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https://f1000research.com/articles/10-931/v1
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16 Sep 21
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{
"type": "Review",
"title": "Digital signature schemes with strong existential unforgeability",
"authors": [
"Jason Chia",
"Ji-Jian Chin",
"Sook-Chin Yip"
],
"abstract": "Digital signature schemes (DSS) are ubiquitously used for public authentication in the infrastructure of the internet, in addition to their use as a cryptographic tool to construct even more sophisticated schemes such as those that are identity-based. The security of DSS is analyzed through the existential unforgeability under chosen message attack (EUF-CMA) experiment which promises unforgeability of signatures on new messages even when the attacker has access to an arbitrary set of messages and their corresponding signatures. However, the EUF-CMA model does not account for attacks such as an attacker forging a different signature on an existing message, even though the attack could be devastating in the real world and constitutes a severe breach of the security system. Nonetheless, most of the DSS are not analyzed in this security model, which possibly makes them vulnerable to such an attack. In contrast, a better security notion known as strong EUF-CMA (sEUF-CMA) is designed to be resistant to such attacks. This review aims to identify DSS in the literature that are secure in the sEUF-CMA model. In addition, the article discusses the challenges and future directions of DSS. In our review, we consider the security of existing DSS that fit our criterion in the sEUF-CMA model; our criterion is simple as we only require the DSS to be at least secure against the minimum of existential forgery. Our findings are categorized into two classes: the direct and indirect classes of sEUF-CMA. The former is inherently sEUF-CMA without any modification while the latter requires some transformation. Our comprehensive review contributes to the security and cryptographic research community by discussing the efficiency and security of DSS that are sEUF-CMA, which aids in selecting robust DSS in future design considerations.",
"keywords": [
"Cryptography",
"Digital Signatures",
"Strong Existential Unforgeability"
],
"content": "Introduction\n\nThe idea of a digital signature scheme (DSS) was proposed by Diffie and Hellman in 1976 as a necessity to design efficient authenticated electronic communications which can serve as legal evidence in the court of law.1 Rivest, Shamir, and Adleman realized the idea in their seminal work known as the RSA cryptosystem,2 the first of many. A DSS consists of three processes, as shown in Figure 1.\n\nFor every (sk,pk) ← keygen(1k) and every m, verify(sign(m,sk),m,pk) = 1 must hold. A σ on m is valid if verify(σ,m,pk) = 1. This is a standard (informal) definition of DSS.3 In the early 90s, a paradigm known as hash-then-sign forms the industry standard for issuing digital signatures.4 The idea is to sign on the hash of a message, h←H(m) instead of the m itself; this has a few benefits for h is constant size, which leads to efficient signing on speed and a constant sized signature. Verification would then require the verifiers to first validate the signed hash, then perform hashing h′←H(m) before finally comparing h′ and h. Concrete examples of the hash-then-sign are discussed in.5-15\n\n\nProperties of DSS\n\nThe following properties are required by DSS3:\n\n• Public verifiability: A signature σ generated from a private key sk can be verified using a public key pk. This property differentiates DSS from other integrity protection mechanisms, such as message authentication codes (MAC). A consequential result from this property is that signatures are also transferrable, meaning a party can copy σ and pk to use it to convince others that the message is authentic from the signer.\n\n• Non repudiation: A signer cannot later deny that they have authenticated a message m once the signature of m, σ is generated and known. This is also another property that separates DSS from MAC, because the only entity that could have plausibly generated the signature in the case of DSS must possess the private key sk; whereas in a MAC scheme, the keys are shared. This property also implies that only the one in posession of sk can generate valid signatures, which disallows forgeries.\n\nNotice that the verification process requires both the message and the signature as inputs, requiring the signer to transmit both. Alternatively, some DSS can support message recovery. DSS with message recovery (DSS-R) has a different sign and verification process, shown in Figure 2; the signer only needs to transmit a packed signature ρ, and the verifier would recover the message m successfully or abort ⊥ depending on signature validity. For practical purposes, |ρ|≤|σ| + |m|. Examples of DSS-R are found in previous literature.16-23\n\nThe security of DSS was first formalized by Goldwasser, Micali and Rivest in 1988.24 Different security goals are used to model the different security guarantees of a DSS when faced with an adversary. The commonly accepted goal to model against is the goal of existential forgery (EUF), which is the easiest for attackers to achieve among other goals (e.g., selective forgery, total break). In addition,24 defined the adversarial capabilities for a DSS, which aims to model what types of attacks can be carried out by an adversary when attempting to break the DSS. The strongest capability, known as adaptive chosen message (CMA) is the widely accepted adversarial capability that is the most used in the literature on DSS. Figure 3 shows the interactions of a challenger and an adversary in the EUF-CMA model. In step (1), the challenger sets up an empty set Q and gives the pk to the adversary. In step (2), the adversary may make oracle queries that model its chosen message attack capability. The queried messages are added to the set Q. In step (3), the adversary announces to the challenger the target message m* it wants to forge. m* must not be an element of Q, nor it can be queried to the oracle; this prevents trivial attacks which uses the oracle to break the security goal. Note, step (4) allows the adversary to use the signing oracle again, which models the adaptive nature of the attack. Finally, in step (5), the adversary outputs a forgery σ*. We say the adversary breaks the DSS if σ* on m* is valid. qs quantifies the number message-signature pair made available to the adversary.\n\nConsider the case for randomized signatures in the EUF-CMA model (e.g., DSA13 or PSS-R18). A randomized DSS allows multiple valid signatures for a single message, which has a subtle implication on the model: Suppose that the adversary queried for a message-signature pair (m,σ). Now, the adversary forges a different valid signature σ′ ≠ σ on the same message m. This is an easier security goal, but could be a critical vulnerability when the DSS is used in a scenario in which the designers assumed that no new signatures can be forged, because a different signature on an existing message is still new. In other words, EUF-CMA does not guarantee that if that an attacker knows (m,σ), it cannot forge (m,σ′) such that σ′ on m is valid. This gave rise to a stronger security model, known as strong existential unforgeability or sEUF-CMA.25 Figure 4 shows the interactions of the adversary with the challenger in the sEUF-CMA model. The main difference is the constraint during the chosen message attacks and in the final step (5). Notably, the adversary can even query for signatures on the challenge message m*, but may not submit any of the signatures obtained from the sign oracle as forgeries. In contrast to EUF-CMA, sEUF-CMA ensures that an adversary cannot produce any new signatures at all; any valid signature must have originated from the signer.\n\n\nWhy does sEUF-CMA matter?\n\nLet’s take a step back and consider why sEUF-CMA is even worth considering in the first place. DSS is very often used as a building block to construct other cryptographic schemes. For example, using the Fiat-Shamir transform,26 a DSS can be turned into an identification protocol. DSS has also been used to create identity-based identification schemes,27 signcryption schemes,25 authenticated key exchanges,28 and identity-based encryption schemes.29 DSS with EUF-CMA security is found to be insufficient in some of the constructions, particularly to build non-malleable cryptographic schemes. In a nutshell, non-malleability refers to the impossibility of an adversary to generate a different ciphertext to some previously known ciphertext that decrypts to the same message, which is a desirable property in cryptographic schemes.30 Thus, if a DSS is sEUF-CMA, it is much more versatile because it can be useful as a building block for many of the schemes which requires the property of non-malleability.\n\nWe show a toy example of a simple attack that can be achieved by an attacker if the DSS used for authentication is not sEUF-CMA. Figure 5 shows honest users Alice and Bob, as well as an attacker Mallory which has hijacked the channel. In step (1), Bob wants to authenticate that Alice is truly on the other end. Mallory launches a chosen message attack in step (2) and (3) on Alice and obtains the message m and signature σ. In step (4), Mallory forwards (m,σ) to Bob, which may initially convince them. After some time elapsed, Bob wants to re-authenticate Alice to ensure that they are still who they claim to be (5). Mallory forges a valid signature σ′ ≠ σ on m and forwards that to Bob (6). From Bob’s perspective, Alice generating a different signature ought to warrant some confidence that Alice is truly Alice. However, if the DSS is not sEUF, this is not the case, as Bob is obviously duped.\n\nWe established sEUF-CMA is of theoretical interest. Here we briefly mention a few real-life needs for sEUF-CMA to emphasize the importance of it. Not too long ago, Stern et al. showed how to duplicate ECDSA signatures based on their malleability.31 A more recent example is the transaction malleability of the popular cryptocurrency, Bitcoin. When a transaction in Bitcoin is signed, the signature does not cover the entire transaction used for hashing; an attacker could perform strong forgery (i.e., maul the signature), then claim that the transaction has failed (because the hash is not valid). The sender would believe it because the signature is valid! This leads to the sender issuing a new transaction, without knowing that the original transaction is valid.32,33 Decker and Wattenhofer pointed out that this subtle flaw could be responsible for a small portion of Bitcoins stolen during the 2014 MtGox attack.34 They remarked that transaction malleability should be carefully considered when implementing Bitcoin clients. In another research, Jackson et al. found that signatures that are not sEUF-CMA may cause the strong session agreement of a well-known authenticated key exchange algorithm, the STS-ISO1 to fail.36 They analyzed STS-ISO using the Tamarin Prover and found that if sEUF is violated, attackers can force the parties in the session to accept message that do not originate from either of the honest parties.\n\n\nDSS secure in sEUF-CMA\n\nThe notion of sEUF-CMA first appeared in the form of non-malleability of ciphertexts in the works of Dolev, Dwork and Naor30 in 1991. The term sEUF-CMA was first introduced by An, Dodis and Rabin which presented it as requirement to construct signcryption schemes.25 Boneh, Shen and Waters were the first DSS that is considered and proven in the sEUF-CMA model,37 but mentions that DSS that are sEUF-CMA have existed earlier such as full domain hash (FDH)-RSA.18 FDH-RSA must be sEUF-CMA because the signatures generated are determined exactly by the message only. This means that FDH-RSA signatures are deterministic. For deterministic signatures, a strong forgery cannot occur without the message m′ being different from the original m, therefore, deterministic signatures are generally sEUF-CMA. We see that this is also the case for the widely used and popular EdDSA which had recently received a provable security treatment.38 Boneh, Shen and Waters shows that non-deterministic signatures may also exhibit sEUF-CMA, such as the Micali-Reyzin signatures,39 Goh-Jarecki signatures40 and Boneh-Boyen signatures.11 The reason for this is that if the forger manages to re-randomize a signature on the same message, the signature constitutes an existential forgery through clever binding of the messages. This is a recurring paradigm to design sEUF-CMA signature schemes.11,41 Since the introduction of the sEUF-CMA model, existing EUF-CMA secure DSS are now re-considered in the sEUF-CMA model. An example of such work is by Fersch, Kiltz and Poettering on the well established DSA.13 DSA was shown to be secure under sEUF-CMA, while ECDSA was not2.43 More recently in 2021, Brendel et al. proved the IETF version of EdDSA to be sEUF-CMA secure.38 Table 1 shows a list of DSS that are secure under sEUF-CMA.\n\nFrom another perspective, we consider DSS with message recovery (DSS-R) candidates under sEUF-CMA. As pointed out by Ateniese and de Mediros, the modified Nyberg-Rueppel signature is sEUF-CMA secure.49 While it is tempting to think that DSS-R must be sEUF-CMA, because modifying the signature will surely modify the message itself given that one can recover the message from the signature. However, we see that this is not the case as Ateniese and de Mediros found the original Nyberg-Rueppel signatures49 to be insecure in sEUF-CMA.\n\nBoneh, Shen and Waters opened a new field in the research of DSS under sEUF-CMA: Interest in sEUF-CMA conversion starts to accumulate with various works being published.41,56-58 Instead of working on individual DSS, the line of research focuses on creating efficient conversions to enhance existing generic DSS with EUF-CMA into sEUF-CMA. Some transforms do not even need EUF-CMA security at minimum, only requiring EUF-GMA, which is a weaker notion than EUF-CMA.59,60 Table 2 shows a list of conversion methods since 2006, including the use of DSS in leakage resilient settings.61-64\n\nConversions that produces DSS with sEUF-CMA.\n\nDSS Req. - Requirement for DSS before using the conversion; Add. Req. - Additional requirements; EUF-GMA - Existential Unforgeability under Generic Chosen Message Attack; GTOW - Given Target One-Wayness (See60); EUF-FLR - Existential Unforgeability with Full Leakage Resilience; sg - signature generation cost; td - trapdoor operation cost; kg - key generation cost; 1k - security parameter; vf - signature verification cost; σ - underlying signature length; pk underlying signature public key length; π - Groth-Sahai proof statement (See66).\n\nThrough our research, we investigated some of the most used DSS in the industry on their security in the sEUF-CMA model. The following are the popular DSS that are not sEUF-CMA secure.\n\n\n\n1. RSA PKCS#1.567\n\n2. ECDSA31,43\n\n3. Ed25519 (Original, not IETF RFC 8032)38\n\n\nChallenges and future direction\n\nIn recent work, there has been several post-quantum cryptographic DSS that incorporates the sEUF-CMA model during design.68-71 DSS in various other contexts (e.g., privacy preserving computation, multiparty computation) such as a homomorphic DSS,72 group DSS,73 and proxy DSS74-76 are being considered in sEUF-CMA as well. In addition, DSS in even more complex cryptographic settings such as in certificateless and identity-based settings are also using sEUF-CMA as their standard model for security.77-80 We see that the security goal post has been moved from EUF-CMA to sEUF-CMA in the span of a decade and believe this is the right direction forward as DSS is increasingly used in intricate security protocols, which cannot tolerate any design flaw that arises from as simple as malleable signatures.\n\n\nConclusion\n\nIn this work, we provided a comprehensive review on what is strong unforgeability in DSS, why is it needed, which of the DSS are secure under the model and how to obtain it if the DSS is only existentially unforgeable. We surveyed and analyzed existing DSS in literature which are secure under sEUF-CMA, and noted the requirements, computational and storage efficiency as well as the security assumptions of each DSS to provide an overview of DSS under the much more secure model.\n\n\nData availability\n\nNo data is associated with this article.",
"appendix": "Acknowledgements\n\nWe would like to acknowledge our research funder: This research is supported by the Ministry of Higher Education of Malaysia through the Fundamental Research Grant Scheme under Grant FRGS/1/2019/ICT04/MMU/02/5 and in part by Multimedia University’s Research Management Fund.\n\n\nReferences\n\nDiffie W, Hellman M: New directions in cryptography. IEEE Trans. Inf. Theor. September 2006; 22(6): 644–654. 0018-9448. Publisher Full Text\n\nRivest RL, Shamir A, Adleman L: A method for obtaining digital signatures and public-key cryptosystems. Commun. ACM February 1978; 21(2): 120–126. 0001-0782. Publisher Full Text\n\nKatz J, Lindell Y: Introduction to Modern Cryptography (Chapman & Hall/Crc Cryptography and Network Security Series). Chapman & Hall/CRC; 2007. 1584885513.\n\nKaliski B: PKCS #1: RSA Encryption Version 1.5. RFC 2313, March 1998. Reference Source\n\nBellare M, Rogaway P: Random oracles are practical: A paradigm for designing efficient protocols. 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Berlin, Heidelberg: Springer Berlin Heidelberg; 2009; pages 703–720. 978-3-642-10366-7.\n\nWang Y, Tanaka K: Generic transformation to strongly existentially unforgeable signature schemes with leakage resiliency. In: Chow SSM, Liu JK, Hui LCK, et al.: editors, Provable Security. Cham: Springer International Publishing; 2014; pages 117–129. 978-3-319-12475-9.\n\nWang Y, Tanaka K: Generic transformation to strongly existentially unforgeable signature schemes with continuous leakage resiliency. In: Foo E, Stebila D: editors, Information Security and Privacy. Cham: Springer International Publishing; 2015; pages 213–229. 978-3-319-19962-7.\n\nHuang J, Huang Q, Pan C: A black-box construction of strongly unforgeable signature schemes in the bounded leakage model. In: Chen L, Han J: editors, Provable Security. Cham: Springer International Publishing; 2016; pages 320–339. 978-3-319-47422-9.\n\nGoldreich O: The foundations of cryptography - volume 2: Basic applications.2001.\n\nGroth J, Sahai A: Efficient non-interactive proof systems for bilinear groups. Cryptology ePrint Archive, Report 2007/155. 2007. Reference Source\n\nMoriarty K, Kaliski B, Jonsson J, et al.: PKCS #1: RSA Cryptography Specifications Version 2.2. RFC 8017.November 2016. Reference Source Section 9.2, Note 2.\n\nRückert M: Strongly unforgeable signatures and hierarchical identity-based signatures from lattices without random oracles. In: Sendrier N: editor, Post-Quantum Cryptography. Berlin, Heidelberg: Springer Berlin Heidelberg; 2010; pages 182–200. 978-3-642-12929-2.\n\nNoh G, Chun JY, Jeong IR: Strongly unforgeable ring signature scheme from lattices in the standard model. J Appl Mathematics, 2014. 2014. 1110-757X. Publisher Full Text\n\nEaton E, Song F: Making existential-unforgeable signatures strongly unforgeable in the quantum random-oracle model. arXiv preprint arXiv:1509.02944. 2015.\n\nCremers C, Düzlü S, Fiedler R, et al.: Buffing signature schemes beyond unforgeability and the case of post-quantum signatures. Cryptology ePrint Archive, Report 2020/1525. 2020. Reference Source\n\nWang F, Wang K, Bao L, et al.: Leveled strongly-unforgeable identity-based fully homomorphic signatures. In: López J, Mitchell CJ: editors, Information Security - 18th International Conference, ISC 2015, Trondheim, Norway, September 9-11, 2015, Proceedings volume 9290 of Lecture Notes in Computer Science. Springer; 2015; pages 42–60. Publisher Full Text\n\nPark H, Lim S, Yie I, et al.: Strong unforgeability in group signature schemes. Computer Standards Interfaces. 2009; 31(4): 856–862. 0920-5489. Publisher Full Text Reference Source\n\nSun Y, Xu C, Yu Y, et al.: Strongly unforgeable proxy signature scheme secure in the standard model. J Syst Soft. 2011; 84(9): 1471–1479. 0164-1212. Publisher Full Text Reference Source Selected papers from the 2009 Joint Working IEEE/IFIP Conference on Software Architecture & European Conference on Software Architecture (WICSA/ECSA 2009).\n\nYu Y, Yi M, Susilo W, et al.: Provably secure proxy signature scheme from factorization. Mathematical and Computer Modelling. 2012; 55(3): 1160–1168. 0895-7177. Publisher Full Text Reference Source\n\nPang L, Zhao H, Zhou X, et al.: Strongly unforgeable and efficient proxy signature scheme with fast revocation secure in the standard model. Int J Distributed Sensor Networks. 2016; 12 (1): 3205206. Publisher Full Text\n\nSato C, Okamoto T, Okamoto E: Strongly unforgeable id-based signatures without random oracles. In: Bao F, Li H, Wang G: editors, Information Security Practice and Experience. Berlin, Heidelberg: Springer Berlin Heidelberg; 2009: pages 35–46. 978-3-642-00843-6.\n\nZhang J, Liu X: An efficient strong id-based signature scheme with unforgeability. 2010 Fifth International Conference on Frontier of Computer Science and Technology. 2010; pages 239–245. Publisher Full Text\n\nYu Y, Yi M, Wang G, et al.: Improved certificateless signature scheme provably secure in the standard model. Information Security, IET. 06 2012; 6: 102–110. Publisher Full Text\n\nLiu Z, Zhang X, Hu Y, et al.: Revocable and strongly unforgeable identity-based signature scheme in the standard model. Sec. and Commun. Netw. September 2016; 9(14): 2422–2433. 1939-0114. Publisher Full Text\n\n\nFootnotes\n\n1 STS stands for Station-to-Station and is an authenticated key exchange protocol due to Diffie et al. 35\n\n2 Brown proved ECDSA to secure under sEUF-CMA, 42 but this was refuted through a series of trivial attacks posed by. 43"
}
|
[
{
"id": "97082",
"date": "03 Nov 2021",
"name": "Denis Chee-Keong Wong",
"expertise": [
"Reviewer Expertise Algebraic cryptography",
"algebra"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 performs a review on existing DSS together with its properties, such as public verifiability, non-repudiation, and ability for message recovering. Furthermore, a detailed discussion on DSS security models are included, which are the EUF-CMA and sEUF-CMA. The differences between both security models are elaborated upon in detail. Finally, the authors provided comprehensive information on existing DSS in Table 1 for comparison purposes. As a survey paper, this work is comprehensive and suitable to be indexed. The authors need to re-check some of the entries in Table 1 to ensure the information stated is correct - please look at the \"GJK +07-1\", and please ensure the group G used is the same for all schemes with |G| in the column of \"sig. len.\".\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
},
{
"id": "162696",
"date": "13 Feb 2023",
"name": "Pin Shen Teh",
"expertise": [
"Reviewer Expertise Biometrics",
"Security",
"Machine Learning",
"Mobile Authentication"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 objective was clear.\n\nThe concept of the work was straightforward.\n\nThe presentation style of the article was clear.\n\nGrammar mistakes are noticeable. The sentence structure and choice of words used can be more concise and precise, some terms used were somewhat inconsistent, making reading and understanding the article quite challenging.\n\nFurther elaboration of why the three popular DSS that are not sEUF-CMA secure would be helpful.\n\nOverall the depth of the work is sufficient for the calibre of this journal.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-931
|
https://f1000research.com/articles/10-930/v1
|
16 Sep 21
|
{
"type": "Software Tool Article",
"title": "AQUA: an Advanced QUery Architecture for the SPARC Portal",
"authors": [
"Niloofar Shahidi",
"Xuanzhi Lin",
"Yuda Munarko",
"Laila Rasmy",
"Tram Ngo",
"Xuanzhi Lin",
"Yuda Munarko",
"Laila Rasmy",
"Tram Ngo"
],
"abstract": "The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program integrates biological and neural information to create anatomical and functional maps of the peripheral nervous system. The SPARC Portal hosts a dynamic storage for the datasets, models, and resources to help the researchers find and produce data. Currently, the SPARC Portal provides a primary search tool, which lacks some features to improve the search experience. To purposefully retrieve the required information from the stored datasets and resources, we have developed an Advanced QUery Architecture (AQUA) for the SPARC Portal. Near-real-time auto-completion of the queries, close-matches suggestions, and multiple filters to narrow or sort the results are the major features of AQUA with the goal to enhance the usability of the SPARC search engine. AQUA is available from: https://github.com/SPARC-FAIR-Codeathon/aqua",
"keywords": [
"AQUA",
"SPARC",
"biological query",
"natural language processing",
"NIFS Ontology",
"text mining",
"Codeathon"
],
"content": "F1000 Research Statement of Endorsement\n\nDavid Nickerson confirms that the author has an appropriate level of expertise to conduct this research, and confirms that the submission is of an acceptable scientific standard. David Nickerson declares he is NF’s primary supervisor and one of the organisers of the 2021 SPARC FAIR Codeathon. Affiliation: Auckland Bioengineering Institute, University of Auckland.\n\n\nIntroduction\n\nThe Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is a platform to assist neuroscientists in developing new medical devices.1 It aims to leverage our understanding of nerve-organ interactions in biological entities and advance existing medical tools. It hosts over a hundred datasets, projects, and resources that are increasing in number, and in the future, there will be a need for a robust tool to explore the expanding content. A targeted data retrieval from the SPARC Portal can boost the researcher-portal interaction experience and help users find the data they seek. However, the search features of the SPARC Portal are limited.\n\nCurrently, the search engine of the SPARC Portal does not account for close-matches or misspelt words. The primitive display of the returned results does not emphasise the matched texts and does not allow users to filter or sort the searched data. This prevents users from easily finding their required resources, and once found, users cannot properly narrow or sort the returned data. Moreover, the current description given for each returned result might not necessarily contain the matched keywords which leads to confusion. We have developed an application that we believe will enhance the SPARC Portal search by addressing the above-mentioned issues to reach a FAIR (Findable, Accessible, Interoperable and Reusable) repository to benefit researchers globally.\n\nAdvanced QUery Architecture (AQUA) is an application that aims at improving the search capabilities of the SPARC Portal. In particular, it makes the search engine smarter at reading and understanding queries. It also enhances the result display feature of the SPARC Portal by making it more user-friendly and providing users with more sophisticated result filtering and sorting options. Our end goal is to improve the visibility of the SPARC datasets exponentially. This, in turn, will benefit the SPARC community as a whole since their datasets will be more discoverable for reuse and subsequent collaborations.\n\nAQUA was initiated and accomplished during the 2021 SPARC FAIR Codeathon held in July, for a time frame of two weeks. In AQUA, we have incorporated Artificial Intelligence tools to process and refine the queries on the SPARC Portal and implement predictive typing to give feasible suggestions. Thereafter, AQUA auto-corrects the queries to match the existing data on the SPARC portal and the Neuroscience Information Framework Standard (NIFS) Ontology. This will return the most probable datasets that match the search keywords and a list of related new keywords. To enhance the current results display, we have added some functional features to first more precisely filter and sort the results, second emphasise the matched texts for easier skimming, and third, in the case of no available matching results, allow the users to enter their email addresses and get notified when their requested dataset is published.\n\nIn this paper, we first review the implementation of AQUA and how its main sectors correlate with the user and the SPARC portal. Next, we provide more details on the sub-sections of each sector and their implemented tools and packages. We mention the added features to the AQUA User Interface (UI) and discuss how it differs from the existing SPARC Portal. Finally, we describe how AQUA can change the search tool on the SPARC Portal and denote the possible future developments to AQUA.\n\n\nMethods\n\nThis section discusses the improvement of the search tool on the SPARC Portal. Figure 1 demonstrates how the AQUA UI (also referred to as frontend) and the AQUA server-side data-access layer (also referred to as backend) bridge between the user and the SPARC Knowledge Base. AQUA UI receives the user’s queries, formulates them in JSON, and transfers to the AQUA backend module. AQUA backend searches for the formulated queries in the SPARC Knowledge Base. Once the matching datasets/resources are detected, the AQUA backend returns the ranked results to the AQUA UI. Thereafter, the AQUA UI displays the results according to the user’s preference of ranking/filtering. The AQUA UI is implemented using the HTML-CSS-JS trio and the main tools utilised for the AQUA backend are Python, Docker, SQLite,2 and SciGraph.\n\nFigure 2 depicts the pipeline of AQUA in three major sections:\n\n• Query refinement:\n\n1. Auto-completion: Based on the term, our tool automatically completes the queries if it partially/completely matches any keywords. It then sends the selected keyword to AQUA backend.\n\n2. Suggestions: If no exact matches are found, it finds close-matches and suggests them to the users by popping up the phrase: “Showing results for ...”. If the users select to search for their initial query, AQUA will send the raw and uncorrected query to the AQUA backend.\n\n• Results filtering:\n\n1. Sort by: When the results for the query are displayed, user will have the option of sorting them based on the Relevance, Date published, and Alphabetical order.\n\n2. Filter by: The results can also be filtered based on Keyword, Author, Category, and Publication date.\n\n3. Matched text emphasised: The searched keywords will be emphasised in the returned results.\n\n• “Notify me”: At the end, if no results are returned by the AQUA backend, our tool asks the user if they want to get notified when a related resource is published or not. For a given email address, the tool checks for its validity and then stores it using SQLite. Thereafter, it will check for any updated/uploaded related resource on the SPARC Portal everyday at 2AM EDT. In case of the requested resource availability, it sends a notification email to the registered user.\n\nThe grey and yellow boxes correspond to the “Query refinement” and “Notify me” modules of the AQUA backend, respectively. The green box corresponds to the “Results filtering” function of the AQUA frontend on displaying the results. The purple boxes illustrate the filters and sorting options.\n\nThe AQUA platform integrates Python libraries, data mining tools, a SQL database engine, and Document Object Model (DOM) API to mimic an environment similar to the SPARC Portal with an improved seach functionality in multiple ways.\n\nThe AQUA backend includes querying the SPARC Knowledge Base for information, delivering data to the frontend, and processing any logic that the AQUA UI requires. The SPARC Knowledge Base comprises of two references: SPARC dataset metadata and NIFS ontology. Metadata is the “Data about data”, i.e., additional information provided about datasets. The SPARC dataset metadata includes information such as title, description, techniques, as well as the number of the files, formats, licenses, etc. (SPARC dataset metadata), and the NIFS ontology is a set of community ontologies used by SPARC to annotate data and models.\n\nThe AQUA backend focuses on two main features: Query refinement and Email notification. Below, we give a brief introduction to these added features.\n\n\n\n• Query refinement:\n\nWhen the initial query term is inserted it goes through two paths: auto-completion (yellow box in Figure 3) and suggestions (purple box in Figure 3).\n\n\n\n1. Auto-completion:\n\nThe AQUA query refinement module auto-completes the queries after the third inserted letter while the user is typing. The idea of auto-completion is to prevent typos occurring and to give a better user experience in the SPARC Portal. We have created an n-gram model for auto-completion and utilised a Python library fast-autocomplete. In spelling correction task, an n-gram is a contiguous sequence of n letters from a given sample of text. An n-gram model is utilised to compare strings and compute the similarity between two words, by counting the number of similar n-grams they share. This technique is language independent. The more similar n-grams between two words exist the more similar they are.3\n\nThe Elasticsearch’s auto-complete suggester is not fast enough and does not do everything that we need. Consequently, we have utilised the fast-autocomplete library in Python which provides us with a much faster process (reducing the average latency from 900 ms to 30 ms). Elasticsearch’s auto-complete suggester does not handle any sort of combination of the words in query terms. For example fast-autocomplete can handle “brainstem neuron in rat” when the words “brainstem”, “neuron”, “in”, “rat” are separately fed into it, while Elasticsearch’s auto-complete needs that whole sentence to be fed to it to show it in auto-complete results.\n\n2. Suggestions:\n\nSimultaneously, AQUA utilises SciGraph for auto-correction and suggestion. SciGraph represents ontologies and ontology-encoded knowledge in a Neo4j graph. However, we found that solely using SciGraph is not sufficient because SciGraph returns alternative queries/suggestions without correcting the initial query. For example, if there is a typo or removed space between the words of a query (scriptio continua), SciGraph returns either no results or irrelevant results from the ElasticSearch. Therefore, we have added a new auto-correction feature to segment queries with missing spaces and fix error spelling by creating a pipeline to SymSpellPy. SymSpellPy is a Python port of SymSpell for spelling correction, fuzzy search and approximate string matching. This improves the performance before sending the request to the ElasticSearch. The auto-correction result is combined with the suggestion results and then executed as the final query search terms. This is demonstrated within the purple box in Figure 3.\n\n\n\nWord segmentation:\n\nWord segmentation divides a string into words by inserting missing spaces at the appropriate positions.\n\nSpelling correction:\n\nSupports spelling correction (word splitting/merging) of multi-word input strings in three cases4:\n\n1) Extra space inserted into a correct word which leads to two incorrect terms; 2) Removed space between two correct words which leads to one incorrect term; 3) Multiple independent input terms with/without spelling errors.\n\nTo read more on AQUA query refinement visit: https://github.com/SPARC-FAIR-Codeathon/aqua/blob/main/Documentation/QueryRefinement.md.\n\n• Email notification\n\nThe primary purpose of this module is to notify users whenever a new dataset is published matching their search terms. However, users can still use the same function to receive a summary table including basic information and links to all datasets currently matching their keywords. Additionally, as the “Notify me” module saves the requests in a database, this information can be further accessed and analysed to improve the content (Figure 4).\n\nWe can summarize the “Notify me” actions as follow:\n\n\n\n1. Adds email requests with keywords;\n\n2. Scans for existing search hits and sends email;\n\n3. Moves the pending requests to a waiting list that is scanned daily;\n\n4. Moves the fulfilled requests to an archive;\n\n5. Any failed requests (that already have matching hits) will remain on the waiting list for one month, during which the “Notify me” module will try to send the email daily. Afterwards, if the email still fails, it will be moved to the archive with a “failed” status.\n\nTo read more visit: https://github.com/SPARC-FAIR-Codeathon/aqua/blob/main/Documentation/NotifyMe.md.\n\nThe purple box corresponds to the path into returned suggestions and the yellow box corresponds to the auto-completion path. The procedure is demonstrated by an example of inserting a misspelt initial query (braistem) into the module.\n\nAQUA UI receives the user’s queries, formulates them, and transfers to the AQUA backend module. When the response from the AQUA backend is received, the AQUA UI interprets it and displays the content on the screen. Like the SPARC Portal web application, the AQUA UI is implemented using VueJS and NuxtJS. Nuxt is an upper-level framework that is built over Vue.js to design and create highly advanced web applications.5 The AQUA UI displays the customised list of results with the emphasised searched keywords.\n\nTo start the application follow the steps in Installation.\n\nHow to use the features added by AQUA to the SPARC Portal search engine?\n\nThe application works like other similar search engines with a user interface mimicking the SPARC Portal environment.\n\n\n\n1. Predictive search typing:\n\nAQUA provides auto-completion for user’s queries as they type. This feature is powered by SciGraph and training data from the SPARC Knowledge Base. AQUA only shows auto-completion after users type three letters or more to avoid too many results being returned, slowing down the application.\n\n2. Advanced search options:\n\nBy expanding the “Advanced search” tab under the search box, users can select whether AQUA searches for Exact match for their query or Any of the words. The default is Any of the words match.\n\n3. Advanced sorting:\n\nThe existing SPARC Portal allows sorting based on dataset titles (alphabetically) and by published date. AQUA adds a “Relevance” sorting criterion that returns results based on how relevant the results are to their search query. This is set as the default sorting option.\n\n4. Advanced filtering:\n\nThe existing SPARC Portal only allows for filtering based on “Dataset status”, which is either Published or Embargoed. AQUA adds more sophisticated filtering options. Users can filter datasets by one or several keywords, authors, and categories. Hit “Enter” after each “Keyword”, “Author”, or “Category” in their respective box to register it. After the entries are registered, click “Apply” to filter dataset results.\n\n5. Email notifications for new matched datasets:\n\nUsers can opt in to receive emails about new datasets that match their search query. We believe this is a much needed option for users to stay updated about their search and SPARC datasets. Simply click on “Create alerts” under the search box and enter an email. AQUA will trigger an email send when newly added dataset(s) that match the search query are published by SPARC. This is a one-time-only email subscription.\n\n6. Emphasise matched texts in result display:\n\nWhen a dataset is returned, any matched text in the dataset title and description will be emphasised for easy and convenient lookup.\n\n\nUse case\n\nWe conducted experiments to compare the performance of the AQUA query refinement module by either deploying SciGraph or fast-autocomplete. We analysed the operation in auto-completing the queries in terms of performance and execution time. We compared these two criteria in two scenarios: correct queries, and queries with one typo. Our experiment revealed that fast-autocomplete returns more completions than SciGraph in both cases of inserting correct queries and queries with typo. Also, fast-autocomplete returned the results 24 times faster in correct queries and 11 times faster in queries with typos.\n\nWe tested the performance of the AQUA spelling correction module and compared the results with the SPARC’s Elasticsearch. To do this, we randomly selected 22 sets of queries from the SPARC dataset, each containing fifty keywords or phrases. The queries were then modified to include different types of typos (deletion, insertion, replacement). We calculated the Mean Average Precision (MAP) of AQUA and the SPARC’s Elasticsearch in spelling correction. Results showed that as the number of terms in a query increases, the performance of AQUA noticeably surpasses the SPARC’s Elasticsearch (Table 1). Same steps were taken on querying the name of author/authors as keywords for 9 test collections. Table 2 shows that AQUA performs better in correcting misspellings that appear in a two-term “author” query. A significant performance difference is AQUA’s ability to fix “author” as a query that loses space where AQUA’s MAP is 0.92 while the SPARC’s Elasticsearch’s MAP is only 0.12.\n\nThe experiment results and description are available here. The code for running the experiments and the data are also available on: https://github.com/SPARC-FAIR-Codeathon/aqua/tree/main/experiment.\n\n\nConclusions and next steps\n\nThis paper demonstrated how the SPARC Portal could be more FAIR by improving its search feature through AQUA. Since the first contact between researchers and a repository of datasets/models/resources is through the website’s search engine, we enhanced the search system’s functionality and the user interface. In AQUA, we deployed multiple tools and packages to make querying the data more precise, convenient, and effective.\n\nWe propose to add a view type to the existing SPARC Portal to enhance the users’ experience with the website. The SPARC Portal’s existing view type is “List”. AQUA proposes to add a “Gallery” view option in the future. Also, we plan to add a new discovering feature to the SPARC Portal to find resources by querying snapshots of simulations. This can be done by segmenting the simulation results into smaller time intervals or any chunk of data. Currently, the AQUA “Notify me” feature is a one-time-only email notification. Options to be alerted more than once can also be added in the future. AQUA can also enhance the SPARC search engine further by improving user’s next query. This will be done by developing a session-based search based on user’s search or clickthrough history on the Portal. The feature will create a personalized experience for users and thus enhance their overall experience with the SPARC Portal.\n\n\nSoftware availability\n\nSource code available from: https://github.com/SPARC-FAIR-Codeathon/aqua/blob/main/LICENSE\n\nArchived source code as at time of publication: https://doi.org/10.5281/zenodo.5352470.6\n\nLicense: MIT\n\nThe AQUA application can be installed and run by cloning the main Github repository and following the command line instructions. Instructions on how to clone a Github repository can be found here.",
"appendix": "Acknowledgements\n\nWe would like to extend our special thanks to the NIH Common Fund’s SPARC Program and to the organisers of the 2021 SPARC FAIR Codeathon for their support during the planning and development of this project.\n\n\nReferences\n\n[1] The Sparc Data and Resource Center: 2021. Reference Source\n\nBhosale ST, Patil T, Patil P: SQLite: Light Database System. Int J Computer Sci Mobile Computing. April 2015; 4(4): 882–885.\n\nAhmed F, De Luca EW, Nurnberger N: Revised n-gram based automatic spelling correction tool to improve retrieval effectiveness. Polibits. December 2009; 40(40): 39–48.\n\nsymspellpy api. Reference Source\n\nNuxt.js and Vue.js: Reasons why they differ and when do they combine.2021. Reference Source\n\nShahidi N, Ngo T, lrasmy Y, et al.: Niloofar-Sh/aqua: First release of AQUA (v1.0.0). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "94519",
"date": "01 Nov 2021",
"name": "Vijay Rajagopal",
"expertise": [
"Reviewer Expertise computational physiology",
"mechanobiology",
"systems biology",
"image analysis",
"bioengineering",
"heart",
"breast"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a search and retrieve tool for the SPARC knowledge database. Overall, the contribution is important and in line with making research data FAIR. The article is also written well but is missing some key components that would make testing and adoption of this tool in SPARC easy to do.\nInstallation already assumes installation of yarn, and I was unable to easily install it. Please include details of popular alternate installation methods (like docker) within the instruction manual.\n\nRelated to the above, what are the minimum required libraries that one needs to build and install to their software to reproduce their results?\n\nTables 1 and 2 need to be more informative. What is the formula for mean average precision? Ideally, they should provide other metrics as well. Perhaps even the distribution of precision for the test collections.\n\nThe authors suggest that AQUA surpasses Elasticsearch as number of queries increases in Table 1. Looking at column \"3 terms\", however, I see that ES has a MAP of ~0.8 vs AQUA's ~0.6 when there is no space. Therefore the claim that AQUA is superior is to Elasticsearch not clear to me.\n\nIn Table 1, what do the NaNs mean in the column \"1 term\"? I can see that \"no space\" does not apply in this case. If this is a typo, it should be resolved. In these cases is a NaN an error produced by both ES (Elasticsearch) and AQUA?\n\nIn Table 2, the \"2 term\" column shows that the MAP is not really that different between ES and AQUA, except for \"no space\". The table does not reflect the significant improvements by using AQUA. I suggest including more comparison metrics to make the case for the performance of AQUA.\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? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No",
"responses": []
},
{
"id": "141807",
"date": "26 Jul 2022",
"name": "Maryann E. Martone",
"expertise": [
"Reviewer Expertise Neuroinformatics. I also am a PI in the SPARC Data and Resource Center so know the SPARC project very well."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors describe a query tool they developed for the SPARC Portal during a code-a-thon held in July 2021. The authors correctly identified several shortcomings of the portal search at that time, and created a service that would address them. However, there are a few issues that limit the utility of this article:\nThe main issue is that, as often happens, the SPARC search interface has evolved since that time, so many of the contentions are no longer true. SPARC has moved to a faceted search interface that goes well beyond the filters employed at that time and here, e.g., anatomical structure, technique, species, sex. The new search functionality uses an Algolio index which could support many of the features that you have developed (although I don't think it is completely open, so that is a minus). So I think for this to be useful beyond describing the technology used, you would have to compare AQUA to the current SPARC interface/services rather than the state in 2021. While I know that it may be impractical to redo all the tests etc with updated SPARC, I would like the author to at least acknowledge the update and address these issues in the discussion.\n\nThe authors lay out several features, e.g., autocomplete, spell checking and e-mail notification. These clearly would be useful, but I don't think that the authors provided evidence in the form of user testing that they are useful, that is, that they give better search results for an average SPARC user. They refer readers to the results in GitHub, but I'd like to see some concrete examples and user feedback. I know there is a Docker image available, but that is not practical for those with domain expertise to test. What are the authors plans to make a version of their interface available through SPARC? e.g., in the Tool and Resource section? I didn't see it listed there.\n\nThe authors don't discuss the generalizability of their approach. Would their code have use beyond the SPARC portal?\nMinor issues:\nWhen the authors refer to \"keywords\", are they specifically referring to the metadata field marked \"keywords\"? What about the other standard metadata that a SPARC acquires and tags in the JSON metadata file?\n\nAdding a reference to the SPARC SDS specification would provide readers with a better idea of the metadata available. Bandrowski et al., 20211.\n\nNIFS should be NIFSTD. A reference for the NIFSTD ontology is Bug et al. 20082.\n\nThe table/figure legends are not adequate. Terms are introduced, e.g., SciGraph in Fig 1, that are not explained either in the legend or in the text. Why are some values bolded in the tables? A reference for SciGraph is Surles-Zeigler et al., 20223 (currently accepted for publication in Frontiers in Neuroinformatics).\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-930
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https://f1000research.com/articles/10-929/v1
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16 Sep 21
|
{
"type": "Research Article",
"title": "Impact of ascorbic acid in reducing the incidence of vancomycin associated nephrotoxicity in critically ill patients: A preliminary randomized controlled trial",
"authors": [
"Nouran Hesham El-Sherazy",
"Naglaa Samir Bazan",
"Sara Mahmoud Shaheen",
"Nagwa A. Sabri",
"Nouran Hesham El-Sherazy",
"Sara Mahmoud Shaheen",
"Nagwa A. Sabri"
],
"abstract": "Background Antioxidants show nephroprotective effect against vancomycin associated nephrotoxicity (VAN) in animals. This study aimed to assess the ascorbic acid nephro-protective role against VAN clinically. Methods Forty-one critically ill patients were randomly assigned to one of two groups: intervention group (vancomycin IV plus ascorbic acid, n=21) or control group (vancomycin IV only, n=20). Primary outcomes were the incidence of VAN and the absolute change in creatinine parameters, while mortality rate was the secondary outcome. Nephrotoxicity was defined as an increase in serum creatinine (S.cr) by at least 0.5 mg/dL or 50% of baseline for at least two successive measurements. This study is registered at Clinicaltrials.gov (NCT03921099), April 2019. Results Mean absolute S.cr increase was significant when compared between both groups, P-value = 0.036, where S.cr increased by 0.05(0.12) and 0.34(0.55) mg/dL in the intervention and control groups, respectively. Mean absolute Cr.cl decline was significant when compared between both groups, P-value = 0.04, where Cr.cl was decreased by 5.9(17.8) and 22.3(30.4) ml/min in the intervention and control groups, respectively. Incidence of VAN was 1/21(4.7%) versus 5/20(25%) in the intervention and control groups, respectively (RR: 0.19; CI: 0.024–1.49; P-value = 0.093). Mortality was higher in the control group; however, it was not statistically significant, P-value = 0.141. Conclusion Co-administration of ascorbic acid with vancomycin preserved renal function and reduced the absolute risk of VAN by 20.3%, however, the reduction in VAN incidence didn’t reach statistical significance level. Further large multicenter prospective trials are recommended.",
"keywords": [
"vancomycin",
"nephrotoxicity",
"critically ill patients",
"ascorbic acid"
],
"content": "Introduction\n\nVancomycin (a glycopeptide antibiotic) has been the first line of treatment for methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant coagulase-negative Staphylococci and Enterococcus faecium since 1970.1 Over the past decades, the use of vancomycin has intensely increased due to the increased incidence of both the community and the health care MRSA infections.2 Moreover, it has been intensively used for the sake of appropriate empirical coverage.3\n\nTrough level between 15–20 mg/L was recommended in complicated infections caused by Staphylococcus aureus as a surrogate marker for the pharmacokinetic/pharmacodynamic ratio (AUC/MIC more than 400).4 However recent guidelines recommend area under the curve (AUC) monitoring using Bayesian software programs instead of trough level as the most accurate way for vancomycin dosing and monitoring.5 In patients suffering serious MRSA infections, an individualized target of the AUC/MIC should be 400 to 600 (assuming MIC= 1 mg/L) in order to achieve clinical efficacy and improve patient safety.5 Doses of 15 to 20 mg/kg (based on actual body weight every 8 to 12 hours) are usually recommended for most patients with normal renal function.5\n\nThe incidence of vancomycin associated nephrotoxicity (VAN) is high and may reach 10–20% upon administering the conventional dose of vancomycin (one gram every 12 hours) and 30–40% upon administering the high dose (15–20 mg/kg every 8–12 hours).6 It usually occurs within 4–8 days after initiating the therapy7 and it is usually reversible within seven days in 44–75% of the patients upon discontinuing the treatment.7 In addition, VAN can be reversed by adjusting doses correctly after renal impairment.8 Some preventive strategies are used such as adequate hydration and therapeutic drug monitoring in high-risk patients9; however, the incidence is still high, especially among critically ill patients.\n\nMany risk factors have been found to increase the risk of VAN such as long duration of treatment (> seven days),7 critical illness,7 obesity (>101.4 kg),10,11 method of administration (intermittent infusion > continuous infusion),12,13 higher trough levels > 20 mg/L14 and the use of two or more concomitant nephrotoxins [e.g. aminoglycosides, angiotensin converting enzyme inhibitors (ACEIs), non-steroidal anti-inflammatory drugs (NSAIDs), furosemide, cyclosporins, amphotericin B, and cisplatin].10,15 Co-administrating piperacillin/tazobactam antibiotic with vancomycin was noted to be a possible risk that may enhance the incidence of VAN compared to administering vancomycin alone in 2011. Then subsequent studies were done but the results are still conflicting.16–18 Also, flucloxacillin has been reported recently to increase the risk for acute kidney injury (AKI) in patients receiving vancomycin.19\n\nOxidative stress has been thought to be the main cause of nephrotoxicity associated with vancomycin. The reactive oxygen species (ROS) generated by the mitochondria initiate renal cell apoptosis, which results in renal dysfunction.7 These generated ROS decrease the activity of superoxide dismutase and catalase enzymes, which have a defensive antioxidative role.7\n\nThe belief that oxidative stress plays a role in renal dysfunction has led to the concept that antioxidants can be beneficial in a nephro-protection approach. Ascorbic acid is an antioxidant that acts as a free radical scavenger, therefore it can reduce renal stress.20 It has been shown to be nephro-protective in animals against the stress generated after cardiac ischemia and by medications (e.g. gentamicin, vancomycin, cisplatin and colistimethate).7,21 With regard to safety, it has been reported to be the least toxic of all vitamins. Generally, it is well tolerated by patients while some may experience minimal gastrointestinal side effects.22 Moreover, it’s cheap and readily available on the market.\n\nAt the moment, no randomized controlled clinical trial has been carried out to investigate the role of ascorbic acid in preventing VAN. Therefore, this pilot study aims to investigate the possible nephro-protective effect of ascorbic acid against VAN in critically ill patients.\n\n\nMethods\n\nThe study was performed to comply with the Declaration of Helsinki principles.23 Approvals were obtained from the Ethics Committee and institutional review board of the Faculty of Pharmacy, Ain Shams University (No: 208) on 10th September 2018, and the council of the critical care medicine department at Cairo University Hospitals. The study is registered at Clinicaltrials.gov (Registration: NCT03921099), April 2019. A written informed consent was obtained from each participating patient or from his/her next first relative.\n\nThis was an open-label prospective, randomized, controlled study conducted on critically ill patients. Patients were recruited from the critical care medicine department at Cairo University Hospitals, Cairo, Egypt, during the period between April 2019 and December 2019.\n\nAll patients suffering from clinical signs of infection in the critical care medicine department were screened for the following inclusion criteria: adults (age >18) of both genders with susceptibility to gram-positive infection (MRSA) that required vancomycin treatment for at least 72 hours. Patients were excluded if they had a known allergy to either vancomycin or ascorbic acid, pregnant or lactating females, baseline serum creatinine ≥2mg/dL, receiving other nephrotoxic drugs (e.g. aminoglycosides, amphotericin B, cisplatin, colistimethate sodium or calcinurine inhibitors) at time of initiating vancomycin, suffer from glucose-6-phosphate dehydrogenase deficiency or urinary tract stones, or were expected to undergo contrast medium administration within seven days.\n\nEligible patients were assigned to either the vancomycin-ascorbic acid (intervention) group or the vancomycin (control) group by block randomization using an online program for randomization (http://www.randomizer.org). Patients were subjected to randomization using sequentially numbered opaque sealed envelopes (SNOSE), to accomplish allocation concealment.24\n\nVancomycin was administered intravenously at a dose of 15–20 mg/kg based on actual body weight every 8–12 hours in both groups. Vancomycin powder was reconstituted by adding 0.9% normal saline (NS) to a final concentration of 2.5–5 mg/ml.5 Reconstituted powder was infused slowly with a maximum rate of 10 mg/min over at least one hour (infusion time was increased to 1.5–2 hours if the patient’s single dose was greater than one gram to avoid Red man syndrome).5\n\nAscorbic acid was administered orally at a dose of two grams twice daily half an hour before the vancomycin dose for the patients assigned to the intervention group.25 No hazardous effects were expected from either administering the ascorbic acid dose or in combination with vancomycin in the vancomycin regimen. For those patients in the intervention group, ascorbic acid was stopped if anuric acute kidney injury occurred to avoid the accumulation of oxalates. Nephrotoxicity was assessed within one week of starting vancomycin therapy in both groups to avoid variation in vancomycin exposure.\n\nPatient demographics (age, gender, weight and height), comorbidities, concurrent medications, urine output, mean arterial pressure and vancomycin related factors (dose, route of administration and regimen) were recorded. Severity of illness was assessed using the APACHE II score (Acute Physiology and Chronic Health Evaluation II) and SOFA score (Sequential Organ Failure Assessment) for all patients within 24 hours of intensive care unit (ICU) admission.\n\nSerum creatinine (S.cr) and blood urea nitrogen (BUN) samples were withdrawn on the starting day of vancomycin (baseline), day three, day seven and at additional times as needed. Creatinine Clearance (Cr.cl) was calculated using the Cockcroft-Gault equation utilizing ideal body weight if BMI was 18.5–24.9), adjusted body weight if BMI was >25 kg/m2 or actual body weight in low body weight patients.26\n\nThe primary outcomes of the study were the incidence of VAN and the absolute change in the creatinine parameters (serum creatinine and creatinine clearance) among the study groups. The guidelines defined VAN as an increase in serum creatinine of at least 0.5 mg/dL or ≥ 50% from baseline within seven days for at least two successive measurements from the starting time of the medication till 72 hours after its end.4 A threshold increment of >0.3 mg/dL in S.cr over 48-hours was adopted by Kidney Disease: Improving Global Outcomes (KDIGO) and the Acute Kidney Injury Network (AKIN) as an indicator of VAN. Herein, VAN refers to the guideline-based definition of nephrotoxicity rather than KDIGO or AKIN criteria. VAN was staged according to the severity of AKI based on KDIGO 2012 guideline.27 Mortality rate was the secondary outcome of the study.\n\nBlood samples were withdrawn to measure vancomycin serum trough level before the fourth dose (where steady state had been reached) by half an hour.4 Blood samples were collected in heparinized blood tubes and were centrifuged immediately for four minutes at 1500 rpm, then the supernatants were separated and stored at -80°C. Plasma vancomycin trough levels were measured within four months using a liquid chromatography mass spectrometry (LC- MS/MS). A Shimadzu Prominence (Shimadzu Scientific Instruments, Columbia, MD, USA) series LC system equipped with degasser (DGU-20A3), solvent delivery unit (LC-20AB) with an auto-sampler (SIL-20 AC) was used to inject the aliquots of the samples on a Luna C18 (Phenomenex Inc., Torrance, CA, USA) 50 × 4.6 mm, 5 μm PS. The guard column was a Phenomenex C18 5 × 4.0 mm, 5 μm PS. All analyses were carried out at room temperature.\n\nA sample size of 40 patients across the two groups was estimated to be needed based upon the assumption that the vancomycin associated nephrotoxicity rate was 40% in the vancomycin (control) group6 and 5% in the vancomycin-ascorbic acid (intervention) group, with 5% type I error and 20% type II error.\n\nStatistics were done using the Statistical Package for Social Sciences (SPSS) Version 25 (IBM SPSS Statistics, RRID:SCR_019096) (An open-access alternative that can perform an equivalent function is the R stats package (R Project for Statistical Computing, RRID:SCR_001905)). Continuous variables were reported as mean (SD) and were compared using Student’s t test as per non-significant Shapiro Wilk test (P-value > 0.05), while non-normally distributed variables (as per significant Shapiro Wilk test (P-value < 0.05) were compared using Mann Whitney U test. Categorical variables were compared using χ2 test or Fisher’s exact test (when the assumptions of χ2 were not fulfilled) and were reported as count (%).\n\nThe comparisons of the primary outcomes (serum creatinine, creatinine clearance and the absolute change in their values) were done using Student’s t-test as per continuous variables while the comparisons of the incidence of VAN (primary outcome) and the mortality rate (secondary outcome) were done using Fisher’s exact test and χ 2 test respectively, as per categorical variables. All data are available at Figshare.28\n\n\nResults\n\nFifty-five critically ill patients with either confirmed or suspected MRSA infection were assessed for their eligibility for the study, however, only forty-one patients met both the inclusion and exclusion criteria and completed the study. They were randomly assigned to one of two groups as described in Figure 1.\n\nAbbreviations: S.cr, serum creatinine; BUN, blood urea nitrogen; Cr.cl, creatinine clearance.\n\nDemographics, baseline clinical characteristics, vancomycin related factors and simultaneous potential nephrotoxins were comparable in both groups as shown in Table 1. The median APACHE II score and SOFA score also didn’t show any significant difference between the two groups. The main cause of infection in all patients was pneumonia (60.9%), and it was comparable in both groups. Other causes of infection are listed in Table 1, and they were all comparable in the two groups. Vancomycin treatment doses were higher in the intervention (ascorbic acid) group; however, they were non-statistically significant as described in Table 1. Total daily fluid intake, urine output, mean arterial pressure and the use of vasopressors were all comparable in both groups.\n\na Based on Student’s t test.\n\nb Based on χ2 test.\n\nc Based on Mann Whitney test.\n\nd Based on Fischer’s Exact test.\n\nSerum creatinine, creatinine clearance (Cr.cl) means and blood urea nitrogen (BUN) median were all comparable at baseline in both groups. However, S.cr and Cr.cl showed a statistically significant difference between both groups when compared at the peak and the lowest values, respectively, Table 2. The mean absolute increase in S.cr concentration was significantly greater in the control group compared to the intervention group (difference of 0.29 mg/dL, 95% CI: 0.02 to 0.54, P-value = 0.036), Table 2. The average time for S.cr to peak was 5 and 4.2 days in the intervention and control group, respectively.\n\na Based on Student’s t test\n\nb Based on Mann-Whitney U test\n\nc Based on χ 2 test\n\nd Based on Fisher’s exact test\n\n* Statistically significant (P-value <0.05)\n\nIn a similar manner, the mean absolute decline in Cr.cl concentration was significantly greater in the control group compared to the intervention group (difference of 16.4 mL/min, 95% CI: −32.12 to −0.79, P-value = 0.04), Table 2. Despite the significant increase observed in S.cr, BUN peak concentrations were not significantly different in either group, Table 2.\n\nAccording to the definition of VAN, acute kidney injury occurred in 6 of 41 patients (14.6%) – 1 of 21 patients (4.7%) in the intervention group and 5 of 20 patients (25%) in the control group (RR: 0.19, CI: 0.024–1.49, P-value = 0.093). By applying the new definition of VAN that is adopted by AKIN and KDIGO, the number of patients suffering VAN didn’t change in either group. AKI categorization is summarized in Figure 2. No adverse effects related to ascorbic acid were detected in the intervention group. The ICU mortality rate within 28 days was higher in the control group compared to the intervention group, however, it didn’t reach a statistically significant level, Table 2.\n\n\nDiscussion\n\nVancomycin associated nephrotoxicity (VAN) in critically ill patients is a topic of debate. Many factors may contribute to increasing VAN incidence in this population such as being infected with more resistant pathogens that require larger doses of treatment, alterations in the volume of distribution and concurrent administration of potential nephrotoxic medications.29,30\n\nIn the current study, the incidence of VAN was 25% in the control group. A comparable incidence of 29.5% was reported in a previous study that was performed on post cardiac surgery patients treated with vancomycin.31 Also, an incidence rate of 27.2% was obtained from a study performed on pediatric critically ill patients.32\n\nSeveral experimental studies have investigated the possible nephroprotective role of many antioxidants and they showed promising results in attenuating proximal renal tubular injury, especially upon ascorbic acid administration.21,33 Therefore, the aim of the current study was to investigate the potential nephro-protective role of ascorbic acid against VAN in critically ill patients.\n\nAscorbic acid is a potent antioxidant capable of scavenging a wide range of reactive oxygen species and prevents their damaging effect to macromolecules such as lipids, DNA, and proteins. It has been reported to have the lowest toxicity of all vitamins.22 It is a known precursor of oxalate that may lead to renal failure secondary to hyperoxaluria, However, acute oxalate nephropathy had been reported to occur after the administration of a single dose of 2.5 grams of intravenous ascorbic acid in patients with previous renal injury.22 Therefore, 4 grams of ascorbic acid per day (divided in two doses) was selected as this dose has been shown to be effective against contrast induced nephrotoxicity (CIN)25 and was reported to be safe without increasing the risk of urinary oxalate.30\n\nIn the present study, the absolute difference in S.cr and Cr.cl levels were significantly lower in the ascorbic acid group in comparison with the control group. These findings were consistent with what was obtained from rats and mice models.21,33 The average time for the S.cr to inflate was five and four days in the intervention and control group, respectively, and this is similar to the range reported by Van Hal et al in their meta-analysis.14\n\nRegarding the incidence of VAN, co-administration of ascorbic acid with vancomycin reduced the absolute risk of VAN incidence by 20.3%, however, this reduction didn’t reach a statistically significant level (RR: 0.19; CI: 0.024–1.49; P-value = 0.093). Nevertheless, a 20.3% reduction in the absolute risk of VAN and an approximate 80% reduction in its relative risk should be considered clinically. Mortality was higher in the control group (40%), but it didn’t show a significant difference when compared to the study group (19%). It has been reported in several studies that the mortality rate due to VAN is between 15–60%, and it varies according to the degree of renal injury that has occurred and the studied population.2\n\nSeveral reasons may have contributed to the lack of a statistically significant reduction in the proportion of patients developing VAN. Firstly, the pilot nature of the study may have been insufficient to detect the reduction in VAN incidence statistically. Therefore, further randomized trials with a larger sample size are recommended. Secondly, because of the lack of ascorbic acid as an intravenous injection dosage form in Egypt at the study time, it was administered orally to patients rather than intravenously. The bioavailability of oral dosage forms of ascorbic acid is 36% for the two-gram dose, which is much lower than the intravenous one.34 This might have affected the expected nephro-protective effect of the antioxidant. Thirdly, although vancomycin doses were statistically comparable in both groups, it was noticed that the mean vancomycin daily dose per body weight was higher in the ascorbic acid group compared to the control group. This can be attributed to the higher number of patients suffering from meningitis and infective endocarditis in the intervention group. Consequently, these higher doses might have contributed in increasing the incidence of VAN in the intervention group.35,36 Other potential confounding influences such as hypotension and the need for vasopressors during the study were minimal and comparable among both groups.\n\n\nConclusion\n\nThis preliminary study revealed that ascorbic acid co-administration with vancomycin reduces the absolute increase in S.cr concentration and the absolute decrease in Cr.cl resulting from vancomycin administration. It also reduced the absolute risk of VAN in critically ill patients by 20.3%, however, it didn’t reach a statistically significant level. Further large multicenter prospective randomized clinical trials are recommended to confirm the efficacy of ascorbic acid as a nephro-protectant against VAN.\n\n\nData availability\n\nFigshare: Underlying data for ‘Impact of ascorbic acid in reducing the incidence of vancomycin associated nephrotoxicity in critically ill patients: A preliminary randomized controlled trial’, https://doi.org/10.6084/m9.figshare.15710004.v1.28\n\nThis project contains the following underlying data:\n\n• Data file 1: Demographic data, underlying diseases, concurrent medications and laboratory data in the study groups.\n\n• Original trial protocol.\n\nFigshare: CONSORT checklist for ‘Impact of ascorbic acid in reducing the incidence of vancomycin associated nephrotoxicity in critically ill patients: A preliminary randomized controlled trial’, https://doi.org/10.6084/m9.figshare.15710004.v1.28\n\nData are available under the terms of Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nConsent\n\nWritten informed consent was obtained from all individual participants included in the study.",
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Antimicrob Agents Chemother. 2013; 57 (2): 734–744. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJeffres MN: The whole price of vancomycin: toxicities, troughs, and time. Drugs. 2017; 77(11): 1143–1154. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeaney CJ, Hynicka LM, Tsoukleris MG: Vancomycin-associated nephrotoxicity in adult medicine patients: incidence, outcomes, and risk factors. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. 2014; 34(7): 653–661. PubMed Abstract | Publisher Full Text\n\nHammond DA, Smith MN, Painter JT, et al.: Comparative incidence of acute kidney injury in critically ill patients receiving vancomycin with concomitant piperacillin-tazobactam or cefepime: a retrospective cohort study. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. 2016; 36(5): 463–471. PubMed Abstract | Publisher Full Text\n\nMcQueen KE, Clark DW: Does combination therapy with vancomycin and piperacillin-tazobactam increase the risk of nephrotoxicity versus vancomycin alone in pediatric patients? J Pediatr Pharmacol Ther. 2016; 21(4): 332–338. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTong SY, Lye DC, Yahav D, et al.: Effect of vancomycin or daptomycin with vs without an antistaphylococcal β-lactam on mortality, bacteremia, relapse, or treatment failure in patients with MRSA bacteremia: a randomized clinical trial. Jama. 2020; 323(6): 527–537. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArdjani TEA, Alvarez-Idaboy JR: Radical scavenging activity of ascorbic acid analogs: Kinetics and mechanisms. Theoretical Chemistry Accounts. 2018; 137(5): 1–8. Publisher Full Text\n\nTakigawa M, Yatsu T, Takino Y, et al.: High-Dose Vitamin C Preadministration Reduces Vancomycin-Associated Nephrotoxicity in Mice. J Nutr Sci Vitaminol (Tokyo). 2019; 65(5): 399–404. PubMed Abstract | Publisher Full Text\n\nMoon JM, Chun BJ: The efficacy of high doses of vitamin C in patients with paraquat poisoning. Hum Exp Toxicol. 2011; 30(8): 844–850. PubMed Abstract | Publisher Full Text\n\nNdebele P: The Declaration of Helsinki, 50 years later. Jama. 2013; 310(20): 2145–2146. PubMed Abstract | Publisher Full Text\n\nDoig GS, Simpson F: Randomization and allocation concealment: a practical guide for researchers. J Crit Care. 2005; 20(2): 187–191. PubMed Abstract | Publisher Full Text\n\nSpargias K, Alexopoulos E, Kyrzopoulos S, et al.: Ascorbic acid prevents contrast-mediated nephropathy in patients with renal dysfunction undergoing coronary angiography or intervention. Circulation. 2004; 110(18): 2837–2842. PubMed Abstract | Publisher Full Text\n\nCockcroft DW, Gault H: Prediction of creatinine clearance from serum creatinine. Nephron. 1976; 16(1): 31–41. PubMed Abstract | Publisher Full Text\n\nKhwaja A: KDIGO clinical practice guidelines for acute kidney injury. Nephron Clinical Practice. 2012; 120(4): c179–c184. PubMed Abstract | Publisher Full Text\n\nElsherazy NH, Bazan NS, Shaheen SM, et al.: Impact of ascorbic acid in reducing the incidence of vancomycin associated nephrotoxicity in critically ill patients: A preliminary randomized controlled trial. Figshare. Dataset. 2021. Publisher Full Text\n\nRoberts JA, Abdul-Aziz MH, Lipman J, et al.: Individualised antibiotic dosing for patients who are critically ill: challenges and potential solutions. Lancet Infect Dis. 2014; 14(6): 498–509. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpapen HD, van Doorn KJ, Diltoer M, et al.: Retrospective evaluation of possible renal toxicity associated with continuous infusion of vancomycin in critically ill patients. Ann Intensive Care. 2011; 1 (1): 26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHutschala D, Kinstner C, Skhirdladze K, et al.: Influence of Vancomycin on Renal Function in Critically Ill Patients after Cardiac SurgeryContinuous versusIntermittent Infusion. Anesthesiology: The Journal of the American Society of Anesthesiologists. 2009; 111(2): 356–365. PubMed Abstract | Publisher Full Text\n\nRagab AR, Al-Mazroua MK, Al-Harony MA: Incidence and predisposing factors of vancomycin-induced nephrotoxicity in children. Infect Dis Ther. 2013; 2(1): 37–46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOcak S, Gorur S, Hakverdi S, et al.: Protective effects of caffeic acid phenethyl ester, vitamin C, vitamin E and N-acetylcysteine on vancomycin-induced nephrotoxicity in rats. Basic Clin Pharmacol Toxicol. 2007; 100(5): 328–333. PubMed Abstract | Publisher Full Text\n\nDavis JL, Paris HL, Beals JW, et al.: Liposomal-encapsulated ascorbic acid: Influence on vitamin C bioavailability and capacity to protect against ischemia–reperfusion injury. Nutr Metab Insights. 2016; 9: NMI. S39764. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurgess LD, Drew RH: Comparison of the incidence of vancomycin-induced nephrotoxicity in hospitalized patients with and without concomitant piperacillin-tazobactam. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. 2014; 34(7): 670–676. PubMed Abstract | Publisher Full Text\n\nHanrahan T, Kotapati C, Roberts M, et al.: Factors associated with vancomycin nephrotoxicity in the critically ill. Anaesthesia and intensive care. 2015; 43(5): 594–599. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "94499",
"date": "21 Sep 2021",
"name": "Abdelrahman Fouda",
"expertise": [
"Reviewer Expertise Translational research"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article by Dr. El-Sherazy et al. examined the effect of concomitant administration of ascorbic acid to reduce the incidence of vancomycin-associated nephrotoxicity in critically ill patients. The study is a prospective randomized open-label trial. The study is well designed and the sample size is adequate. The authors found that co-administration of ascorbic acid with vancomycin preserved renal function and reduced the absolute risk of VAN by 20.3%, however, the reduction in VAN incidence was not statistically significant. There were some limitations in the study which the authors addressed in the discussion section such as using ascorbic acid as an oral dose instead of intravenous injection due to lack of availability.\nMy comment is that the study would benefit from representing some of the key data as figures in addition to the numbers in tables at least for the primary outcomes. For example, a graph showing the incidence of VAN and change of S.cr and Cr.cl over time in the control and intervention groups would give the reader an idea of the change in these parameters with and without ascorbic acid administration. In addition, graphical representation of the numbers of absolute increase in S.cr and decrease in Cr.cl would help the reader appreciate the magnitude of change.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "94495",
"date": "28 Sep 2021",
"name": "Mona F. Schaalan",
"expertise": [
"Reviewer Expertise Clinical Pharmacology in the areas of diabetes",
"hypertension",
"and Metabolic Syndrome",
"and Kidney diseases."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst, I appreciate this opportunity to review this interesting article \" Impact of ascorbic acid in reducing the incidence of vancomycin associated nephrotoxicity in critically ill patients: A preliminary randomized controlled trial.\"\nThis study assessed the nephro-protective effect of oral ascorbic acid against VAN in critically ill patients. The current study is a prospective randomized open-label trial. Generally, the study is appropriately designed with sufficient sample size. The results revealed that concomitant administration of oral ascorbic acid with vancomycin preserved renal function and reduced the absolute risk of VAN by 20.3%, yet did not reach statistical significance. This is appropriately discussed and rationalized. The authors also addressed their limitations of the study at the end of the discussion.\nHowever, there are some minor comments that need to be clarified and added to the manuscript.\nThe authors used 2g ascorbic acid twice daily half an hour before the vancomycin dose for the patients assigned to the intervention group.25 Reading the reference no. 25, they used a different dose. The authors should discuss the difference in the dosing used. The authors should also discuss how the dosage used, 2g twice daily would not put the patients at risk of oxalate accumulation.\n\nThe presentation of results in Table 2 needs to be better illustrated in figures and graphs to track the changes in values; e.g. a graph showing the incidence of VAN and change of S.cr and Cr.cl over time in the control and treated groups would help the reader observe the extent of change.\n\nFigure 2. is not sufficiently described and needs the histogram to be more clear in terms of units in the y axis and the magnitude of bars in both arms.\n\nIn the discussion section, 4th paragraph, third line; however, should be written small initial and preceded by semi colon. \"It is a known precursor of oxalate that may lead to renal failure secondary to hyperoxaluria, However, acute oxalate nephropathy ….\"\n\nTo this end, my decision is approval 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?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-929
|
https://f1000research.com/articles/10-186/v1
|
08 Mar 21
|
{
"type": "Research Article",
"title": "Vaccine hesitancy among mothers of under-five children in Coastal South India: a facility-based cross-sectional study",
"authors": [
"Rekha Thapar",
"Nithin Kumar",
"Priya Surendran",
"Aleemath Shahdiya",
"Vibha Mahendran",
"Ranjitha Ramesh",
"Deepali J. Shetty",
"Bhaskaran Unnikrishnan",
"Prasanna Mithra",
"Ramesh Holla",
"Darshan Bhagwan",
"Avinash Kumar",
"Rekha Thapar",
"Priya Surendran",
"Aleemath Shahdiya",
"Vibha Mahendran",
"Ranjitha Ramesh",
"Deepali J. Shetty",
"Bhaskaran Unnikrishnan",
"Prasanna Mithra",
"Ramesh Holla",
"Darshan Bhagwan",
"Avinash Kumar"
],
"abstract": "Background: Vaccine hesitancy (VH) has been identified by the World Health Organization as one among the top ten threats to global public health. There is limited literature regarding VH from developing countries like India. Methods: In this facility based cross-sectional study, 172 mothers of under-five children were assessed regarding VH using the parental attitude towards childhood vaccination questionnaire. Results: The prevalence of VH was 3.4% (n=6). Only 7.6% (n=13) of the study participants had refused vaccination for their child and the most common reason cited for vaccine refusal was that they thought it was not safe (n=6). Government health facilities was the place of routine immunization for 60.5% (n=104) participants. Health care providers (n =79, 46%) were the major source of information regarding vaccines.\nConclusions: Our study highlights the presence of very low prevalence of VH in Mangalore compared to similar studies from India and other parts of the world. The limited number of participants had refused vaccination due to concerns related to vaccine safety.",
"keywords": [
"Vaccine Hesitancy",
"PACV",
"Mothers",
"Vaccination coverage",
"Mangalore"
],
"content": "Introduction\n\nImmunization is one of the most effective and economical health interventions in recent times, which has brought down the incidence of under-five morbidity and mortality attributed to infectious diseases worldwide. The effectiveness of a vaccine is subject to a significant number of people in the community being immunized. Unvaccinated children are at a greater risk of developing diseases. These children make those vaccinated susceptible to a disease due to waning herd immunity, as seen in poliomyelitis (Grassly et al., 2012). In order to achieve maximum coverage of this intervention, the Global Vaccine Action Plan 2011-2020 (GVAP) called for countries to achieve =90% immunization coverage by 2020 for all vaccines by incorporating it in their National Immunization Schedule (Peck et al., 2019). Only 129 out of 194 World Health Organization (WHO) member countries have achieved or surpassed the GVAP national vaccination coverage goal. Immunization coverage across the world since 2010 has been steady at 85% to 86% (Lawrence, 2019). The highly ambitious Sustainable Development Goals (SDGs), to be achieved by 2030, includes two immunization indictors to measure the progress made by countries in their journey towards ensuring healthy lives and promote well-being of all age groups. The percentage of the target population covered by all vaccines included in the national immunization schedule (3.b.1) indirectly reveals the capacity of a nation to access and achieve universal coverage of newer vaccines. Immunization is one among the tracer indicators within the coverage of essential health services or “Universal health Coverage - Index” (3.8.1). The percentage of children up to one year of age who have received three doses of diphtheria-tetanus and pertussis vaccine (DTP3) is taken as proxy indicator for full immunization (WHO, 2017). These estimates of DTP3 are used to monitor the performance of the health system, measure the effectiveness of the immunization program in terms of service delivery, and implement strategies for disease eradication and elimination (Measure Evaluation, n.d.). The global coverage for DTP1 and DTP3 in 2018 was estimated to be 90% and 86% and 86% for the first dose of measles-containing vaccine (MCV1). These estimates, however do not reflect the marked regional differences in vaccination coverage. The DTP1 and DTP3 coverage varied from 84% and 76% in African countries to 97% and 94% in European regions (Peck et al., 2019). The routine immunization coverage has been lower than expected in India where maternal and neonatal tetanus has been eliminated and has also been certified polio-free (UNICEF,n.d.). Only 62% of children were fully immunized, with the coverage of DTP3 and measles first dose estimated at 78.4% and 81.1%, respectively (Ministry of Health and Family Welfare, [MoHFW, 2015a]). However, with programs like mission Indradhanush, India has been able to marginally improve its vaccination coverage (Gurnani et al., 2018).\n\nThe lower vaccination coverage and dropouts may be attributed to populations who are either hard to reach or hard to vaccinate. Hard to reach are those residing in conflict zones or in difficult geographical terrain where vaccination is poor due to inadequate or irregular supply of vaccines. Hard to vaccinate population are those who despite having access to vaccination do not get their children immunized. This group poses a big challenge to immunization programs across the world. The attitude of these individuals, who may be influenced by religious beliefs or distrust, can make them hesitant to accept immunization (Peck, 2019).\n\n“Vaccine hesitancy [VH] refers to the delay in acceptance or refusal of vaccinations despite availability of vaccination services” (WHO, 2014). Vaccine hesitant individuals may be those who have doubts about the vaccine but still get their children vaccinated, or individuals who either refuse or delay a vaccine but receive others, or individuals who reject all vaccines. VH is usually suspected to be present when the immunization coverage is low despite having adequate health services and provision of regular health communication by grass root level workers. This has threatened to reverse the progress made over the years in achieving adequate immunization coverage (WHO, n.d.1). VH has been identified by the WHO as one among the top ten threats to global public health (WHO, n.d.2), and was reported to be a significant problem by 74% of WHO member countries. These countries cited issues related to risk and benefits of vaccines as the most important reason for VH (MacDonald, Butler & Dube, 2018). However, VH is a complex and context specific phenomenon driven by behavioral and social factors which influence an individual’s decision of accepting a vaccine, and not just limited to the safety concerns regarding a vaccine (MacDonald, Butler & Dube, 2018, Thomson, Robinson & Vallee-Tourangeau, 2016). The reason for VH also varies across geographical regions and for different vaccines. The reasons for VH have been explained by the three ‘C’s model - confidence, complacency and convenience. Lack of confidence in health systems providing immunization services, or the health professionals providing information regarding the vaccine or delivering the services can influence an individual’s immunization uptake behavior. The acceptance of vaccines is high when a new vaccine is introduced against any disease. This is reflected in an increase in vaccine coverage and a decrease in the incidence of disease over a period of time. This leads to complacency resulting in a belief that the vaccine is no longer needed. This results in refusal for vaccination (Edwards and Hackelle, 2016). Vaccination convenience in terms of quality of services provided, its ease of availability and geographical accessibility, affordability, ability to understand the communication offered by health workers and appeal of services can also affect vaccination uptake (MacDonald, 2015).\n\nThere are many factors influencing vaccine uptake among parents. Adverse effects of the vaccines, and pain and fever following immunization are the reasons for VH in many countries. Wrong and misleading information from mass media or unfavorable incidents following immunization reported by relatives and friends may lead parents to question the necessity of providing vaccination to their children. Some parents withhold, delay or in extreme situations refuse to vaccinate their children even though they believe in the effectiveness of vaccines. Many parents also believe that natural immunity, prolonged breastfeeding, maintaining proper hygiene and sanitation or isolating the sick are better ways of protecting their children than vaccination. Lack of awareness and social factors like religious beliefs which contradict the use of vaccines also play an important role in VH (LaClair, Smith & Woodword, 2014).\n\nThere is limited literature regarding VH from Mangalore, where the proportion of children fully immunized (children between 12-23 months who have received measles, BCG and 3 doses of DPT and OPV) is 77.3% This is higher than the overall state average of 62.6% (Ministry of Health and Family Welfare, [MoHFW, 2015c]) and the National average of 62.9% (Ministry of Health and Family Welfare, [MoHFW, 2015a]). However, for a district with high literacy rate and, the immunization coverage rates are expected to be more than 80%.\n\nWith this background, we carried out this study to find the prevalence and reasons for VH among mothers of under-five children in Mangalore.\n\n\nMethods\n\nMangalore, the major commercial and district headquarter of Dakshina Kannada in the South Indian state of Karnataka, India is known for its numerous educational institutes. It has a literacy rate of 93.4% with male literacy being 96.03% and female literacy 90.84%, which is better than the national urban average of 85% (Census, 2001). The performance of the district in achieving key health care indicators including immunization coverage is also better than the state and national average.\n\nIn this facility-based cross-sectional study, mothers of under-5 children visiting hospitals affiliated to Kasturba Medical College, Mangalore were assessed regarding VH. The sample size was calculated considering proportion of vaccine hesitancy among mothers to be 40.2%, based on a previous study (Dube et al., 2016), relative precision of 20%, confidence level of 95%, power 80% and adding a non-response error of 20%. It was calculated using the formulae: N= 4pq/d2 where P = Prevalence, q = 100-P, d = Precision. The study was carried out during the months of March and April 2017.\n\nParticipants were approached in the waiting area of the outpatient departments of the hospitals and were briefed about the purpose and objectives of the study. Data was collected by questionnaire from the willing participants after obtaining written informed consent to participate. Mothers with at least one child visiting the obstetric and pediatrics outpatient departments were included in the study using non-random (convenient) sampling technique.\n\nThis study was approved by the Institutional Ethics Committee of Kasturba Medical College, Mangalore (IEC KMC MLR 03-17).\n\nInformation was collected using a semi-structured questionnaire which had the following sections:\n\n- Section A: Socio-demographic information of the participants (age, education, occupation, marital status, education and occupation of spouse, family income, number of family members, religion, place of residence, place of routine immunization, number of children, gender of the children);\n\n- Section B: Core VH survey questions (Larson et al., 2015);\n\n- Section C: Parental attitude towards childhood vaccination (PACV) (Opel et al., 2011). The PACV is a validated questionnaire which assesses the attitude of mothers towards vaccination under three domains: immunization behavior, beliefs about vaccine safety and efficacy and trust.\n\nThe questionnaire was translated to the local vernacular language, Kannada (Extended data (Rekha et al., 2021)) and was pretested and content validated for the language. The pretesting was done on 30 mothers visiting the outreach clinics of the department of community medicine. Based on the responses, the questionnaire was modified for the language without changing the content. The content validation of the questionnaire was done by the subject expert. Socioeconomic status was evaluated using Modified B.G Prasad scale (Singh, Sharma & Nagesh, 2017). Questionnaires were checked for completeness and only the completed questionnaires were considered for final analysis.\n\nThe collected data was entered in and analyzed using IBM SPSS (Statistical Package for Social Sciences) Statistics for Windows Version 25.0. Armonk, NY: IBM Corp) and expressed using mean (Standard Deviation), and proportions. The calculated PACV scores ranged from 0-100: participants who scored between 0-49 were considered to have no VH, and those with scores from 50-100 were considered to be vaccine hesitant. The factors associated with VH was assessed using Chi-square test and P<0.05 was considered a statistically significant association.\n\n\nResults\n\nA total of 172 mothers were assessed regarding VH. The mean age of the participants was 29.4 (±5.2) years, with majority (n=75, 63.0%) in the age group between 26-35 years. A higher proportion (n=61, 35.5%) of the participants had completed high school and were from middle socio-economic status. (n=30, 30%) Government health facilities were the place of routine immunization for 60.5% (n=104) of the participants. The socio-demographic characteristics of the study participants is depicted in Table 1.\n\nHealth care providers (n =79, 46%) were the major source of information regarding vaccines, followed by the child’s primary doctor (n= 52, 30.2%). Family members, television, newspaper magazine and internet comprised the rest of the sources.\n\nTable 2 shows the findings of the baseline VH survey among the study participants. Only 7.6% (n=13) of the study participants had refused vaccination for their child and the most common reason cited for vaccine refusal was that they thought it was not safe (n=6).\n\n* Multiple responses\n\nThe perception of the participants regarding vaccine safety and efficacy, trust and their immunization behavior as assessed by PACV is shown in Table 3. A lower proportion of the participants (14%, n=24) opined that children get more vaccines than that are good for them. A higher proportion (80.8%, n=139) of the participants worried about their child having serious side effects from the vaccine. However, the majority (91.8%, n=158) of the participants trust the information provided to them regarding vaccines. A very small proportion (n=6, 3.5%) of the study participants had refused getting their child immunized and 5.8% (n=10) were hesitant about childhood vaccination.\n\nThe median PACV score among participants was 10.0 with a total of 166 parents (96.5%) scoring a value < 50 and were defined as not vaccine hesitant. Only 6 (3.5%) participants had a PACV score = 50 and were labelled as vaccine hesitant. Among the participants who were found to have no VH, a higher proportion were under the age of 30 years, urban residents, belonged to Hindu religion and utilized government facility for immunization ( Table 4).\n\n\nDiscussion\n\nThe success of immunization programs relies on high vaccination coverage and vaccine uptake rates. Maintaining a high timely vaccination coverage has resulted in effective control of vaccine preventable diseases (VPDs), among those vaccinated, as well as the unvaccinated by virtue of herd immunity. However, recent outbreaks of VPDs like measles and diphtheria in both developed and developing countries, has undermined the progress made by immunization programs implemented all over the world. High vaccination coverage rates are misleading and do not reflect the number of under-vaccinated and unvaccinated section of the population (Kumar et al., 2016). The global vigilance on immunization programs in developed countries has attributed recent outbreaks of measles to VH (Shukla, 2019). However, the trend of VH is universal and not just limited to developed countries. The analysis of WHO/ UNICEF Joint Reporting Form data for VH for the years 2015-2017 revealed that VH was reported by more than 90% of the WHO member countries (Lane et al., 2018).\n\nIn our study, a very low proportion (3.5%) of the participants were found to be vaccine hesitant. The lower VH among the participants could be due to high literacy rate, better immunization coverage and services, and creation of awareness by grass root level workers which has resulted in high vaccine uptake rates. With an educational index of 0.958 and an overall Human Development Index (HDI) of 0.830, Mangalore has always been one of the better performing regions in the State of Karnataka (Shodhganga. Profile of Dakshina Kannada, n.d.) There is huge variation in the estimates of VH reported in primary studies from various parts of the world. This variation may be attributed to the use of different questionnaires and cut-off scores to categorize VH among the population. Assessment of hesitancy for an individual vaccine or the entire immunization schedule, as well as the age group of target population may also result in VH estimates of varying proportions. The VH reported in studies from different parts of India ranged between 14.1% to 83% (Krishnamoorthy et al., 2019, Agarwal et al., 2019, Narayanan, Jayaraman & Gopichandran, 2018, Dasgupta et al., 2018). Similar variation in the prevalence of VH is also observed in studies from other parts of the world. The VH was as low as 1.1% in a study in Guatemala (Domek et al., 2018) while in a study in Nigeria it was 76% (Larsen et al, 2015b). Other studies have reported VH in the range of 11.6% to 66% (Dube et al, 2016, Lane et al., 2018, Mohd Azizi, Kew, Moy, 2017, Giambi et al., 2018, Ferrante et al., 2019, Napolitano, D’Alessandro & Angelilo, 2018, Ray et al., 2018, Paterson, Chantler & Larson, 2018). It is evident that irrespective of the measurement tool used, VH is widely prevalent across countries, having an impact on the coverage rates of immunization and vaccine uptake among the targeted population. Hence, it is imperative to first identify these vaccine hesitant groups, and strategically work towards restoring their trust and belief towards the health system in general and vaccination (Marti et al., 2017). Although by definition, it includes people who delay or refuse vaccination, people who chose to vaccinate in spite of having doubts about the same should also be identified and their concerns addressed. This will ensure a better immunization coverage in the future.\n\nIdentifying and overcoming the reasons for VH is one of the most important challenge faced by immunization and program managers. VH is usually limited to a subgroup of the population whose decision-making process is driven by their socio-cultural, religious, and political standing and cannot be overcome by strengthening the health system or increasing vaccination services alone. Studies have shown that there is not one particular reason for refusing or delaying vaccination. The reasons are diverse and can vary from one person to another in a vaccine hesitant population. Globally, the three most common reasons cited for VH during the year 2015, 2016 and 2017 were concerns related to vaccine safety (22%, 23%, 23%), lack of knowledge and awareness regarding immunization and its benefit (15%, 13%, 10%), and religious and cultural beliefs (10%, 9%, 12%) (Marti et al., 2017).\n\nThe reasons for VH varied across WHO regions and socio-economic status of the countries within these regions. In the European Region, South East Asian Region and Western Pacific Region, concerns about safety of vaccines and fear of side effects were predominant, while issues revolving around religion and cultural beliefs were common in the Americas. Inadequate knowledge or information regarding vaccines and their benefits as well as poor awareness were mainly reported from African Region and Eastern Mediterranean Region. Adverse events following immunization and safety of the vaccine were the most important driver for VH in upper-middle income countries, while inadequate knowledge and awareness regarding vaccines and immunization services were predominantly seen in lower-middle income countries. VH due to religious influences were seen across countries of all strata of income and in most of the WHO regions (The History of Vaccines. n.d.).\n\nApprehensions regarding the risks and benefit of vaccines were the most common reasons for VH in our study which was also reported by a study in Chennai. The other reasons for influencing VH cited in that study were lack of trust for the newer vaccines (Narayanan, Jayaraman & Gopichandran, 2108). In a study in Siliguri, unwillingness and having no reliable information on the vaccine were the major reasons cited for VH (Dasgupta et al., 2018). Primary studies from different part of the world have also reported a heterogeneous group of reasons. The most frequently cited reason leading to VH in a study in England were the presence of porcine gelatin in the vaccine and issues related to vaccine effectiveness and side effects (Lane et al., 2018). Meanwhile, in a study in Guatemala, health system related factors like distance of the clinic, cost incurred to get to the clinic and timing of the clinic and waiting at the clinic were the predominant reasons for VH (Domek et al., 2018). A study conducted in Quebec found that fear of adverse effects and low perceived vulnerability of the child or severity of the disease were the most common reasons for VH (Dube et al., 2016).\n\nReligious influences for VH are the most challenging to address in any immunization program since they arise out of individual’s core belief and driven by their faith. Use of human tissues in creating a vaccine or the belief that the body should be healed naturally by God and not by chemicals are some of the points for refusing vaccines (McKee & Bohannon, 2016). Unlike other reasons for VH, they do not arise out of lack of knowledge or awareness regarding immunization, but is a by-product of an individual’s or a group’s religious conviction thus making it difficult to change their attitude towards immunization (McKee & Bohannon 2016).\n\nIssues related to vaccine safety and side effects is one of the most important reasons for refusal of vaccines by the parents. Parents are bombarded with information on vaccine safety and adverse effects, and opinions on vaccination through mass media and social media. Such information can be overwhelming at times, creating enough doubts to make an informed decision, thus leading them to ultimately refuse vaccination (McKee & Bohannon 2016).\n\nIn our study, mothers aged less than 30 years, residing in an urban area, belonging to Hindu religion, and availing immunization services from a government facility were found to be non-vaccine hesitant, though these factors were not significant (P>0.05). Mother’s age (Krishnamoorthy et al., 2019), lower educational status of mother (Agarwal et al., 2019, Dasgupta et al., 2018) nuclear family (Agarwal et al., 2019, Dasgupta et al., 2018), and past history of incomplete immunization (Agarwal et al., 2019) were found to be significantly associated with VH in other studies from India. Some of the factors associated with VH reported in studies from other parts of the world include younger parents (Mohd Azizi, Kew & Moy, 2017), unemployed parents (Mohd Azizi, Kew & Moy, 2017), higher educational status (Ferrante et al., 2019), contact with parents of children who had experienced serious side effects (Giambi, 2018), not advised by a pediatrician to complete the full course of immunization (Giambi, 2018), and lack of trust on the pediatrician (Napolitano, 2018).\n\nThis being a facility-based study, our findings cannot be extrapolated to the general population.\n\n\nConclusion\n\nOur study highlights the presence of very low prevalence of VH in Mangalore compared to similar studies from India and other parts of the world. The limited number of participants who had refused vaccination, refused due to concerns related to vaccine safety.\n\nHesitancy to vaccines follows the iceberg phenomenon, with the tip of the iceberg representing the population who refuse vaccination, while the submerged proportion representing the vaccine hesitant population. Identifying these vaccine hesitant subgroups is important for the success of any immunization program. Rather than single site studies, multi-centric studies with robust methodology needs to be carried out to get an actual estimate of the problem. Such studies also give an insight into the various reasons for VH existing in different population groups. Use of digital technology in the form of mobile health apps for tracking immunization can help in identification of vaccine hesitant individual or subgroup depending on their immunization uptake behavior. VH arises out of attitudes and concerns of parents regarding immunization which cannot be overcome by strengthening the health services alone. Behavior change communication and educational intervention needs to be inbuilt into the immunization programs. Health care workers should address the needs and concerns of the target population and beneficiaries regarding vaccines and reinforce their trust on the health system.\n\n\nData availability\n\nOpen Science Framework: Vaccine Hesitancy among mothers of Under-5 children in Coastal South India - A facility-based study, https://doi.org/10.17605/OSF.IO/A3XJU (Rekha et al., 2021).\n\nOpen Science Framework: Vaccine Hesitancy among mothers of Under-5 children in Coastal South India - A facility-based study, https://doi.org/10.17605/OSF.IO/A3XJU (Rekha et al., 2021).\n\nThis project contains the following extended data:\n\n- Questionnaire as asked in the local language.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nWe thank the Department of Community Medicine, Kasturba Medical College, Mangalore, and the Manipal Academy of Higher Education for their support for this research and its publication.\n\n\nReferences\n\nAgarwal AK, Sengar A, Gupta P, et al.: A Study of Vaccine Hesitancy among Mother & Care Provider During MR Vaccine Campaign. Natl J Community Med 2019; 10(11): 605–611.\n\nDasgupta P, Bhattacherjee S, Mukherjee A, et al.: Vaccine Hesitancy for childhood vaccinations in slum areas of Siliguri, India. Indian J Public Health 2018; 62: 253–8. PubMed Abstract | Publisher Full Text\n\nDomek GJ, O’Leary ST, Bull S, et al.: Measuring Vaccine Hesitancy: Field testing the WHO SAGE Working Group on Vaccine Hesitancy survey tool in Guatemala. Vaccine 2018; 36(35): 5273–5281. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDubé E, Gagnon D, Zhou Z, et al.: Parental Vaccine Hesitancy in Quebec (Canada). PLoS Currents 2016; 8. ecurrents. outbreaks. 9e239605f4d320c6ad27ce2aea5aaad2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEdwards KM, Hackell JM: Countering Vaccine Hesitancy. Paediatrics 2016; 138(3): e20162146. PubMed Abstract | Publisher Full Text\n\nFerrante M, Cristaldi A, Cormaci L, et al.: Vaccine Hesitancy among parents in the general population in Sicily (South Italy): A survey study: Maria Fiore. Eur J Public Health 2019; 29(4): ckz186-504. Publisher Full Text\n\nGiambi C, Fabiani M, D’Ancona F, et al.: Parental Vaccine Hesitancy in Italy - Results from a national survey. Vaccine 2018; 36(6): 779–787. PubMed Abstract | Publisher Full Text\n\nGurnani V, Haldar P, Aggarwal MK, et al.: Improving vaccination coverage in India: lessons from Intensified Mission Indradhanush, a cross-sectoral systems strengthening strategy. BMJ 2018; 363: k4782. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrassly NC, Jafari H, Bahl S, et al.: Waning intestinal immunity after vaccination with oral poliovirus vaccines in India. J Infect Dis 2012; 205(10): 1554–1561. PubMed Abstract | Publisher Full Text\n\nKumar D, Chandra R, Mathur M, et al.: Vaccine Hesitancy: understanding better to address better. Isr J Health Policy Res 2016; 5: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrishnamoorthy Y, Kannusamy S, Sarveswaran G, et al.: Factors related to Vaccine Hesitancy during the implementation of Measles-Rubella campaign 2017 in rural Puducherry-A mixed-method study. J Family Med Prim Care 2019; 8: 3962–3970. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLane S, MacDonald NE, Marti M, et al.: Vaccine Hesitancy around the globe: Analysis of three years of WHO/UNICEF Joint Reporting Form data-2015-2017. Vaccine 2018; 36(26): 3861–3867. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaClair BJ, Smith SL, Woodword J: Attitudes and Concerns of Kansas Parents related to Childhood Immunization. Immunize Kansas Kids 2014Reference Source\n\nLarson HJ, Jarrett C, Schulz WS, et al.: Measuring Vaccine Hesitancy: The development of a survey tool. Vaccine 2015; 33(34): 4165–75. PubMed Abstract | Publisher Full Text\n\nLarson HJ, Schulz WS, Tucker JD, et al.: Measuring vaccine confidence: introducing a global vaccine confidence index. PLoS Currents 2015; 25, 7: ecurrents. outbreaks. ce0f6177bc97332602a8e3fe7d7f7cc4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLorenz J: Global Vaccination Coverage Remains Unchanged at 86% Since 2010.2019Reference Source Accessed on 11/04/2020.\n\nMacDonald NE; SAGE Working Group on Vaccine Hesitancy: Vaccine Hesitancy: Definition, scope and determinants. Vaccine 2015; 33(34): 4161–4. PubMed Abstract | Publisher Full Text\n\nMacDonald NE, Butler R, Dubé E: Addressing barriers to vaccine acceptance: an overview. Hum Vaccin Immunother 2018; 14(1): 218–224. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMangalore urban region: Census.2011Reference Source\n\nMarti M, de Cola M, MacDonald NE, et al.: Assessments of global drivers of Vaccine Hesitancy in 2014-Looking beyond safety concerns. PLoS One 2017; 12(3): e0172310. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcKee C, Bohannon K: Exploring the reasons behind parental refusal of vaccines. J Pediatr Pharmacol Ther 2016; 21(2): 104–109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeasure evaluation: Immunization coverage rate by vaccine for each vaccine in the national schedule.n.d.Reference Source\n\nMinistry of Health and Family Welfare (MoHFW 2015): National Family Health Survey-4.2015-2016Reference Source\n\nMinistry of Health and Family Welfare (MoHFW 2015): National Family Health Survey-4. District Fact Sheet Dakshina Kannada, Karnataka2015-2016Reference Source\n\nMinistry of Health and Family Welfare (MoHFW 2015): National Family Health Survey-4. State Fact Sheet - Karnataka 2015-2016Reference Source.\n\nMohd Azizi FS, Kew Y, Moy FM: Vaccine Hesitancy among parents in a multi-ethnic country, Malaysia. Vaccine 2017 May 19; 35(22): 2955–2961. PubMed Abstract | Publisher Full Text\n\nNapolitano F, D’Alessandro A, Angelillo IF: Investigating Italian parents' Vaccine Hesitancy: A cross-sectional survey. Hum Vaccin Immunother 2018; 14(7): 1558–1565. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNarayanan SS, Jayaraman A, Gopichandran V: Vaccine Hesitancy and attitude towards vaccination among parents of children between 1-5 years of age attending a tertiary care hospital in Chennai, India. Indian J Community Family Med 2018; 4(2): 31–36. Publisher Full Text\n\nOpel DJ, Mangione-Smith R, Taylor JA, et al.: Development of a survey to identify vaccine-hesitant parents: the parent attitudes about childhood vaccines survey. Hum Vaccin 2011; 7(4): 419–25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaterson P, Chantler T, Larson HJ: Reasons for non-vaccination: Parental Vaccine Hesitancy and the childhood influenza vaccination school pilot programme in England. Vaccine 2018 Aug 28; 36(36): 5397–5401. PubMed Abstract | Publisher Full Text\n\nPeck M, Gacic-Dobo M, Diallo MS, et al.: Global Routine Vaccination Coverage, 2018. MMWR Morb Mortal Wkly Rep 2019; 68(42): 937–942. PubMed Abstract | Publisher Full Text\n\nRekha T, Kumar N, Surendran P, et al.: Vaccine Hesitancy among mothers of Under-5 children in Coastal South India - A facility-based study.2021, January 26. Publisher Full Text\n\nRey D, Fressard L, Cortaredona S, et al.: Vaccine hesitancy in the French population in 2016, and its association with vaccine uptake and perceived vaccine risk-benefit balance. Euro Surveill 2018; 23(17): 17–00816PubMed Abstract | Publisher Full Text | Free Full Text\n\nShodganga (n.d.): Profile of Dakshina Kannadano dateReference Source\n\nShukla M: The Global Threat of VH. Yale Global Online 2019Reference Source\n\nSingh T, Sharma S, Nagesh S: Socio-economic status scales updated for 2017. Int J Res Med Sci 2017 Jul; 5(7): 3264–3267. Publisher Full Text\n\nThe History of Vaccines: Cultural Perspectives on Vaccination.no dateReference Source\n\nThomson A, Robinson K, Vallée-Tourangeau G: The 5As: A practical taxonomy for the determinants of vaccine uptake. Vaccine 2016; 34(8): 1018–24. PubMed Abstract | Publisher Full Text\n\nUnited Nations International Childrens Emergency Fund: Immunization.no dateReference Source\n\nWorld Health Organization (WHO 2014): Report of the SAGE working group on VH. 2014Reference Source\n\nWorld Health Organization (WHO): Sustainable Development Goals (SDGs) Immunization indicator selection.2017Reference Source\n\nWorld Health Organization (WHO): Improving vaccination demand and addressing hesitancy.Reference Source\n\nWorld Health Organization: Ten threats to global health in 2019.no dateReference Source"
}
|
[
{
"id": "81112",
"date": "22 Mar 2021",
"name": "Giriyanna Gowda",
"expertise": [
"Reviewer Expertise epidemiology",
"clinical trials"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments:\nThe introduction is too lengthy; please make it specific and concise and based on the needs of the study.\n\nIn the abstract, it is mentioned that the prevalence of vaccine hesitance is 3.4 % and also that 7.6 % had refused vaccination for their child. Please clarify this.\n\nRecommendations are not based on results. Kindly specify it.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6893",
"date": "09 Jul 2021",
"name": "Nithin Kumar",
"role": "Author Response",
"response": "We thank you for taking out your valuable time to review our article. We have incorporated all the changes and corrections suggested by you in the manuscript. Kindly find the response letter below. Response to the Comments: 1.The introduction is too lengthy; please make it specific and concise and based on the needs of the study. Thank you for the suggestion. We have made the introduction concise and specific, in line with the objectives of the study. 2. In the abstract, it is mentioned that the prevalence of vaccine hesitance is 3.4 % and that 7.6 % had refused vaccination for their child. Please clarify this.One of the questions in the Core vaccine hesitancy Survey tool directed towards the mothers was “Have you ever refused a vaccination for your child? Yes/No”. Only 7.6% of the study participants had refused vaccination for their child at some point of time. The prevalence of vaccine hesitancy was calculated based on the scores obtained from the Parental Attitude Towards Childhood Vaccination Questionnaire (PACV). Participants who scored between 50 -100 were vaccine hesitant. Only 3.4% of the study participants were vaccine hesitant. We have clarified it in abstract. 3. Recommendations are not based on results. Kindly specify it. Recommendations have been made specific to the conclusions drawn from the study."
}
]
},
{
"id": "82849",
"date": "04 May 2021",
"name": "Aida Kalok",
"expertise": [
"Reviewer Expertise Maternal health",
"General Obstetrics."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe introduction is quite lengthy.\n\nSample size - please state the number of participants required based on the sample size calculation. Did this study reach its required sample size?\n\nWhat was the study hypothesis?\n\nData collection: Did the participants complete the questionnaire themselves? What about the illiterate mothers?\n\nData analysis: Was there any association between VH and maternal employment/level of education/socio-economic status? Please include this in the results/discussion.\n\nDiscussion:\nPlease discuss why with such a low VH rate, the proportion of immunised children in Mangalore is still around 77%.\n\nThe study was conducted in a health facility; women who sought/received health care were most likely to demonstrate a lower level of vaccine hesitancy.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6894",
"date": "09 Jul 2021",
"name": "Nithin Kumar",
"role": "Author Response",
"response": "We thank you for taking out your valuable time to review our article. We have incorporated all the changes and corrections suggested by you in the manuscript. Kindly find the response letter below. The introduction is quite lengthy. Thank you for the suggestion. We have made the introduction concise and specific, in line with the objectives of the study. Sample size - please state the number of participants required based on the sample size calculation. Did this study reach its required sample size? Based on the sample size calculation, a total of 172 participants were required to be included in the study. We were able to achieve the sample size. The same has been added to the Methods section in the manuscript. What was the study hypothesis? Even though the study area has a good health system and a literacy rate that is higher than the national figures, the immunization coverage has consistently remained below 90 per cent. The study hypothesis was “Vaccine hesitancy is present in the study area”. Data collection: Did the participants complete the questionnaire themselves? What about illiterate mothers? All the participants were interviewed while they were waiting in the respective OPDs. The same has been included in the methods section of the manuscript. Data analysis: Was there any association between VH and maternal employment/level of education/socio-economic status? Please include this in the results/discussion. Crosstabulation between the presence of vaccine hesitancy and educational status, employment status and socioeconomic status is incorporated in the results and discussion section. However, no statistically significant association was observed between VH and maternal employment, level of education and socio-economic status. Discussion: Please discuss why with such a low VH rate, the proportion of immunized children in Mangalore is still around 77%. Being a health facility-based study, our finding of low VH among the study participants does not reflect the status of VH in Mangalore. Population-based studies covering a larger sample / multicentric studies would throw more evidence towards the presence of VH as a reason for a lower vaccination coverage in the study area. Also, since the study was conducted in a health facility; the women who sought/received health care were most likely to demonstrate a better health seeking behavior which is also reflected in a lower vaccine hesitancy among the participants. The study was conducted in a health facility; women who sought/received health care were most likely to demonstrate a lower level of vaccine hesitancy. Yes. we agree with the observation."
}
]
}
] | 1
|
https://f1000research.com/articles/10-186
|
https://f1000research.com/articles/9-591/v1
|
11 Jun 20
|
{
"type": "Research Article",
"title": "An embedded randomised controlled retention trial of personalised text messages compared to non-personalised text messages in an orthopaedic setting",
"authors": [
"Alex S. Mitchell",
"Liz Cook",
"Alexandra Dean",
"Caroline Fairhurst",
"Matthew Northgraves",
"David J. Torgerson",
"Mike Reed",
"Liz Cook",
"Alexandra Dean",
"Caroline Fairhurst",
"Matthew Northgraves",
"David J. Torgerson",
"Mike Reed"
],
"abstract": "Background: Several studies have investigated whether personalising trial documentation can aid recruitment and retention. We did a ‘study within a trial’ (SWAT) evaluating the effectiveness of a personalised text message compared to a non-personalised text message, on the retention rate in a large orthopaedic trial. Methods: The SWAT was embedded in the Knee Replacement Bandaging Study (KReBS) trial. The primary outcome was the proportion of 12-month questionnaires returned. Secondary outcomes were the proportion of questionnaires completed and time to questionnaire return. Binary data were analysed using logistic regression and time to return using Cox proportional hazards regression. Odds ratios (OR) and hazard ratios (HR) are presented, with associated 95% confidence intervals (CI) and p-values. Results: In total, 1465 participants were included in the SWAT. In the personalised group, 644/723 (89.1%) of participants returned a questionnaire, compared to 654/742 (88.1%) in the non-personalised group. The absolute difference in return rate was 0.9% (95% CI: -2.3% to 4.2%; p=0.57). There was no evidence of a difference between the groups in the likelihood of returning a questionnaire (OR 1.09; 95% CI: 0.79 to 1.51; p=0.61), the likelihood of returning a complete questionnaire (OR 1.11; 95% CI: 0.82 to 1.51; p=0.50) nor in time to return (HR 1.05; 95% CI: 0.94 to 1.17; p=0.40). Conclusion: This SWAT adds to the growing evidence base for whether personalised text messages are effective. Registration: ISRCTN87127065 (20/02/2017); SWAT 35 (01/12/2015)",
"keywords": [
"SWAT",
"Study Within A Trial",
"attrition",
"SMS",
"text messages"
],
"content": "Introduction\n\nClinical trialists have identified the recruitment and retention of participants as key issues for randomised controlled trials (RCT)1,2.\n\nSeveral studies have investigated whether personalising trial documentation can aid recruitment and retention3,4. Recently, Cochrane et al. looked at the effect of personalised text messages compared to standard text messages in improving retention rates5. This study was carried out in response to a number of embedded trials evaluating the effectiveness of SMS messages in improving retention rates6–11, alongside a study suggesting personalised messages increased the payment of delinquent fines12.\n\nTo further add to the evidence on the effectiveness of personalised text messages, we did a ‘study within a trial’ (SWAT) evaluating the effectiveness of a personalised text message compared to a non-personalised text message on postal questionnaire response rates in a large orthopaedic trial.\n\n\nMethods\n\nThis paper details the methods and results of a SWAT embedded within the prospectively registered Knee Replacement Bandaging Study (KReBS) RCT (ISRCTN87127065, registered on 20 February 2017). KReBS evaluated the effectiveness of a two-layer compression bandage compared with a standard wool and crepe bandage applied post-operatively on patient-reported outcomes in total knee replacement patients13.\n\nThe SWAT was conducted in 26 NHS hospital trust sites and was implemented at the start of the study. All KReBS participants were eligible for this SWAT provided they had opted in to receiving SMS messages and were not deceased or withdrawn from follow-up before being due to be sent their 12-month postal questionnaire.\n\nParticipants in the SWAT were sent either a personalised or non-personalised text message (Table 1) four days after their 12-month questionnaire was sent.\n\nKReBS - Knee Replacement Bandaging Study\n\nThe primary outcome was the proportion of participants who returned a 12-month questionnaire. Secondary outcomes were the proportion of participants who completed the questionnaire and time to questionnaire return. A questionnaire was considered complete if the participant had answered 11 or more questions of the 12-item host trial primary outcome, the Oxford Knee Score14.\n\nSince this was an embedded trial, the sample size was determined by the number of participants in the main KReBS trial13, which aimed to recruit 2600 participants.\n\nParticipants were randomised into the SWAT using simple randomisation in a 1:1 allocation ratio. The allocation schedule was generated by a researcher at the York Trials Unit not involved in the recruitment or follow-up of participants.\n\nParticipants were not informed of their explicit participation in the SWAT, but due to the nature of the intervention could not be blinded to whether the text was personalised or non-personalised. Similarly, it was not possible to blind research staff to SWAT allocation.\n\nThe SWAT was approved by the Research Ethics Committee North East – Newcastle and North Tyneside on 13/04/2018 (REC Number 16/NE/0400; Amendment Number 16/NE/0400/AM14). As the SWAT was deemed to be low risk, explicit informed consent was not obtained for participation.\n\n\nStatistical analysis\n\nAnalyses were carried out using Stata v16.015. A diagram detailing the flow of participants through the SWAT is provided, and baseline characteristics are presented by SWAT allocation. Outcomes are summarised descriptively. Statistical tests were two-sided using a 5% significance level, and were done on an intention to treat basis. All analyses (except the calculation of the absolute difference in return rate which was estimated using the two-sample test of proportions) used mixed effects regression, adjusting for SWAT allocation and host trial allocation as fixed effects and trial site as a random effect. Relevant parameter estimates are presented with associated 95% confidence intervals and p-values.\n\nThe proportion of participants who returned a 12-month questionnaire, and proportion complete, was analysed using logistic regression. A second SWAT evaluating receipt of a pen on response rates was also embedded in KReBS at 12 months16. In a sensitivity analysis, we additionally adjusted the primary model for pen SWAT allocation.\n\nTime to questionnaire return was analysed using a Cox proportional hazards shared frailty model. Participants who did not return a questionnaire were censored at 90 days.\n\n\nResults\n\nIn total, 2335 participants were recruited into the KReBS trial and 1470 were randomised to the SWAT (Figure 1). The average age was 66.8 years and 54.0% were female (Table 217). Five participants died or withdrew following randomisation and as a result 723 participants in the personalised group, and 742 in the non-personalised group, were sent a 12-month questionnaire and were included in the analysis. Of these, 680 (94.1%) of the 723 participants in the personalised group, and 701 (94.5%) of the 742 in the non-personalised group, were sent a text.\n\nIn the personalised group, 644/723 (89.1%) participants returned a questionnaire, compared to 654/742 (88.1%) in the non-personalised group (Table 317). The absolute difference in return rate was 0.9% (95% CI: -2.3% to 4.2%; p=0.57). There was no evidence of a difference between the groups in the likelihood of returning a questionnaire (OR 1.09; 95% CI: 0.79 to 1.51; p=0.61), the likelihood of returning a complete questionnaire (OR 1.11; 95% CI: 0.82 to 1.51; p=0.50) nor in time to return (HR 1.05; 95% CI: 0.94 to 1.17; p=0.40). In total, 1465 participants were also randomised to the pen SWAT. When the primary model was repeated with the addition of pen SWAT allocation, the results remained the same.\n\n\nDiscussion\n\nThis embedded trial found little evidence to suggest personalised text messages are more effective than non-personalised text messages in encouraging return and completion of questionnaires. The trial did not find evidence of a statistically significant difference between groups in any of the outcomes, although effect size estimates favoured the personalised group. On the other hand, while Cochrane and colleagues also did not find evidence of a statistically significant difference between groups, estimates of effect mostly favoured the non-personalised group5.\n\nThe SWAT had a large sample size, which means the results can be generalised to other orthopaedic studies. However, completion rate was calculated as a proportion of all SWAT participants rather than all SWAT participants who returned a questionnaire, and as a result questionnaire completion was highly correlated with questionnaire return. In addition, some participants included in the analysis did not receive a text message.\n\n\nConclusion\n\nThis SWAT adds to the growing evidence base for whether personalised trial documentation, in particular text messages, are effective.\n\n\nData availability\n\nOpen Science Framework: Underlying data and CONSORT diagram for an embedded randomised controlled retention trial of personalised text messages compared to non-personalised text messages in an orthopaedic setting. https://doi.org/10.17605/OSF.IO/KHJ8E17\n\nThis project contains the following underlying data:\n\n- KReBS_Text_SWAT_Clean.sas (Study data in SAS compatible format)\n\n- KReBS_Text_SWAT_Clean.csv (Study data in .csv format)\n\n- KReBS_Text_SWAT_Clean_Key.xlsx (Key for datasets)\n\nOpen Science Framework: CONSORT checklist for ‘An embedded randomised controlled retention trial of personalised text messages compared to non-personalised text messages in an orthopaedic setting’ https://doi.org/10.17605/OSF.IO/KHJ8E17\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\nBower P, Brueton V, Gamble C, et al.: Interventions to improve recruitment and retention in clinical trials: a survey and workshop to assess current practice and future priorities. Trials. 2014; 15: 399. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHewitt CE, Kumaravel B, Dumville JC, et al.: Assessing the impact of attrition in randomized controlled trials. J Clin Epidemiol. 2010; 63(11): 1264–1270. PubMed Abstract | Publisher Full Text\n\nEdwards PJ, Roberts I, Clarke MJ, et al.: Methods to increase response to postal and electronic questionnaires. Cochrane Database Syst Rev. 2009; (3): MR000008. PubMed Abstract | Publisher Full Text\n\nMcCaffery J, Mitchell A, Fairhurst C, et al.: Does handwriting the name of a potential trial participant on an invitation letter improve recruitment rates? A randomised controlled study within a trial [version 1; peer review: 2 approved]. F1000Res. 2019; 8: 659. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCochrane A, Welch C, Fairhurst C, et al.: An evaluation of a personalised text message reminder compared to a standard text message on postal questionnaire response rates: an embedded randomised controlled trial [version 1; peer review: 2 approved]. F1000Res. 2020; 9: 154. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAshby R, Turner G, Cross B, et al.: A randomized trial of electronic reminders showed a reduction in the time to respond to postal questionnaires. J Clin Epidemiol. 2011; 64(2): 208–212. PubMed Abstract | Publisher Full Text\n\nBrabyn S, Adamson J, MacPherson H, et al.: Short message service text messaging was feasible as a tool for data collection in a trial of treatment for irritable bowel syndrome. J Clin Epidemiol. 2014; 67(9): 993–1000. PubMed Abstract | Publisher Full Text\n\nClark L, Ronaldson S, Dyson L, et al.: Electronic prompts significantly increase response rates to postal questionnaires: a randomized trial within a randomized trial and meta-analysis. J Clin Epidemiol. 2015; 68(12): 1446–1450. PubMed Abstract | Publisher Full Text\n\nKeding A, Brabyn S, MacPherson H, et al.: Text message reminders to improve questionnaire response rates. J Clin Epidemiol. 2016; 79: 90–95. PubMed Abstract | Publisher Full Text\n\nMan MS, Tilbrook HE, Jayakody S, et al.: Electronic reminders did not improve postal questionnaire response rates or response times: a randomized controlled trial. J Clin Epidemiol. 2011; 64(9): 1001–1004. PubMed Abstract | Publisher Full Text\n\nRichmond SJ, Keding A, Hover M, et al.: Feasibility, acceptability and validity of SMS text messaging for measuring change in depression during a randomised controlled trial. BMC Psychiatry. 2015; 15: 68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaynes LC, Green DP, Gallagher R, et al.: Collection of delinquent fines: An adaptive randomized trial to assess the effectiveness of alternative text messages. J Policy Anal Manag. 2013; 32(4): 718–730. Publisher Full Text\n\nCook L, Northgraves MJ, Fairhurst C, et al.: Knee Replacement Bandaging Study (KReBS) evaluating the effect of a two-layer compression bandage system on knee function following total knee arthroplasty: study protocol for a randomised controlled trial. Trials. 2019; 20(1): 261. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDawson J, Fitzpatrick R, Carr A, et al.: Questionnaire on the perceptions of patients about total hip replacement. J Bone Joint Surg Br. 1996; 78(2): 185–190. PubMed Abstract | Publisher Full Text\n\nStataCorp: Stata Statistical Software: Release 16. College Station, TX: StataCorp LLC, 2019.\n\nMitchell A, Cook L, Dean A, et al.: Using pens as an incentive for questionnaire return in an orthopaedic trial: an embedded randomised controlled retention trial [version 1; peer review: 1 approved with reservations]. F1000Res. 2020; 9: 321. Publisher Full Text\n\nMitchell A, Cook L, Dean A, et al.: Underlying data and CONSORT diagram for an embedded randomised controlled retention trial of personalised text messages compared to non-personalised text messages in an orthopaedic setting. 2020. http://www.doi.org/10.17605/OSF.IO/KHJ8E"
}
|
[
{
"id": "64613",
"date": "03 Jul 2020",
"name": "Michelle E Kho",
"expertise": [
"Reviewer Expertise Research methodology",
"trial design and reporting"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMitchell et al. elegantly describe a SWAT of personalized vs. non-personalized reminder text messages embedded in a randomized orthopaedic trial. The primary outcome was questionnaire return at 12 months, and the secondary outcomes were proportion of completed questionnaires, and time to questionnaire return. There was no difference in any outcome between groups.\n\nMinor issues:\nThere is a large body of evidence outlining strategies to improve return rates of postal questionnaires1. The primary outcome in this study, questionnaire return at 12 months, could be confounded by the host trial efforts to improve postal questionnaire return. Can the authors report more information on the host trial efforts to optimize postal questionnaire return?\n\nThe questionnaire return rates for this subgroup of host trial participants was very high (~89%). Can the authors report the questionnaire return rates for the 809 people in the host trial who were not included in the SWAT, or if this is not available, the overall questionnaire return rate for the host trial?\n\nIn Figure 1, can you please clarify the difference between those excluded in the first box for “did not provide a valid mobile phone number” and those who were sent a questionnaire and “did not provide a valid phone number”?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7106",
"date": "15 Sep 2021",
"name": "Alex Mitchell",
"role": "Author Response",
"response": "We thank the reviewer for her positive feedback and constructive comments, to which we have responded below. In addition to responding to the comments, we have made a minor amendment to the results of the paper, as since publication a duplicate randomisation was found, and therefore 2334 participants were randomised to the host trial, not 2335. This does not impact the results of the SWAT, as the duplicate randomisation was not given an allocation in the SWAT. There is a large body of evidence outlining strategies to improve return rates of postal questionnaires1. The primary outcome in this study, questionnaire return at 12 months, could be confounded by the host trial efforts to improve postal questionnaire return. Can the authors report more information on the host trial efforts to optimize postal questionnaire return? Thank you, we have added text under the Intervention section of the paper, describing the strategies used in the host trial to optimise questionnaire return. The questionnaire return rates for this subgroup of host trial participants was very high (~89%). Can the authors report the questionnaire return rates for the 809 people in the host trial who were not included in the SWAT, or if this is not available, the overall questionnaire return rate for the host trial? In total, 864 participants were not randomised to the SWAT. This number consists of the 806 who did not opt-in to receive SMS, and the 58 who had either withdrawn, did not provide a valid mobile phone number or were missed. Of these 864, 827 had not withdrawn by the 12-month time point and were sent a questionnaire. 704 returned the questionnaire, which corresponds to a response rate of 85.1%. This is slightly lower than the response rate observed in the SWAT, which may be due to participants who didn’t opt-in to receive SMS or didn’t provide a valid mobile phone number being less engaged with the study. Due to this being a post-hoc analysis, we have decided not to include this result in the publication. In Figure 1, can you please clarify the difference between those excluded in the first box for “did not provide a valid mobile phone number” and those who were sent a questionnaire and “did not provide a valid phone number”? We have added text describing the two stages of mobile phone number verification in the Intervention section of the paper."
}
]
}
] | 1
|
https://f1000research.com/articles/9-591
|
https://f1000research.com/articles/10-871/v2
|
15 Sep 21
|
{
"type": "Research Article",
"title": "Driving-induced lower back pain: Investigation of causes and recommendations with TRIZ",
"authors": [
"Poh Kiat Ng",
"Muhammad Syafiq Syed Mohamed",
"Jian Ai Yeow",
"Muhammad Syafiq Syed Mohamed",
"Jian Ai Yeow"
],
"abstract": "Background: Driving-induced lower back pain (DLBP) is associated with long driving times and awkward postures. Nonetheless, its actual causes and solutions remain unclear due to intervening causes from activities of daily living and traumatic injuries. This study investigated the causes and recommendations for DLBP using the theory of inventive problem solving (TRIZ). Methods: A cause-and-effect chain analysis (CECA) was conducted based on discussions with 19 ergonomics experts from Malaysia. Engineering contradictions were formulated according to the causes and associated with the parameters of the TRIZ system. These parameters were then intersected in the contradiction matrix to extract the inventive principles. Finally, recommendations were made based on these principles. Results: CECA uncovered the design- and posture-related causes of DLBP. It was implied that missing seat adjustment controls might cause drivers to sit with their knees positioned higher than their hips. This issue causes an excessive posterior pelvic tilt, resulting in DLBP. To address this issue, an inert atmosphere involving the addition of inflatable bubble wraps to elevate the posterior position was recommended. Conclusion: While there have been studies on DLBP, the present study demonstrated originality by using TRIZ to preliminarily but systematically investigate and resolve DLBP. Further triangulations, prototyping, experimentations, and verifications were not possible due to time and budgetary constraints. Nevertheless, this research uncovered the TRIZ-integrated perspectives on ergonomic solutions to DLBP that are more cost-effective than medical treatments or design overhauls.",
"keywords": [
"TRIZ",
"lower back pain",
"driving",
"posterior pelvic tilt",
"ergonomics",
"awkward posture",
"inventive principles",
"engineering contradiction"
],
"content": "Introduction\n\nLower back pain (LBP) involves pain felt below the costal margin and above the inferior gluteal folds.1 In Australia, the healthcare cost for LBP varies if the patient is admitted to the hospital (AUD$ 14,949) or discharged from an emergency department (AUD$ 584).2 In addition, LBP also radically changes one’s life and identity over time.3,4\n\nWhile there are findings on the risk factors for DLBP, there is limited evidence supporting that whole-body vibrations directly increase DLBP risks.5 DLBP is attributable to accelerated muscle fatigue due to the upright driving posture that is maintained for a long time.6,7\n\nAlthough improving seat designs limits the effects of DLBP,8–11 the causes and solutions for DLBP remain ambiguous due to the presence of outliers from daily living activities. For example, the causes may be complicated due to trauma effects. If a driver sustains injuries from an accident, factors such as airbag deployment and the vehicles involved can affect the pain location.12 Therefore, it is important to create proper exclusion criteria before exploring the causes and recommendations for DLBP. While DLBP is often researched using surveys,13–16 these alone may not sufficiently provide the information needed to address the issue.17\n\nThe theory of inventive problem solving (TRIZ) is an algorithmic problem-solving approach used in various areas, such as technology and business.18–21 The use of such a systematic yet adaptable approach in the context of DLBP has not been explored. Hence, this study aimed to investigate the causes and recommendations for DLBP using TRIZ.\n\n\nMethods\n\nThe exclusion criteria were established first because DLBP is a specific kind of LBP. These criteria were determined through a focus group discussion among three medical doctors who were selected using purposive sampling. Each doctor has had at least 10 years of experience in treating LBP. Based on the discussion, the following criteria should be excluded when deliberating the causes of DLBP:\n\n\n\n• Pre-existing back injuries (e.g. herniated disc, prolapsed disc);\n\n• Fractures;\n\n• Overweight or obesity;\n\n• Congenital spine abnormalities (e.g. ankylosing spondylitis, seronegative spondylarthritis);\n\n• Limb deformities (e.g. talipes equinovarus, congenital polio)\n\n• Other health issues (e.g. spinal stenosis, prostate issues);\n\n• Pregnancy;\n\n• Pain from activities besides driving (e.g. sports, sitting in front of a work desk)\n\nThese exclusion criteria were referenced in the main focus group discussion. A cause-and-effect chain analysis (CECA) was used, with the causes extracted from the main focus group comprising 19 ergonomics experts from Malaysia who were selected using purposive sampling. Each expert has had at least 10 years of experience in ergonomics and DLBP.\n\nThe experts suggested that drivers commonly complain about temporary LBP around the L5–S1 region after driving for 10–15 min due to increased disc pressure caused by a slouched driving posture. This posture is attributable to a posterior pelvic tilt from an increased hip flexion angle when sitting with the hips positioned below the knees. The experts added that this condition occurs if there are no seat adjustment controls for the posterior position. These causes are summarised in the CECA diagram (see Figure 1).\n\n\nResults\n\nFrom the posture-related causes, the first engineering contradiction (EC1) was formulated.\n\nEC1: If the hip is positioned lower than the knees, then the driver sinks his/her weight into the seat (#2: Weight of stationary object), but the increased disc pressure causes LBP (#11: stress or pressure).\n\nThe “then” and “but” phrases were linked to two system parameters22,23 and intersected in the contradiction matrix24 to obtain four inventive principles:\n\n13: The other way around\n\n29: Pneumatics and hydraulics\n\n10: Preliminary action\n\n18: Mechanical vibration\n\nPreliminary action (essential change on the object before needed) was found to be suitable for resolving EC1. Specifically, seat controls can be used to elevate the posterior portion before driving25 for the hips to be positioned above the knees, thereby preventing the risk for LBP. However, some vehicles do not have this type of seat control. For this design-related cause, the EC2 was formulated.\n\nEC2: If the seat controls are omitted, then the cost is reduced (#39: Productivity), but a compromised sitting posture causes LBP (#13: Stability of the object’s composition).\n\nSimilarly, the parameters were intersected in the matrix to obtain these four principles:\n\n35: Parameter changes\n\n3: Local quality\n\n22: Blessing in disguise\n\n39: Inert atmosphere\n\nAn inert atmosphere (adding neutral parts or “nothing” into a system) is suitable for resolving EC2. Adding “nothing” can include adding air (e.g. inflatable bubble wraps to elevate the posterior position and alleviate disc pressure).\n\nMeanwhile, a hard object is not suitable because it causes discomfort and pain around the waist and buttocks.26,27 Conversely, a soft object is not suitable as the driver will sink into the seat, negating the original purpose of the solution.\n\nApart from that, a soft high-density foam is also an option.28 The object should be hard enough to prevent drivers from sinking back into the original posture and soft enough to maintain cushioning.\n\n\nConclusions\n\nThis study preliminarily investigated the causes and recommendations for DLBP using TRIZ. This aim was achieved using the CECA and inventive principles. Although DLBP has been studied previously, the present study demonstrated originality by using TRIZ to preliminarily but methodically investigate and resolve DLBP.\n\nCECA revealed that DLBP arises from sitting with the hips positioned lower than the knees or without seat controls. The preliminary action principle proposed that seat controls should be included in the seat design to allow the lumbar region to be elevated and reduce the posterior pelvic tilt. Considering that not all cars have these seat controls, the inert atmosphere principle was recommended by adding inflatable bubble wraps to elevate the seat’s posterior portion. In summary, rapidly-synthesised and cost-effective solutions for DLBP were successfully proposed using TRIZ.\n\nThis was a preliminary study. Triangulation, prototyping, and experimentation were not possible due to time and budgetary constraints. In the future, further apparatus development and testing should be considered.",
"appendix": "Acknowledgements\n\nThe authors would like to thank the Faculty of Engineering and Technology, Multimedia University (MMU) for allowing this study to be conducted. The authors thank the organising committee of MECON 2021 and DIFCON 2021 for facilitating the review and submission of the works related to this study. Special thanks go to the anonymous medical doctors and ergonomics experts who participated in the focus group discussion sessions. Lastly, the authors are exceptionally grateful to Ms. Chiew Fen Ng for the constructive criticism of the manuscript.\n\n\nAuthor contributions\n\nPoh Kiat Ng\n\nRoles: Conceptualisation, data curation, formal analysis, investigation, methodology, project administration, writing – original draft preparation, writing – review, and editing\n\nMuhammad Syafiq Syed Mohamed\n\nRoles: Conceptualisation, investigation, project administration, writing – original draft preparation, writing – review and editing\n\nJian Ai Yeow\n\nRoles: Project administration, methodology, writing – review and editing\n\n\nReferences\n\nKoes BW, van Tulder MW, Thomas S: Diagnosis and treatment of low back pain. BMJ. 2006; 332(7555): 1430–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoombs DM, Machado GC, Richards B, et al.: Healthcare costs due to low back pain in the emergency department and inpatient setting in Sydney, Australia. Lancet Reg Health West Pac. 2021; 7: 100089. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRossen CB, Høybye MT, Jørgensen LB, et al.: Disrupted everyday life in the trajectory of low back pain: A longitudinal qualitative study of the cross-sectorial pathways of individuals with low back pain over time. Int J Nursing Studies Advances. 2021; 3: 100021. Publisher Full Text\n\nShin D: Correlation between non-specific chronic low back pain and physical factors of lumbar and hip joint in office workers. Med Hypotheses. 2020; 144: 110304. PubMed Abstract | Publisher Full Text\n\nGallais L, Griffin MJ: Low back pain in car drivers: A review of studies published 1975 to 2005. J Sound Vibration. 2006; 298(3): 499–513. Publisher Full Text\n\nBartuzi P, Tokarski T: The Influence of Body Posture on Muscle Fatigue and Reaction Time during Truck Driving. Proceedings of the 6th World Congress of Biomechanics. 2010; 31: 119–22. Publisher Full Text\n\nOkunribido OO, Shimbles SJ, Magnusson M, et al.: City bus driving and low back pain: A study of the exposures to posture demands, manual materials handling and whole-body vibration. Appl Ergon. 2007; 38(1): 29–38. PubMed Abstract | Publisher Full Text\n\nLecocq M, Lantoine P, Bougard C, et al.: Neuromuscular fatigue profiles depends on seat feature during long duration driving on a static simulator Applied Ergonomics.2020; 87: 103118. PubMed Abstract | Publisher Full Text\n\nMatsuo T: Automobile seat for people with low back pain. Japan patent JP4341845B2. 14 October 2009.\n\nMercier C: Seat for motor vehicle, has adjusting unit adjusting inclination, towards front and/or rear, for upper surface of base with respect to horizontal plane and including transversal pivoting axle positioned at rear of base. France patent FR2911305A1. 26 February 2010.\n\nCardoso M, McKinnon C, Viggiani D, et al.: Biomechanical investigation of prolonged driving in an ergonomically designed truck seat prototype. Ergonomics. 2018; 61(3): 367–380. PubMed Abstract | Publisher Full Text\n\nUrits I, Burshtein A, Sharma M, et al.: Low Back Pain, a Comprehensive Review: Pathophysiology, Diagnosis, and Treatment. Curr Pain Headache Rep. 2019; 23: 23. PubMed Abstract | Publisher Full Text\n\nBovenzi M, Rui F, Negro C, et al.: An epidemiological study of low back pain in professional drivers. J Sound Vibration. 2006; 298(3): 514–39. Publisher Full Text\n\nJadhav AV: Comparative cross-sectional study for understanding the burden of low back pain among public bus transport drivers. Indian J Occup Environ Med. 2016; 20(1): 26–30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMiyamoto M, Shirai Y, Nakayama Y, et al.: An Epidemiologic Study of Occupational Low Back Pain in Truck Drivers. J Nippon Med Sch. 2000; 67(3): 186–90. PubMed Abstract | Publisher Full Text\n\nTiemessen IJH, Hulshof CTJ, Frings-Dresen MHW: Low back pain in drivers exposed to whole body vibration: analysis of a dose–response pattern. Occup Environ Med. 2016; 65: 667–75. PubMed Abstract | Publisher Full Text\n\nStarr S: Survey research: we can do better. J Med Libr Assoc. 2012; 100(1): 1–2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIlevbare IM, Probert D, Phaal R: A review of triz, and its benefits and challenges in practice. Technovation. 2013; 33(2-3): 30–7. Publisher Full Text\n\nLee C-H, Chen C-H, Trappey AJC: A structural service innovation approach for designing smart product service systems: Case study of smart beauty service. Advanced Engineering Informatics. 2019; 40: 154–67. Publisher Full Text\n\nPokhrel C, Cruz C, Ramirez Y, et al.: Adaptation of triz contradiction matrix for solving problems in process engineering. Chemical Eng Res Design. 2015; 103: 3–10. Publisher Full Text\n\nSouchknov V, Hoeboer R, Zutphen MV: TRIZ for Business: Application of Rca+ to Analyze and Solve Business and Management Problems. The ETRIA TFC. 2006; 9-11 October 2006; Kortrijk, Belgium2007.\n\nYeoh TS: TRIZ: Systematic Innovation in Business and Management.1st ed. Selangor, Malaysia: Firstfruits Publishing; 2014.\n\nYeoh TS, Yeoh TJ, Song CL: TRIZ: Systematic Innovation in Manufacturing. 1st ed. Selangor, Malaysia: Firstfruits Publishing; 2015.\n\nAltshuller G: 40 Principles: TRIZ Keys to Technical Innovation. 3rd ed. Worcester, MA: Technical Innovation Centre; 2002.\n\nCarlsson A, Pipkorn L, Kullgren A, et al.: Real World Adjustments of Driver Seat and Head Restraint in Saab 9–3 Vehicles. Traffic Injury Prevention. 2016; 18(4): 398–405. PubMed Abstract | Publisher Full Text\n\nKim S, Jee Y: Effects of 3D Moving Platform Exercise on Physiological Parameters and Pain in Patients with Chronic Low Back Pain. Medicina. 2020; 56(7): 351. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMulyadi, Nurwahidah A, Satria DN: Ergonomic risk analysis of lecture chairs at the engineering faculty, Hasanuddin University. IOP Conference Series: Materials Science and Engineering. 2020; 885: 012033.\n\nGumasing MJJ, Villapando AC, Abalajon APP: An Ergonomic Design of Passenger Cabin for Public Utility Jeepney. Proceedings of the 2020 2nd International Conference on Management Science and Industrial Engineering.2020: 273–8. Publisher Full Text\n\nNg PK, Mohamed MSS, Yeow JA: Driving-induced lower back pain: Investigation of causes. [Dataset]: Figshare; 2021 [10 June 2021]. Publisher Full Text"
}
|
[
{
"id": "94374",
"date": "20 Sep 2021",
"name": "Chandrakantan Subramaniam",
"expertise": [
"Reviewer Expertise Occupational Safety and Health"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe area of examination is seen as important and needs immediate attention. However, the background of the study needs to be improved as it needs to show some evidence or statistics from valid sources that the issue is rampant or important to be investigated. This will very much help future readers to understand the issue from a practical viewpoint.\nThe methodological section could be further improved to show the rigorousness of how the data was obtained. This is a qualitative study and many would like to understand the methodology better. This will help to demonstrate the scientific part of this present study.\nFinally, The results section needs some improvement as readers must understand the results easily. How were the findings derived? What was the technique used? How was the inference made? Who were the respondents? Any inclusion or exclusion criteria?. These are some of the important things that were missing in this paper. The authors(s) could also probably present a simpler way to explain the results.\nThe Vinodkumar and Bhasi (2010)1 article is a suggested reference as it also studies safety behaviour from the human factors angle thus would be helpful inclusion to explain the current phenomenon too.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "98546",
"date": "16 Nov 2021",
"name": "Markus Hartono",
"expertise": [
"Reviewer Expertise Kansei Engineering",
"Ergonomics",
"New Product & Service Design",
"Service Quality."
],
"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 lacks the details of research urgency, research gaps, and state-of-the-art. It is unclear to see what the rationales of this study are, why DLBP has been investigated, what the urgency of this study was, and why TRIZ was proposed to solve the problem.\n\nThere were no literature reviews of physical problems (such as musculoskeletal disorders/MSD or DLBP), methods used for product design and development (such as TRIZ or similar methods), ergonomics principles.\n\nIt's unfortunate that the rationale of DLBP being studied was insufficient.\n\nAlso, why TRIZ was being applied seems to be insufficient in explanation. Let say, we have many similar potential methods, they should have been reviewed, and how the TRIZ has been focused. Unfortunately, they were unavailable.\nOverall, this article lacks the details and critical points (in terms of method/approach and research gap).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7451",
"date": "16 Nov 2021",
"name": "Poh Kiat Ng",
"role": "Author Response",
"response": "I understand the comments of the reviewer. However, this article (through RSF) was meant to be a short report (less than 1000 words). Therefore it was not possible to summarise all the details, research gaps, and literature review since the authors were trying to fulfil the word limit. Nonetheless. we still thank the reviewer for his comments."
}
]
},
{
"id": "102348",
"date": "04 Jan 2022",
"name": "Anca Draghici",
"expertise": [
"Reviewer Expertise industrial ergonomics",
"occupational health and 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\nI would like to see how the TRIZ method has been applied because it is the first time that I see such an application connected with driving-induced lower back pain!\nSo, I suggest extending the ”Methods” chapter with relevant information on how the TRIZ method has been used (including the specific software tool for this) and how the results were achieved and interpreted. Thus, in the Conclusions part... may be added some recommendations (or limits) of using the research approach described in the paper.\nThis is a really innovative approach...congratulations on your creativity.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 2
|
https://f1000research.com/articles/10-871
|
https://f1000research.com/articles/10-919/v1
|
14 Sep 21
|
{
"type": "Research Article",
"title": "SARS-CoV-2 genome datasets analytics for informed infectious disease surveillance",
"authors": [
"Moses Effiong Ekpenyong",
"Ifiok James Udo",
"Mercy Ernest Edoho",
"EnoAbasi Deborah Anwana",
"Francis Bukie Osang",
"Joseph Ikim Geoffery",
"Emmanuel Ambrose Dan",
"Aliu Bolanle Momodu",
"Nnamso Michael Umoh",
"Kingsley Christopher Udonyah",
"Ifiok James Udo",
"Mercy Ernest Edoho",
"EnoAbasi Deborah Anwana",
"Francis Bukie Osang",
"Joseph Ikim Geoffery",
"Emmanuel Ambrose Dan",
"Aliu Bolanle Momodu",
"Nnamso Michael Umoh",
"Kingsley Christopher Udonyah"
],
"abstract": "Background: The COVID-19 pandemic has ravaged economies, health systems, and lives globally. Concerns surrounding near total economic collapse, loss of livelihood and emotional complications ensuing from lockdowns and commercial inactivity, resulted in governments loosening economic restrictions. These concerns were further exacerbated by the absence of vaccines and drugs to combat the disease, with the fear that the next wave of the pandemic would be more fatal. Consequently, integrating disease surveillance mechanism into public healthcare systems is gaining traction, to reduce the spread of community and cross-border infections and offer informed medical decisions. Methods: Publicly available datasets of coronavirus cases around the globe deposited between December, 2019 and March 15, 2021 were retrieved from GISAID EpiFluTM and processed. Also retrieved from GISAID were data on the different SARS-CoV-2 variant types since inception of the pandemic. Results: Epidemiological analysis offered interesting statistics for understanding the demography of SARS-CoV-2 and helped the elucidation of local and foreign transmission through a history of contact travels. Results of genome pattern visualization and cognitive knowledge mining revealed the emergence of high intra-country viral sub-strains with localized transmission routes traceable to immediate countries, for enhanced contact tracing protocol. Variant surveillance analysis indicates increased need for continuous monitoring of SARS-CoV-2 variants. A collaborative Internet of Health Things (IoHT) framework was finally proposed to impact the public health system, for robust and intelligent support for modelling, characterizing, diagnosing and real-time contact tracing of infectious diseases. Conclusions: Localizing healthcare disease surveillance is crucial in emerging disease situations and will support real-time/updated disease case definitions for suspected and probable cases. The IoHT framework proposed in this paper will assist early syndromic assessments of emerging infectious diseases and support healthcare/medical countermeasures as well as useful strategies for making informed policy decisions to drive a cost effective, smart healthcare system.",
"keywords": [
"Disease surveillance",
"infectious disease",
"genome pattern mining",
"SARS-CoV-2",
"self-organizing map"
],
"content": "Introduction\n\nCoronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen, was initially detected in Wuhan, China in December 2019 and has progressively become a global pandemic with continuous negative impacts on health policies, education, social relationships, and national economies. The rapid rate of transmission with no medically proven prophylaxis and high numbers of recorded deaths has kept the scientific community apprehensive, working towards understanding the virus and possibly finding avenues to contain the virus. Epidemiological studies have recognized the variations in demographic, clinical and genomic features of COVID-19 among and within continents, countries, and regions. This variation has led to a wide range of outcomes where a proportion of people with positive reverse transcription polymerase chain reaction (RT-PCR) tests have been found to be asymptomatic and symptomatic patients have also reportedly exhibited different symptoms ranging from a mild cold to intense illness and in some cases, death. Hence, understanding the underlying mechanism of variation appears crucial.\n\nA myriad of studies has characterized epidemiologic and genomic features in hospitalized patients in specific regions while some inter-regional/continental studies have utilized COVID-19/SARS-COV-2, curated, and published primary and secondary data (in open access databases). In the literature, the Global Initiative on Sharing All Influenza Data (GISAID) (Elbe and Buckland-Merrett, 2017) has been the most frequently accessed for genomic data mining. The criticism cast on the World Health Organization’s (WHO’s) Global Influenza Surveillance Network, on the limited global access to avian H5N1 influenza virus sequence data managed by the Los Alamos National Laboratories in the United States of America brought into focus the need for optimal transparency in data sharing with no infringement of intellectual property rights. In addition to GISAID, 34 of such databases and computational resources together with their resource description and data types have been outlined by the Office of Data Science Strategy, National Institute of Health. The data, which predominantly includes genomic, chemical structure, epidemiologic data and digital images, have been made available for sharing, verification, and collaborative research through the efforts of medical personnel and researchers. Besides medical scientists, digital technologists have also strived to play a role in tackling the pandemic, in areas such as risk assessment and patient prioritization, screening and diagnosis, contact tracing, supporting drug discovery and treatment. This technological effort stems from the artificial intelligence (AI) community and thrives on data from open-source repositories as its essential element. However, the inherent constrictions of these repositories possess some systematic challenges, as possible limitations in sample sizes of biomedical data, incompatible data extensions and schemas as well as non-uniformity of data elements of similar features across repositories impede the integration of data from different sources.\n\nProviding capacity to contain emerging and recurrent outbreaks of infectious diseases is insufficient to satisfy effective medical countermeasures such as diagnostics, therapeutics, and vaccines. Often, non-pharmaceutical interventions such as contact tracing, outbreak investigation, isolation, social distancing, and the use of face masks remain the only viable options/tools for slowing down an emerging outbreak in the absence of such medical countermeasures. Once a novel infectious threat is identified, surveillance of the disease transmission becomes paramount for immediate risk assessment. The COVID-19 pandemic has presented the urgent need for governments, healthcare decision makers, providers, and others, to refocus on balancing their response with wider health needs. The increased availability of novel web-based data sources can substantially improve infectious disease surveillance (Choi et al., 2016; Ainsworth et al., 2021). Globally, web-based surveillance tools and epidemic intelligence methods are providing new prospects to facilitate risk assessment and timely outbreak detection. These tools are increasingly adopted for rapid detection of changes in the incidence rate of endemic diseases and the early detection and characterization of syndromes caused by previously unknown pathogens of epidemic potential. Furthermore, customized systems utilizing robotics (Yang et al., 2020) are appearing in infectious disease situations to manage disease situations in the areas of clinical care (telemedicine and decontamination), logistics (delivery and handling of contaminated waste), and reconnaissance (monitoring compliance with voluntary quarantines); and are actively being deployed in Asian countries such as China and Israel, as well as in Western countries such as the United States.\n\nWhile the ‘Big Data’ revolution is ongoing, most public health systems such as those in low- and medium-income countries (LMICs) still rely on traditional surveillance. Simonsen et al. (2016) advocate increased use of hybrid systems that combine traditional surveillance information and Big Data sources, to ensure a faster system that is more relevant to local needs. Today AI and data science are redefining our response to infectious disease situations, by powering existing devices to deliver cost effective services through predictive modelling (a data mining and probability method for estimating more granular, specific outcomes) and effectively complementing forecasting methods (trend analysis for estimating future events based on past and present data) for proper service integration into decision-making processes of surveillance systems. Consequently, decision-making under emerging infectious disease situations has greatly improved using appropriate data and advanced analytics (George et al., 2019) for reinforced public health actions such as resource requirement determination, situational awareness refinement, and control efforts monitoring (Chretien, Riley, and George, 2015; Rainisch et al., 2015; CDC FluSight; Meltzer et al., 2016).\n\nOne major challenge facing the response, recovery, and resilience to emerging pandemics is the weak system for collecting timely, disaggregated data related to the pandemic. Underfunding, mixed data standards, data integration, and the need to share quality data at local, national, regional, and international levels, are challenging epidemiological protocols, hence, undermining health system capacity, and decreasing support for open access tools. Nevertheless, with the availability of other data sources such as social media data, mobile phone data, satellite data and citizen-generated data, there is hope that these gaps can be addressed in real-time. We summarize in Table 1 the effective technologies and resources used at national and international levels for predicting and controlling emerging infectious disease threats. Examples of each resource are highlighted as well as their main applications.\n\nIncreased uncertainty of SARS-CoV-2 mutation and the ability of the virus to adapt to changing environments has confirmed the emergence of novel sub-types and strains (Wang et al., 2020, 2021; Grabowski, Kochanczyk, M., and Lipniacki, 2021, Richmond et al., 2020; Koyama et al., 2020). Furthermore, inadequate capacity of under-resourced countries to contain the sudden spread of emerging infectious diseases has diminished sound medical protocol and is gradually breeding a ‘careless’ society that resorts to self-help activities such as patronizing quacks.\n\nThis research study seeks a patient-centered healthcare system with smart components for driving robust decisions on emerging infectious disease surveillance. To initiate this investigation, the following hypotheses are proposed:\n\nH1:Localizing transmission routes of intra-country sub-strains to immediate countries and continents would most likely assist early contact tracing and stem the spread of infectious diseases.\n\nH2:Implementing a smart healthcare system powered by Internet of Things technology would support disease surveillance in overburdened and poor health systems.\n\nH3:Implementing a healthcare system powered by Internet of Things technology offers patient-centered services and enhances healthcare policy decisions.\n\nThis paper tackles the first hypothesis by mining retrieved genome datasets from GISAID, to provide a demography and transmission routes of SARS-CoV-2 viral sub-strains among infected patients, by gender. An Internet of Things (IoT) framework with collaborative components for driving robust decisions on emerging infectious disease surveillance including a feasible workflow for implementing same is proposed to initiate the second and third hypotheses. To actualize the later hypotheses, a research project grant is currently being pursued. The research is expected to impact the research community and society in the following areas:\n\n• Localized transmission route discovery – Whereas Ekpenyong et al. (2021a) adopted a global transmission route classification, with a greater proportion of the genome sequences belonging to the intra-country sub-strains cluster, this paper localizes the transmission routes of intra-country sub-strains to immediate countries and continents for enhanced contact tracing and supports the deployment of early countermeasures to prevent further transmissions. Furthermore, Governments’ understanding of the source of the disease or infection will guide enhanced border regulations and ascertain which sub-strain(s) is (are) spreading within their countries.\n\n• Disease information sharing and AI-knowledge extraction – Retrieval of datasets has always been met with complexity imposed by unstructured data, hence, increasing the difficulty of restructuring the database for AI-knowledge extraction. A novel taxonomy re-defining the unique annotation of entries into clinical information databases is demonstrated in this paper, to aid knowledge simplification and minimization of inconsistencies.\n\n• Processed global disease datasets – The datasets provided in this paper are useful for accurate characterization and prediction of SARS-CoV-2 genome pattern(s)/sub-strain(s) by gender, a contribution that is currently missing in the literature. This data would benefit computational scientists in the development of classification models as well as expert/recommendation systems for global disease surveillance. Clinicians/physicians and pharmacists can also exploit the proposed expert system framework, to support efficient decisions on contact tracing, disease diagnosis, and recommendations. Furthermore, by providing access to processed clinical (control) SARS-CoV-2 data, research could be advanced towards individualized/precision medicine. Finally, the developed models and algorithms would provide open-source tools with domain adaption and research replication possibilities.\n\n• Optimized response and recovery system for patient diagnosis, care, and management – The proposed Internet of Health Things (IoHT) framework will support overburdened and poor health systems with insufficient numbers of health workers, when responsibly deployed. It will provide better logistics for resource allocation, support self-diagnosis, psychosocial care, and enhance the timely communication of protocols such as real-time medical response and quality policy decisions, contact tracing, and early information on treatment tips/recommendations.\n\n\nMethods\n\nA total of 29225 complete, high coverage genome sequences (sequences with lengths of above 29000 bp and <1% undefined or ambiguous bases, ‘N’s, and <0.05% unique amino acid mutations), were retrieved as a single FASTA file from GISAID EpiFluTM between December 2019 and March 15, 2021. Statistics of retrieved genomes are distributed by continent as follows; Africa: 2288, Europe: 8592, Asia: 13210, North America: 1829, South America: 3289, and Oceania: 17. Only sequences with patient status (age and gender) and complete collection date were filtered and retained for the study, resulting in 9164 genome sequences consisting of 5269 male and 3895 female samples from 61 different countries of the world, across six continents, Antarctica exempt (as no SARS-CoV-2 data deposits were found from Antarctica at the time of retrieval).\n\nPython 3.9.5 was used to extract individual genome sequences from the retrieved FASTA file. The following functions/libraries/packages were used to aid extraction process: Pandas (a library for data manipulation and analysis, used to convert the extracted sequences to CSV file); PyCountry (a library containing ISO information about countries of the world, used for converting country names and their long-forms into their ISO-alpha-3 form); re (the Python regular expression library, used to match characters and sequence of characters during the extraction and cleaning process); os module (a module with several functions for interacting with host’s operating system, used for creating directories, moving and deleting files during the cleaning process). The Python code used for the extraction is provided in Algorithm 1 (Extended data).\n\nMetadata was compiled to document specific isolate details including: Isolate Code (three-letter country code_isolate number), Country, Accession Number, Gender, Age (Child: <18 y, Adult: 18-59 y, Senior: >59 y), Status, Specimen Source and Additional Information. The Additional Information column holds both location and host information such as transmission history, treatment history, date sample was taken, etc. Specimen sources include swabs (nasal, oral, throat, nasal and oral), fluids (bronchoalveolar lavage, saliva, sputum, stool) and unknown. FASTA files of the genome isolates can be located at GISAID using the accession numbers (see Data availability). The statistical methods used to analyze the metadata were summation, simple measures of central tendencies (mean and mode), as well as additional logical statements for conditional count, sum, and approximate and exact matching. These were achieved using the following Microsoft Excel functions: SUM, AVERAGE, MODE, COUNTIF, SUMIF, and VLOOKUP.\n\nUsing Python, raw genome sequences of male and female patients/isolates were retrieved and processed into vertical columns of individual genomes and stored in a CSV file for the various continents under study, in the following order: Africa, Europe, Asia, North America, South America and Oceania. During the retrieval, we observed that the GISAID database was inconsistent at rendering the patient status and specimen sources, and numerous incoherent annotations introduced inherent redundancy. To assist efficient documentation and processing of data for intelligent analytics, taxonomies re-classifying these two fields are given in Figure 1 and Figure 2, respectively. A semi-automated method was used to develop the taxonomies. To obtain patient status, the mode function of Microsoft Excel was used to obtain the most frequent occurring status (unique status) and such similar comparisons manually verified before the search and replace function was used to replace redundant statuses with unique ones. Hence, our taxonomies subsume incoherent or redundant annotations (annotations in square text boxes) into unique specifications (annotations in oval shapes), ready for efficient data mining (Edoho et al., 2020). Hence, for patient status (Figure 1), the unique annotation sequence used to relabel the datasets includes:\n\n• Symptomatic -> Hospitalized -> [Live, Mild, Moderate, Severe, Critical, Recovering, Recovered, Released, Deceased].\n\n• Symptomatic -> Not Hospitalized (Outpatient) -> [Home]\n\n• Symptomatic -> [Isolation]\n\n• Symptomatic -> [Quarantine]\n\n• Asymptomatic\n\n• Unknown\n\nGISAID, Global Initiative on Sharing All Influenza Data; COVID-19, coronavirus disease 2019; ICD, International Classification of Diseases; EHPAD, Établissement d'hébergement pour personnes âgées dépendantes.\n\nGISAID, Global Initiative on Sharing All Influenza Data; COVID-19, coronavirus disease 2019; VTM, viral transport medium.\n\nFor specimen sources (Figure 2), the unique annotations used to relabel the datasets include:\n\n• Pharyngeal Swab\n\n• Pharyngeal Swab, Serum\n\n• Pharyngeal Swab, Serum, Urine\n\n• Saliva\n\n• Saliva, Pharyngeal Swab\n\n• Serum\n\n• Serum, Urine\n\n• Urine\n\n• Sputum\n\n• Autopsy Material\n\n• Brain Tissue\n\n• Cerebrospinal Fluid\n\n• Anal Fluid\n\n• Lung Tissue\n\n• Unknown\n\nIn June 2021, WHO designated seven variants of interest (VOIs) and four variants of concern (VOCs) (Konings et al., 2021). Submissions and statistics documenting SARS-CoV-2 VOIs/VOCs were retrieved as a Microsoft Excel workbook using the GISAID EpiCovTM download option. The retrieved Workbook documents VOI/VOC cases between December 16, 2019 and August 8, 2021. Using Microsoft Excel SUM and VLOOKUP functions the following number of SARS-CoV-2 VOIs/VOCs cases were retrieved and processed; VOI Lambda: 647826, VOI Kappa: 981843, VOI Iota: 974080, VOI Eta: 1472927, VOI Zeta: 19012, VOI Gamma: 1036999, VOC Beta: 659580, VOC Alpha: 2200327, and VOC Delta: 89961.\n\nOur pattern visualization model is defined by a self-organizing map (SOM) – a single neural network with neurons defined along the grids, that projects data into a low-dimensional space (Kangas et al., 1990). Using an unsupervised, competitive learning process, a low-dimensional, discretized representation of the input space or training samples, known as the feature map, is produced. During training, weights of the winning neuron and neurons in a predefined neighborhood are adjusted towards the input vector using equation (1),\n\nwhere r is the learning rate and fiq is the neighborhood function, with value 1 at the winning neuron q and decreasing as the distance between i and q increases. At the end, the principal features of the input data are retained. The batch unsupervised weight/bias algorithm of MATLAB 2017b (trainbu) with mean squared error (MSE) performance evaluation, was adopted to drive the proposed SOM. This algorithm trains a network with weight and bias learning rules using batch updates. The training was carried out in two phases: a rough training with large (initial) neighborhood radius and large (initial) learning rate, followed by a finetuned training phase with smaller radius and learning rate. A freely available alternative software that can be used to replicate this study is Python with the following data science libraries: NumPy–a fundamental package for scientific computing in Python. Pandas. Matplotlib.pyplot–a collection of functions that make matplotlib work like MATLAB.\n\nEach genome sequence was mapped or transformed into an equivalent genomic signal (a discrete numeric sequence) using the following encoding of the individual nucleotide (i.e., A = 1; C = 2; G = 3; T = 4). As base input, we maintained nucleotide pairs above 29000 bp (the input vector), indicating approximate (maximum) length of DNA sequences of the SARS-CoV-2 genome. Next, all ambiguous sequences were removed. A vector representation for pairwise Euclidean distance computation among the vectors in the form of a distance matrix was achieved using the SOM algorithm implemented in MATLAB 2017b. As the distance matrix is highly dimensional, a suitable representative sequence of each isolate was adopted and the individual component planes transformed into a cognitive map using their similarity scores, useful for labelling classification targets for predictive systems.\n\nKnowledge mining is an emerging field in AI and has had huge benefits for quick learning from Big Data. We applied natural language processing to the genome datasets and extracted knowledge of similar viral sub-strain(s). An iterative technique (using Python Similarity, and Microsoft Excel’s COUNTIF and CORRELATION commands/functions) was then imposed on the SOM isolates (i=1,2,3,…,n), where n is the maximum number of isolates. For each isolate pattern, similar patterns with the rest of the isolates (i.e., i+1,i+2,…,n) were compiled. Compiled isolate(s) were concatenated into a list (j1,j2, … ,jm) where j is an element of the list. The compiled list was dumped into CogMap(ki∈j1,j2, … ,jm).\n\n\nResults\n\nEpidemiological analysis was carried out on the Metadata file. Table 2 documents the continent, isolate distribution by country, isolate distribution by gender, and total number of samples/isolates retrieved. Using Python, the following statistics were compiled:\n\nSymptomatic and asymptomatic cases\n\nTable S1 (Extended data) shows statistics for symptomatic and asymptomatic cases. We observed more hospitalized cases (7625/9164, 83.21%) than not-hospitalized cases (391/9164, 4.27%), with more male patients hospitalized (M = 4338/7625, 56.89%; F = 3287/7625, 43.11%). Furthermore, more males died of COVID-19 than females (M = 541/9164, 5.90%; F = 248/9164, 2.71%). Asymptomatic cases represent 0.76% (40/5269) and 1.05% (41/3895) of total male and female patients, respectively.\n\nPatient age and status across continents\n\nDistribution of patients by age and status across African countries is shown in Table S2 (Extended data). It was observed that South Africa had the highest number of entries (M = 503/1804, 27.88%; F = 1004/1804, 55.65%). Regarding age, the highest number of patients came from the Adult class (M = 506/1804, 28.05%; F = 869/1804, 48.17%). Regarding patient status, the highest proportion of patients belonged to the Live category (M = 599/1084, 33.20%; F = 1039/1840, 56.47%), followed by the Released category (M = 97/1804, 5.38%; F = 63/1804, 3.50%).\n\nDistribution of patients by age and status across European countries is shown in Table S3 (Extended data). It was observed that Italy had the highest number of entries (M = 308/1545, 19.94%; F = 253/1545, 16.38%). Regarding age, adults (M = 395/1545, 25.57%; F = 392/1545, 25.37%) and seniors (M=381/1545, 24.66%; F = 327/1545, 21.17%) shared the highest proportion (about 24%) of the total patients. Regarding patient status, the highest proportion of patients belonged to the Live category (M = 441/1545, 28.54%; F = 436/1545, 28.22%) followed by the Mild category (M = 122/1545, 7.90%; F = 109/1545, 7.06%).\n\nDistribution of patients by age and status across Asian countries is shown in Table S4 (Extended data). It was observed that India had the highest number of entries (M = 1041/4078, 25.53%; 557/4078, 13.66%). Regarding age, adults (M = 2169/4078, 53.19%; F = 914/4078, 22.41%) constituted the highest proportion of patients. Regarding patient status, the highest proportion of patients belonged to the Live category (M = 1744/4078, 42.77%; F = 740/4078, 18.15%), followed by the Released category (M = 636/4078, 15.60%; F = 340/4078, 8.34%).\n\nDistribution of patients by age and status across North American countries is shown in Table S5 (Extended data). It was observed that USA had the highest number of entries (M = 318/978, 32.52%; 181/978, 18.51%). Regarding age, adults (M = 392/978, 40.08%; F = 222/978, 22.70%) constituted the highest proportion of patients. Regarding patient status, the highest proportion of patients belonged to the Live category (M = 165/978, 16.87%; F = 123/978, 12.58%), followed by the Home category (M = 159/978, 16.26%; F = 120/978, 12.27%).\n\nDistribution of patients by age and status across South American countries is shown in Table S6 (Extended data). It was observed that Brazil contributed the highest number of entries (M = 258/741, 34.82%; 261/741, 35.22%). Regarding age, adults (M = 232/741, 31.31%; F = 219/741, 29.55%) had the highest proportion of patients. Regarding patient status, the highest proportion of patients belonged to the Live category (M = 100/741, 13.50%; F = 109/741, 14.71%), followed by the Deceased category (147/741, 19.84%; 120/741, 16.19%).\n\nDistribution of patients by age and status across Oceanian countries is shown in Table S7 (Extended data). Although there is paucity of data in this continent, we observed that Australia contributed the highest number of entries (M = 9/18, 50%; 6/18, 33.33%). Regarding age, adults (M = 9/18, 50%; F = 3/18, 16.67%) had the highest proportion of patients. Regarding patient status, the highest proportion of patients belonged to the Recovering category (M = 6/18, 33.33%; F = 3/18, 16.67%), followed by the Recovered category (M = 3/18, 16.67%; F = 1/18, 5.56%).\n\nSpecimen sources across continents\n\nTable S8 (Extended data) reveals that in the highest proportion of cases, pharyngeal swabs (M = 2925/9164, 31.92%; F = 2850/9164, 31.10%) were used as sequence samples. However, annotation evidence indicates the use of saliva (3/9164, 0.03%) in Europe (Spain), Asia (Turkey), and North America (Canada). The use of sputum (98/9164, 1.07%) as a sequence sample was found in Africa (Ghana and Nigeria), Asia (China, Indonesia, Japan, Lebanon, Mongolia, South Korea, Sri Lanka, and Thailand), and Oceania (New Zealand and Australia). Lung tissue (69/9164, 0.75%) was used as sequence sample in Asia (China and Japan), Europe (Austria, Belgium, Czech Republic, France, Italy, Russia, and Spain), and South America (Colombia and Ecuador). Anal fluid (14/9164, 0.15%) was used as sequence samples in Asia (China) and North America (USA). Serum or blood, and urine (4/9164, 0.15%) were used as sequence samples in Asia (India). A hybrid of samples (32/9164, 0.35%) was collected for sequencing SARS-CoV-2 virus in Africa (Nigeria), and Asia (India). Other forms of sequence samples (9/9164, 0.10%) came from Europe (Russia). Statistics also show that unknown sequence samples formed 31.21% (2860/9164) of the total sequence samples collected.\n\nIntra- and inter-country transmissions across countries\n\nAnalysis of intra- and inter-country transmissions was performed on the Additional Information column of the metadata and are documented in Table 3. In Africa, we found that more intra-country transmissions were reported, especially in South Africa. Senegal had few family cluster transmissions, while few imported cases or inter-country transmissions were observed in Madagascar, Nigeria, and Senegal.\n\nIn Europe, intra-country transmissions were mostly observed in the Czech Republic and Spain, while inter-country transmissions were observed in Italy, China, and France.\n\nContact with patient zero (0), family clusters, congregations, seafood wholesale markets, local communities, passengers on a Nile river cruise ship, and medical college hospitals were means of intra- and inter- country transmissions in Asia. Inter-country transmissions specifically came from Africa, Europe, and North America.\n\nEvidence of reinfection was reported in North America, specifically the US. Private events, contact with infected patients, local communities and local airports, were avenues of intra- and inter- country transmissions. Europe and South America were the sources of transmission.\n\nEvidence of reinfection was also reported in South America, specifically Brazil. Local hospitals and international travel were the means of inter- and intra-country transmissions in this continent.\n\nOceania witnessed intra- and inter-country transmissions from Asia, specifically Iran and China.\n\nThe SOM component planes allowed an investigation of countries that share similar genome pattern expressions of SARS-CoV-2 and which patterns permeate the different regions. To account for the variability of SOM neighborhood structure at every SOM run, the reference genome was included in the experiment datasets during each training phase. Our topologies possess random (but controllable) discontinuities that permit more flexible self-organization with high-dimensional data, thus, preserving the ensuing map structure as much as possible. The training was performed by gender, per continent, for clean whole genome sequences (>29000 bp), i.e., without ambiguous nucleotides. During the training, the male and female samples were trained separately for each continent. However, due to the paucity of data in the Oceanian region, its dataset was merged with South America, resulting in 10 different maps (Figures 3-7). We observed that globally, there are inter- and intra- country transmissions evident in the pattern (dis) similarities exhibited by the various SOM maps. Most component planes exhibiting intra-country sub-strains show highly disparate and variable cluster patterns with well separated boundaries, indicating emergence of new sub-strain(s) with rapid nucleotide mutations. However, component planes exhibiting inter-country sub-strain patterns possess clear patterns without sharp boundaries, indicating fewer nucleotide changes. Interestingly, the gradual evolution of the cluster patterns into well separated boundaries can be traced, hence providing opportunities for predicting the emergence of new sub-strains. Furthermore, some of the patients retained the reference genome pattern (i.e., had similar pattern as component plane 1, encircled in red), indicating no significant mutation in the nucleotide composition.\n\nComponent plane 1 is the reference genome pattern. (a) Male patients – Component planes: [2-129] are patterns from South Africa; [130] is the pattern from Gambia; [131] is the pattern from Algeria; [132-136] are patterns from Egypt; [137-143] are patterns from Tunisia; [144-145] are patterns from Morocco; [146-147] are patterns from Mozambique; [148] is the pattern from Nigeria; [149-160] are patterns from Senegal. (b) Female patients: Component planes [2-219] are patterns from South Africa; [220] is the pattern from Algeria; [221-222] are patterns from Egypt; [223-228] are patterns from Tunisia; [229] is the pattern from Mogadishu; [230-233] is pattern from Nigeria; [234-237] are patterns from Senegal.\n\nComponent plane 1 is the reference genome pattern. (a) Male patients – Component planes [2] is the pattern from Switzerland; [3-5] are patterns from Faroe Islands; [6] is the pattern from Belgium; [7-8] are patterns from Poland; [9-21] are patterns from Romania; [22-56] are patterns from Spain; [57-58] are patterns from Georgia; [59-110] are patterns from Italy; [111-123] are patterns from Russia; [124-154] are patterns from France; [155] is pattern from Slovakia; [156-159] are patterns from Hungary; [160-163] is pattern from Ukraine; [164] is the pattern from Sweden; [165] is the pattern from Bosnia and Herzegovina; [166-179] are patterns from Czech Republic. (b) Female patients: Component planes [2] is the pattern from Switzerland; [3-4] are patterns from Faroe Islands; [5-6] is pattern from Belgium; [7-12] are patterns from Germany; [13-33] are patterns from Romania; [34-62] are patterns from Spain; [63] are patterns from Georgia; [64-95] are patterns from Italy; [96-118] are patterns from Russia; [119-146] are patterns from France; [147-148] is pattern from Slovakia; [149-153] are patterns from Hungary; [154-157] is pattern from Ukraine; [158] is the pattern from Austria; [159-169] are patterns from Czech Republic.\n\nComponent plane 1 is the reference genome pattern. (a) Male patients – Component planes: [2-11] are patterns from Singapore; [12] is the pattern from Iraq; [13-53] are patterns from China; [54] is the pattern from Kuwait; [55-71] are patterns from Malaysia; [72] is the pattern from Sri Lanka; [73-82] are patterns from Bangladesh; [83-167] are patterns from India; [168-169] are patterns from South Korea; [170] is the pattern from Kazakhstan; [171-176] are patterns from Indonesia; [177-181] are patterns from Turkey; [182-187] are patterns from Taiwan; [188-196] are patterns from Vietnam; [197] is the pattern from Israel; [198-215] are patterns from Saudi Arabia; [216-222] are patterns from Oman; [223-225] are patterns from Lebanon; [226-229] are patterns from United Arab Emirates; [230-299] are patterns from Japan. (b) Female patients: Component planes: [2-5] are patterns from Singapore; [6-40] are patterns from China; [41-53] is pattern from Malaysia; [54-58] are patterns from Bangladesh; [59-154] are patterns from India; [155-160] is pattern from Kazakhstan; [160-169] are patterns from Indonesia; [170-172] are patterns from Turkey; [173-184] are patterns from Taiwan; [185-201] are patterns from Vietnam; [202-215] are patterns from Saudi Arabia; [216-217] are patterns from Pakistan; [218-225] are patterns from Oman; [226-227] are patterns from Lebanon; [228] is the pattern from United Arab Emirates; [229-300] are patterns from Japan.\n\nComponent plane 1 is the reference genome pattern. (a) Male patients – Component planes: [2-17] are patterns from Mexico; [18-101] are patterns from USA; [103-104] are patterns from Saint Martin; [105-108] are patterns from Guadeloupe; [109-110] are patterns from Canada; [111-127] are patterns from Costa Rica. (b) Female patients – Component planes: [2-15] are patterns from Mexico; [16-64] are patterns from USA; [65-67] are patterns from Saint Martin; [68-74] are patterns from Guadeloupe; [75-79] are patterns from Canada; [80-87] are patterns from Costa Rica.\n\nComponent plane 1 is the reference genome pattern. (a) Male patients – Component planes: [2] is the pattern from Chile; [3] is the pattern from Argentina; [4-15] are patterns from Colombia; [16-19] are patterns from Ecuador; [20] is the pattern from Peru; [21-79] are patterns from Brazil. (a) Female patients – Component planes: [2] is the pattern from Venezuela; [3] is the pattern from Argentina; [4-21] are patterns from Colombia; [22-78] are patterns from Brazil.\n\nNext, we decoupled the SOM correlation hunting matrix space (Vesanto and Ahola, 1999), and attributed these associations to disparate clusters of discovered viral sub-strains, resulting in a cognitive map that links similar transmission routes. Table S9 (Extended data) and Table S10 (Extended data) distinguish transmission routes for male and female patients (columns 3 and 4), respectively. Also shown in the tables are dominant transmission cases, and patients that retained the reference genome pattern (column 1). For male patients (Table S9, Extended data), no dominant intra-country transmission or spread is observed in Africa, while only South African and Tunisian patients retained the refence genome pattern. Dominant intra-country transmission is observed in Europe (Faroe Islands, France, Sweden, and Czech Republic), while the reference genome pattern appears dominant in Poland, Romania, Spain, Italy, Russia, and France. In Asia, dominant intra-country spread is observed in Singapore, China, Indonesia, Israel, and Japan, while the reference genome pattern is retained in China, Sri Lanka, Bangladesh, Taiwan, Saudi Arabia, and The United Arab Emirates. In North America, intra-country transmission occurs in Mexico and USA, while the reference genome is retained only in Mexico and USA. Dominant intra-country patterns are found in Brazil, while the reference genome pattern is retained in Chile, Ecuador, and Brazil. In Oceania, intra-country transmission is observed in Australia, while the reference genome is retained in Guam.\n\nFor female patients (Table S10, Extended data), no dominant intra-country transmission is observed in Africa, while only South African patients retained the refence genome pattern. Intra-country transmission is observed in Europe (Faroe Islands, Belgium, Russia, France, with dominant transmission in the Czech Republic), while the reference genome pattern appears dominant in Belgium, Romania, Spain, Italy, France, with only one copy in the Czech Republic. In Asia, dominant intra-country spread is observed in Japan with few intra-country transmissions occurring in Singapore, China, Bangladesh, India, Indonesia, Taiwan, Saudi Arabia, Pakistan, and Oman, while the reference genome pattern is retained in China, Sri Lanka, Bangladesh, Taiwan, Saudi Arabia, and United Arab Emirates. In North America, intra-country transmission appears dominant in Mexico and USA with few transmissions in Saint Martin, Guadalupe, and Canada, while the reference genome is retained in Mexico and USA. Intra-country patterns are found in Colombia and Brazil, while the reference genome pattern is also retained in Colombia and Brazil. In Oceania, no intra-country transmission or reference genome patterns are observed.\n\nThe benefits of our cognitive map cannot be overemphasized. While manual annotation of transmission routes indicates few recorded cases (see Table 3), our cognitive map efficiently traced each patient and groups the patient according to two transmission routes, i.e., inter- and intra-country transmissions. The map would benefit contact tracing and early disease surveillance for informed medical decisions if integrated into current epidemiological protocol.\n\nTwo classes of SARS-CoV-2 variants namely, Variant of Interest (VOI) and Variant of Concern (VOC) have been defined by World Health Organization (WHO) and US Centers for Disease Control and Prevention (CDC). The B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) variants have been classified as variants of concern (Campbel et al., 2021) and are circulating around the world. Another variant classification type known as Variant of High Consequence (VOHC) has recently been introduced by US CDC, and to date, no VOHC have been identified (Chadha et al., 2021). As attention on the pandemic shifts to the emergence of new VOC, understanding the variability between new variants and non-VOC lineages is becoming increasingly important for surveillance and maintaining the effectiveness of public health as well as vaccination programs (Jewell, 2021).\n\nAnalysis of the variants type by continent is presented in Figure 8. We observe that Europe records the highest number of VOCs as follows (VOC Gamma: 606955, VOC Beta: 407879, VOC Alpha: 1338089, and VOC Delta: 72290). North America follows with (VOC Gamma: 36441, VOC Beta: 195360, VOC Alpha: 683838, and VOC Delta: 9181). Asia follows with (VOC Gamma: 41946, VOC Beta: 8112, VOC Alpha:130662, and VOC Delta:1570). South America follows with (VOC Gamma: 21860, VOC Beta: 538, VOC Alpha: 31848, and VOC Delta: 325). Africa follows with (VOC Gamma: 78, VOC Beta: 6645, VOC Alpha: 12388, and VOC Delta: 249). And Oceania follows with (VOC Gamma: 38, VOC Beta: 56, VOC Alpha: 3467, and VOC Delta: 1343). Oceania appears to be experiencing increased proportion of VOC Delta over its closest form, VOC Alpha (1343/3667 = 38.74%) compared to Africa (249/12388 = 2.01%), South America (325/31848 = 1.02%), Asia (1570/130662 = 1.20%), North America (9181/683838 = 1.34%), and Europe (72290/1338089 = 5.40%).\n\n\nDiscussion\n\nResults of epidemiological and surveillance analysis revealed increased intra-country transmissions, demanding localized strategic planning and informed response to the pandemic. Understanding how, when and in what circumstances the virus spreads is crucial to developing effective public health measures for infection prevention and control. Genetic variants of SARS-CoV-2 are circulating around the world with routine surveillance (cases, deaths, health workers, hospitalizations) becoming more critical to monitor viral mutations and variants through sequence-based analysis, laboratory studies, and epidemiological investigations.\n\nA novel IoHT framework is proposed in this section to support our drive towards a smart healthcare system. The proposed framework as shown in Figure 9 is a multi-layer expert system architecture that coordinates a set of collaborative components or layers, namely, 1) smartphone/end-user, 2) IoHT, 3) data warehouse and knowledge base (KB), and 4) medical expert opinion.\n\nDS, data source; DW, data warehouse; KB, knowledge base.\n\n\n\n1) The smartphone/end-user layer is intended to offer medical services to end-users (individuals, epidemiologists, physicians, policymakers, government), and serve two major functions: a) assist in primary collection of demographic data–as users register and signup for medical services (e.g., syndrome check/confirm), physiological data–symptoms, medical history, and any other data–assisted by the IoHT); and b) assist in secondary data processing (deposited genomes or any other data of emerging infectious diseases). This layer communicates with the IoHT layer and the data warehouse and KB layers to perform analysis of syndromes, perform global disease surveillance, display disease status and produce surveillance reports.\n\n2) The IoHT layer holds smart health objects in the form of intelligent apps or plug-in devices that provide personal health records to the KB layer of the framework. It consists of interconnected objects with the capacity to exchange and process data to improve patient health. An interface/plug-in that aids communication between sensors and the mobile layer is proposed. Sensors are required to assist this interface to measure physiological parameters such as temperature, blood pressure, pulse rate, and oxygen level, for use in the diagnosis of infectious diseases. This synergy can transform the mobile layer for regulated display, transfer, storage, or conversion of patient-specific medical data from a connected device.\n\n3) The data warehouse and KB layer curates and stores clinical datasets (e.g., genome sequences) voluntarily donated by patients or deposited by clinicians or any other data the world over. This layer also contains data modelling tools and data marts (subsets of data). Data can be crowdsourced for disease databases for the purpose of intelligent disease surveillance facilitated by intelligent (machine learning, ML) algorithms, to produce surveillance reports (epidemiological analysis, genome pattern analysis and cognitive knowledge map) useful for tracking disease transmission routes and supporting inter- and intra-country contact tracing. The KB is a collection of data generated by end-users, including rules and intelligent algorithms, for diagnostics and surveillance analytics. The KB layer therefore represents the engine room of the proposed framework and communicates with all other layers for efficient storage and retrieval purposes as well as coordinated health information processing.\n\n4) The knowledge opinion layer enables contributions from medical experts for knowledge simplification and evidence-based practice that defines thresholds for diagnosis and prevention of emerging infectious diseases. These contributions are processed by the KB, to offer reference labels to input datasets. In this paper, the taxonomies created to normalize patient status and specimen source will improve the precision of feature labelling in intelligent system classification.\n\nTo achieve layer 1, the Python programming language and Node.js could be used to develop a Smart Medical Assistant and the app interface for early syndromic assessment of infectious disease situations. To achieve layer 2, a cloud-based system embedding the various devices to guarantee ubiquitous computing, context-awareness and wireless communication could be adopted. The objects would be interconnected for exchanging and processing data for improved patient’s healthcare services. Embedded soft sensors could also be programmed for the purpose of collecting physiological measurements such as temperature, blood pressure, and oxygen level. Synergy between the IoHT and the smartphone layers will transform the mobile layer into a regulated retrieval and storage system. To achieve layer 3, AI/data science tools/models (neural network, multi-criteria, fuzzy, and tree-based models) could be applied to mine experiential knowledge from primary/secondary datasets into informed decision charts/reports. To achieve layer 4, contributions from medical experts for knowledge simplification and evidence-based practice that defines the ‘universe of discourse’ for diagnosis and prevention of emergent infectious diseases could be performed. To achieve context-awareness, a location-based system could be implemented using two major steps: spatial database design – satellite image acquisition, identification, and abstraction of relevant features within the study area, start and end boundary extraction; and geo-modelling, GIS mapping and testbed/prototype design – mapping the location information and details from the health registry data to the testbed/prototype using a geo-analysis software such as ArcGIS. Steps to achieving this activity include geolocation superimposition on the extracted surface after image digitalization, geodatabase modeling and integration and prototype/testbed development.\n\nTo test and evaluate the proposed system (for end-users’ acceptance), data could be crowdsourced from patients/participants and healthcare workers for the purpose of building an intelligent disease surveillance system facilitated by ML/AI algorithms.\n\nThe following subsections discuss the data collection procedures, inference/evaluation criteria and expected research outcomes of the smart medical/healthcare system proposal.\n\nData collection procedures\n\nTo achieve the smart healthcare system, researchers would be drawn from multidisciplinary fields including Computing, Medical, Engineering and Social Sciences. The core system’s design, implementation and evaluation will be carried out by researchers in the computing and engineering fields. Experiential knowledge of symptoms, assessments and end-users’ evaluation would be obtained from patients and medical experts. Community interaction, development of data instruments, and instruments evaluation would be performed by social scientists.\n\nTo ensure that activities are properly monitored during implementation, coordinators from participating/collaborating universities in Nigeria would be appointed. The research population would be drawn from various states and cover a sizable number of participants. Stratified random sampling could be adopted to select required participants for the study.\n\nInference/evaluation criteria\n\nTo test and evaluate the proposed IoHT system for end-users’ acceptance, data could be crowdsourced from male and female participants (patients and healthcare workers). A user acceptance test, where actual end-users test the system to determine its ability to carry out the required tasks it was designed to address in real-world situations or validate whether all the specific requirements are satisfied, with appropriate inference/evaluation of the system, would also be carried out.\n\nExpected research outcomes\n\nThis research is expected to produce four major outcomes to support investigation of the second and third hypotheses, as follows:\n\n1) Improved healthcare services. A smart healthcare system powered by IoHT with Smart Medical Assistant, which connects patients and healthcare resources in real-time and aids the syndromic assessment of infectious disease(s), is expected. As healthcare informatics research seeks a nexus between theory and practice, the research promises to engage and build a critical mass of early career researchers from the North-South region of Nigeria to actualize the most-needed knowledge-driven healthcare system that will create national, regional, and global impact.\n\n2) Enhanced healthcare decision support. A proposed location-based (spatial) system in the form of an app will enable real-time and accurate localization of available healthcare facilities as well as services offered by these facilities. Another deliverable is an expert recommendation system, which will provide useful information such as disease surveillance reports from crowdsourced data for enhanced healthcare decisions. By integrating a decision support system that influences society, the community/society will be involved, and Government policies will be re-modelled towards a smart and healthy society. With this breakthrough, the capacity of the university system will be strengthened to impact the various sectors of the economy and restore confidence in the various stakeholders.\n\n3) Increased number and quality of research outputs. Quality research publications and patents are expected from this research that will advance science, technology, and innovation, as well as research progress, for the dissemination of innovative and reproducible research results. The method/design, findings, and results will have a wider impact on the global community.\n\n4) New breed of experienced mentees. This research will produce strong and independent mentees with multidisciplinary experience to sustain the research into the future.\n\nThis work is limited to disease surveillance analysis using secondary data, pattern visualization and generic grouping of transmission routes for discovery of intra-country sub-strains. Although our proposed IoHT framework integrates a hybrid solution for collaborative data analytics, practical implementation of this proposal is required to derive the full benefits of the framework.\n\n\nConclusions\n\nCommunity transmission and antiretroviral treatments can engender novel mutations in a virus, potentially resulting in more virulent strains with higher mortality and strains resistant to treatment. Hence, systematic tracking of demographic and clinical data as well as sub-strain information is indispensable to effectively contain infectious diseases. Mutant variability analysis and precise sub-strain prediction can also serve as useful precursors to emerging viral sub-strain discovery and quality vaccine formulation. This work identified the existence and spread of SARS-CoV-2 viral sub-strains among infected patients. Using cognitive knowledge mining, transmission routes (inter- and intra-country transmissions) were efficiently separated by gender. Clinicians and medical experts could exploit the epidemiology and genome pattern analysis, as well as the proposed system framework, to support efficient medical decisions on real-time contact tracing, disease diagnosis and global disease surveillance.\n\n\nData availability\n\nSequence data are available from GISAID (Elbe and Buckland-Merrett, 2017). GISAID accession numbers are presented in the Acknowledgment Table. Access to the data requires registration and agreement to the conditions for use at: https://www.gisaid.org/registration/register/.\n\nOpen Science Framework: SARS-CoV-2 Genome Datasets Analytics. https://doi.org/10.17605/OSF.IO/U7G4D. (Ekpenyong et al., 2021b).\n\nThis project contains the following underlying data:\n\n- gisaid_hcov-19_acknowledgement_table_2021_08_11_04.pdf (GISAID Acknowledgement table)\n\nOpen Science Framework: SARS-CoV-2 Genome Datasets Analytics. https://doi.org/10.17605/OSF.IO/U7G4D (Ekpenyong et al., 2021b).\n\nThis project contains the following extended data:\n\n- Appendix.pdf (Algorithm 1 and Tables S1-10)\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\nAinsworth B, Miller S, Denison-Day J, et al.: Infection control behavior at home during the COVID-19 pandemic: observational study of a web-based behavioral intervention (Germ defence). Journal of Medical Internet Research. 2021; 23(2): e22197. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCampbell F, Archer B, Laurenson-Schafer H, et al.: Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021. Eurosurveillance. 2021; 26(24): 2100509. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChadha J, Khullar L, Mittal N: Facing the wrath of enigmatic mutations: A review on the emergence of SARS-CoV-2 variants amid COVID-19 pandemic. Environ Microbiol . 2021. PubMed Abstract | Publisher Full Text\n\nChoi J, Cho Y, Shim E, et al.: Web-based infectious disease surveillance systems and public health perspectives: a systematic review. BMC Public Health. 2016; 16(1): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChretien JP, Riley S, George DB: Mathematical modeling of the West Africa Ebola epidemic. Elife. 2015; 4: e09186. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChristaki E: New technologies in predicting, preventing and controlling emerging infectious diseases. Virulence . 2015; 6(6): 558–565. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDong E, Du H, Gardner L: An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020; 20(5): 533–534. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEdoho ME, Ekpenyong ME, Momodu AB, et al.: Mining the Human Metabolome for Precision Oncology Research. Proceedings of the 4th International Conference on Medical and Health Informatics . 2020: 8–17. Reference Source\n\nEkpenyong ME, Edoho ME, Inyang UG, et al.: A hybrid computational framework for intelligent inter-continent SARS-CoV-2 sub-strains characterization and prediction. Sci Rep. 2021a; 11(1): 1–25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEkpenyong ME, Udo IJ, Edoho ME, et al.: SARS-CoV-2 Genome Datasets Analytics. 2021b. Publisher Full Text\n\nElbe S, Buckland-Merrett G: Data, disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall. 2017; 1(1): 33–46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGeorge DB, Taylor W, Shaman J, et al.: Technology to advance infectious disease forecasting for outbreak management. Nat Commun. 2019; 10(1): 1–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGrabowski F, Kochanczyk M, Lipniacki T: L18F substrain of SARS-CoV-2 VOC-202012/01 is rapidly spreading in England. medRxiv . 2021; Publisher Full Text\n\nJewell BL: Monitoring differences between the SARS-CoV-2 B. 1.1. 7 variant and other lineages. Lancet Public Health . 2021; 6(5): e267–e268. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKonings F, Perkins MD, Kuhn JH, et al.: SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse. Nat Microbiol. 2021; 6: 821–823. PubMed Abstract | Publisher Full Text\n\nKangas J, Kohonen T, Laaksonen J: Variants of self-organizing maps. IEEE Transactions on Neural Networks. 1990; 1(1): 93–99. PubMed Abstract | Publisher Full Text\n\nKoyama T, Weeraratne D, Snowdon JL, et al.: Emergence of drift variants that may affect COVID-19 vaccine development and antibody treatment. Pathogens. 2020; 9(5): 324. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeltzer MI, Santibanez S, Fischer LS, et al.: Modeling in Real Time During the Ebola Response. MMWR Suppl . 2016; 65(Suppl-3): 85–89. PubMed Abstract | Publisher Full Text\n\nRainisch G, Asher J, George D, et al.: Estimating ebola treatment needs, United States. Emerg Infect Dis. 2015; 21(7): 1273–1275. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRichmond CS, Sabin AP, Jobe DA, et al.: Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa. MedRxiv. 2020; Publisher Full Text\n\nSimonsen L, Gog JR, Olson D, et al.: Infectious disease surveillance in the big data era: towards faster and locally relevant systems. J Infect Dis. 2016; 214(suppl_4): S380–S385. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVesanto J, Ahola J: Hunting for Correlations in Data Using the Self-Organizing Map. Proceeding of the International ICSC Congress on Computational Intelligence Methods and Applications . 1999: 279–285.\n\nWang R, Chen J, Gao K, et al.: Analysis of SARS-CoV-2 mutations in the United States suggests presence of four substrains and novel variants. Commun Biol. 2021; 4(1): 1–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang R, Chen J, Gao K, et al.: Characterizing SARS-CoV-2 mutations in the United States.2020; arXiv preprint arXiv: 2007.12692. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang GZ, Nelson BJ, Murphy RR, et al.: Combating COVID-19—The role of robotics in managing public health and infectious diseases. Sci Robot . 2020; 5(40). PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "100582",
"date": "09 Dec 2021",
"name": "Mario Coccia",
"expertise": [
"Reviewer Expertise COVID-19 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\nSARS-CoV-2 genome datasets analytics for informed infectious disease surveillance\nThe topics of this paper are interesting, but the structure and content must be revised, and results have to be better explained by authors before to be reconsidered for publication.\nTitle has to be shorter. Abstract has to be shorter focusing on results and explaining reliable health and social implications.\n\nIntroduction has to better clarify the research questions of this study and provide more theoretical background. Authors have to better describe the different sources of transmission dynamics of COVID-19 (e.g., mobility, environment, pollution, etc.) and risk factors in society, that can accelerate diffusion of this novel coronavirus. In addition, the application of a collaborative Internet of Health Things (IoHT) is one of the strategies of control of COVID/19 and support of disease surveillance in poor health systems because it has to be associated with a certain level of Health expenditure. IN any case this tool has to be discussed in a general strategy of prevention to cope with COVID/19 transmission (See suggested readings that must be all read and used in the text).\n\nHypotheses are too general and vague and have to be better defined and specified.\n\nMethods of this study is not clear. The section of Materials and methods must be re-structured with following sections:\nSample and data\n\nMeasures of variables\n\nModels and Data analysis procedure.\n\nResults has a lot of subheadings that create fragmentation of the paper and confusion. All subheadings can be removed.\n\nTable 2 and 3 have to indicate the period of data.\n\nFigure 3-7 are too small, and they are unreadable so I suggest putting in Appendix and authors can explain better results in the text .\nFigure 8 has to indicate the period in the title and all data should be presented per 100 0000 people to be comparable…\n\nDiscussion can remove subheadings. Figure 9….is messy. The paper has a lot of figures that are difficult to digest, they have to be reduced inserting in the text the most important ones, the other if appendix.\n\nTo reiterate, avoiding in the just mentioned sections, sub-headings that create fragmentation of the paper. The small paragraph of Limitations can be put in conclusions.\nConclusion has not to be a summary, but authors have to focus on manifold limitations of this study and provide suggestions of health and social policy.\nOverall, then, the paper is interesting, but structure is confused. Theoretical framework is weak, and some results create confusion… structure of the paper has to be improved; study design, discussion and presentation of results have to be clarified using suggested comments.\n\nIf the paper is improved, by using all comments, maybe it can be considered.\n\nSuggested readings of relevant papers that have to be read and all inserted in the text and references.\nAhmed, A., Boopathy, P., Sudhagara Rajan, S. 2022. Artificial intelligence for the novel corona virus (COVID-19) pandemic: Opportunities, challenges, and future directions, International Journal of E-Health and Medical Communications 13(2)\nCoccia M. 2021. Preparedness of countries to face covid-19 pandemic crisis: Strategic positioning and underlying structural factors to support strategies of prevention of pandemic threats, Environmental Research, n. 111678, https://doi.org/10.1016/j.envres.2021.111678\nSaini, G., Swahn, M.H., Aneja, R. 2021. Disentangling the Coronavirus Disease 2019 Health Disparities in African Americans: Biological, Environmental, and Social Factors )(2021) Open Forum Infectious Diseases, 8 (3).\n\nFountain-Jones, N.M., Appaw, R.C., Carver, S., Didelot, X., Volz, E., Charleston, M. 2020. Emerging phylogenetic structure of the SARS-CoV-2 pandemic ()(2020) Virus Evolution, 6 (2), art. no. veaa082\nCoccia M. 2021. The relation between length of lockdown, numbers of infected people and deaths of Covid-19, and economic growth of countries: Lessons learned to cope with future pandemics similar to Covid-19. Science of The Total Environment, n. 145801. https://doi.org/10.1016/j.scitotenv.2021.145801\nPan, D., Sze, S., Minhas, J.S., Bangash, M.N., Pareek, N., Divall, P., Williams, C.M., (...), Pareek, M. 2020. The impact of ethnicity on clinical outcomes in COVID-19: A systematic review )(2020) EClinicalMedicine, 23, art. no. 100404\nGomes, L., Jeewandara, C., Jayadas, T.P., (...), Waggoner, J., Malavige, G.N. 2022. Surveillance of SARS-CoV-2 variants of concern by identification of single nucleotide polymorphisms in the spike protein by a multiplex real-time PCR, Journal of Virological Methods300,114374\nCandido, D.S., Claro, I.M., de Jesus, J.G., Souza, W.M., Moreira, F.R.R., Dellicour, S., Mellan, T.A., (...), Faria, N.R. 2020. Evolution and epidemic spread of SARS-CoV-2 in Brazil (), (2020) Science, 369 (6508), pp. 1255-1260.\nCoccia M. 2021. Effects of the spread of COVID-19 on public health of polluted cities: results of the first wave for explaining the dejà vu in the second wave of COVID-19 pandemic and epidemics of future vital agents. Environmental Science and Pollution Research. 28(15), 19147-19154. https://doi.org/10.1007/s11356-020-11662-7\nNana-Sinkam, P., Kraschnewski, J., Sacco, R., Chavez, J., Fouad, M., Gal, T., Auyoung, M., (...), Behar-Zusman, V. 2021. Health disparities and equity in the era of COVID-19 )(2021) Journal of Clinical and Translational Science, art. no. e99.\nCoccia M. 2021. Pandemic Prevention: Lessons from COVID-19. Encyclopedia of COVID-19, 1, pp. 433–444. https://doi.org/10.3390/encyclopedia1020036\nForde, A.T., Crookes, D.M., Suglia, S.F., Demmer, R.T. 2019. The weathering hypothesis as an explanation for racial disparities in health: a systematic review(2019) Annals of Epidemiology, 33, pp. 1-18.e3.\nDavies, N.G., Jarvis, C.I., van Zandvoort, K., Clifford, S., Sun, F.Y., Funk, S., Medley, G., (...), Keogh, R.H. 2021. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 () (2021) Nature, 593 (7858), pp. 270-274\nCoccia M. 2021. High health expenditures and low exposure of population to air pollution as critical factors that can reduce fatality rate in COVID-19 pandemic crisis: a global analysis. Environmental Research, vol. 199, Article number 111339, https://doi.org/10.1016/j.envres.2021.111339\nJeewandara, C., Jayathilaka, D., Ranasinghe, D., Hsu, N.S., Ariyaratne, D., Jayadas, T.T., Panambara Arachchige, D.M., (...), Malavige, G.N. 2021. Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka ()(2021) Frontiers in Microbiology, 12, art. no. 722838\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-919
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https://f1000research.com/articles/10-230/v1
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23 Mar 21
|
{
"type": "Research Article",
"title": "COVID-19 measures and the Japanese Constitution",
"authors": [
"Hajime Akiyama"
],
"abstract": "Since March 2020, the Act on Special Measures for Pandemic Influenza and New Infectious Diseases Preparedness and Response has been a significant statute in dealing with COVID-19 in Japan. The Act mandates requests and orders for business suspension and shortened business hours, as well as stay-at-home requests. Although there have been no penalties as of January 2021, these requests and orders limit freedom of movement and establishment, guaranteed rights under the Japanese Constitution. This article poses the following research question: “Does the Japanese Constitution allow measures against COVID-19 such as requests and orders for business suspension and shortened business hours, and stay-at-home requests?” It also asks: “Are measures with penalties allowed by the Constitution?” This paper introduces constitutional concepts that guarantee or limit individual freedom. Concepts that guarantee individual freedoms include freedom of establishment and movement. These freedoms derive from the constitutional values of freedom to choose one’s occupation and choose and change one’s residence (Art. 22) and the right to own or hold property (Art. 29). Concepts that limit individual freedom include the right to life (Art. 13), welfare rights and public health (Art. 25), and public welfare (Art. 13). Individual freedom that threatens right to life, welfare rights and public health, and public welfare may not be guaranteed. This paper argues that since measures against COVID-19 are considered public welfare, the Constitution allows the limiting of freedom of establishment and movement. Furthermore, from the perspectives of the right to life, welfare rights, and public health, the government is responsible for reducing the risk to life from COVID-19. It also argues that the Constitution permits measures with penalties, while proportionality needs to be considered.\n2020年3月以来、日本においては新型インフルエンザ等対策特別措置法がCOVID-19対策の中心的な役割を果たしてきた。同法に基づき、休業や営業時間短縮の要請・指示、外出自粛要請が行われている。2021年1月時点で、罰則はないものの、これらの要請・指示には日本国憲法が保障する営業の自由や移動の自由を制限する側面がある。そこで本稿は、「COVID-19対策としての休業や営業時間短縮の要請・指示及び外出自粛要請に、憲法上の制約もしくは要請はあるか」をリサーチ・クエスチョンとして検討を行った。また、「罰則のある措置は憲法上認められるか」との論点も扱った。本稿は「個人の自由を保障する概念」及び「個人の自由を制限しうる概念」に分けて検討した。個人の自由を保障する概念としては、営業の自由と移動の自由が挙げられる。これらの自由は主に居住、移転及び職業選択の自由（憲法22条）及び財産権（同29条）により保障される。また、生命権（同13条）、生存権・公衆衛生（同25条）及び公共の福祉（同13条）への脅威となる個人の自由は制限されうる。本稿は、COVID-19対策が公共の福祉に適合するため、憲法は営業の自由及び移動の自由の制限を許容していると主張した。また、生命権、生存権・公衆衛生の視点から、政府がCOVID-19に起因する生命へのリスクを低減させる責任を負っていると述べた。さらに比例原則を検討する必要はあるものの、憲法は罰則のある措置を許容していると論じた。",
"keywords": [
"新型コロナウイルス感染症",
"日本国憲法",
"新型インフルエンザ等対策特別措置法",
"人権",
"営業の自由",
"移動の自由",
"生命権",
"生存権",
"公衆衛生",
"公共の福祉",
"COVID-19",
"the Constitution of Japan",
"the Act on Special Measures for Pandemic Influenza and New Infectious Diseases Preparedness and Response",
"human rights",
"freedom of establishment",
"freedom of movement",
"right to life",
"welfare rights",
"public health",
"public welfare"
],
"content": "はじめに\n\n2020 年から 2021 年にかけて、世界各国で新型コロナウイルス感染症 （以下、COVID-19） の感染確認者数が増加している。2021 年 1 月の時点で、日本を含め多くの国では COVID-19 のワクチンがまだ承認されておらず、今後確保できるワクチン数、変異したウイルスへのワクチンの効力等は不明である。そこで各国政府は感染拡大予防のために、様々な対策を採っている。例えば各国の COVID-19 対策を分析している Our World in Data によれば、2020 年 12 月 31 日現在、124 の国や地域で外出自粛要請や外出制限などの措置が取られている1。\n\n日本においては、2020 年 3 月以来「新型インフルエンザ等対策特別措置法 （以下、特措法） 」が COVID-19 対策の中心的な役割を果たしてきた。同法に基づき、休業や営業時間短縮の要請・指示、外出自粛要請が行われてきた。2021 年 1 月時点で、罰則はないものの、これらの要請・指示には日本国憲法が保障する営業の自由や移動の自由を制限する側面がある。その一方で、COVID-19 対策が憲法に規定される公共の福祉に適合しており、自由の制限はやむを得ないとの見解もあり得る。\n\n2021 年 1 月現在、日本の COVID-19 対策の憲法上の論点について包括的に検討した論文は限られている2。その一つが、江藤祥平による論文である3。江藤は「公共の福祉」と「個人の人権」という図式を提示し、感染症対策のための私権の制限の合憲性について詳細かつ批判的に検討している。同論文は憲法における公衆衛生、表現の自由、営業の自由、個人の尊厳、自己決定権にとどまらず、国際人権法における健康への権利にも言及しており、多角的に COVID-19 対策について検討を行っている。しかし、江藤論文における分析に加えて、以下の二点の検討が必要である。第一に、憲法 13 条に規定される生命権を検討する必要がある。通説では生命権について議論されてこなかったが、COVID-19 の感染拡大は人権の基盤である生命への脅威となり、生命権の概念を含めて COVID-19 対策を検討し直す必要がある。第二に、「公共の福祉」と「個人の人権」という分類の妥当性を再検討する必要がある。江藤の述べる通り、この二項対立は憲法学では「お馴染みの図式」である4。しかし COVID-19 対策においては、公共の福祉と人権でなく、人権規範同士が衝突することも想定される。例えば COVID-19 が生命権への脅威であるとすれば、感染拡大予防策により生命権の保障が見込まれる一方で、江藤が「個人の人権」とする自由権的な権利が制限される可能性がある。すなわち、「公共の福祉」と「個人の人権」でなく、権利の性質を考慮しつつ、「個人の自由を保障する概念」及び「個人の自由を制限しうる概念」に整理し直し、COVID-19 対策の憲法上の論点を再検討する必要性がある。\n\n本稿のリサーチ・クエスチョンは、「COVID-19 対策としての休業や営業時間短縮の要請・指示及び外出自粛要請に、憲法上の制約もしくは要請はあるか」である。また、COVID-19 の感染拡大により、罰則のある措置を盛り込んだ特措法の改正が議論されている 2021 年 1 月現在の状況を踏まえ5、「罰則のある措置は憲法上認められるか」との論点も検討する6。\n\nなお、本稿は特措法に基づく対応に着目して検討する。特措法以外にも、感染症法上の指定感染症7、検疫法上の措置、予防接種法上のワクチン等の論点があるが、これらは別稿に譲りたい。その上で、本稿は特措法に基づく対策の総論的な論点の整理に留め、各論的な議論の詳細には立ち入らない。例えば首長による要請・指示については、行政法の視点を導入する必要があるが、論点が散逸するため詳細には扱わない。また、本稿は 2021 年 1 月 10 日以前の情報を基盤としており、COVID-19 の状況、政府の対応は刻一刻と変化することにご留意いただきたい。\n\n第 1 節では、特措法に基づき採られた COVID-19 対策を紹介する。第 2 ・ 3 節は、COVID-19 対策に関連する、個人の自由を保障する概念及び個人の自由を制限しうる概念を指摘する。第 4 節では、上記の概念を COVID-19 対策に適用し、COVID-19 対策を検討する際の憲法的論点を整理する。\n\n\nI. 特措法と COVID-19 対策\n\n2021 年 1 月現在、日本における COVID-19 対策の基盤となっているのは、特措法である。特措法は、2009 年に新型インフルエンザが世界的に流行し、医療資源が逼迫したことを契機として、2012 年に成立し、2013 年に施行された8。特措法の対象は新型インフルエンザ、再興型インフルエンザ及び新感染症である9。ここで重要なのは、特措法の対象となる感染症は、国民の多くが免疫を獲得していないため、急速な蔓延により国民の生命及び健康に重大な影響を与える恐れがある点である10。そのために、既知の感染症より強い措置が必要となる。\n\n当初、特措法は COVID-19 に適用されず、感染症法及び検疫法を基盤とした対応が想定されていた11。特措法の特徴は、緊急事態宣言や外出自粛要請、施設の使用制限要請・指示が可能になることであるが、厚生労働省幹部によれば、日本で初めて COVID-19 の感染者が確認された 2020 年 1 月時点では特措法の適用が必要であるとの認識は共有されていなかったようである12。同年 2 月 1 日に、COVID-19 は感染症法に基づく二類相当の「指定感染症」とされ、感染の疑いがある患者の入院措置が可能になった13。また同日、COVID-19 が検疫法上の「検疫感染症」となり、強制力を伴う入国時の診察・検査が可能になった14。\n\nしかし同年 2 月 21 日に国内感染者数が 100 人を超えると社会的な緊張が高まり、2 月 27 日には当時の安倍首相が、感染拡大抑制のために必要な法案を早急に準備するよう指示した15。そして 3 月 13 日に特措法が改正され、翌 14 日より COVID-19 が特措法の対象となった16。\n\n特措法は二段階構造により、新型感染症のまん延予防を試みている17。第一段階は政府対策本部の設置である。従来のインフルエンザより症状が深刻である新型感染症が発生した際に、政府対策本部、都道府県対策本部が設置される18。都道府県対策本部長となる都道府県知事は、特措法 24 条 9 項に基づき、団体、個人に必要な協力を要請する事ができる。\n\n第二段階が緊急事態宣言である。首相は、感染症が全国的なまん延により、かつ国民社会、国民生活に甚大な影響を及ぼす場合に緊急事態宣言を発出し、緊急事態措置を実施すべき期間、区域を指定する19。特措法は緊急事態宣言発出時の専門家の役割に触れていないが、首相が専門家に諮問することが想定されている20。緊急事態措置の対象となった地域では、都道府県知事が不要不急の外出自粛要請及び施設使用制限の要請を行う事ができる21。施設の使用制限要請に応じない場合、知事は施設管理者に法的義務を課す指示を行うことができる22。これらの要請・指示に従わなくとも罰則はない。しかし、45 条に基づく施設使用制限が要請・指示された場合は、その旨が公表される23。公表が可能になることが、緊急事態宣言発出による大きな変化である。しかし、政府対策本部が設置されていれば都道府県知事は必要な協力を要請できるため、緊急事態宣言の発出は社会的に大きなインパクトがあるものの、要請の法的な効力が変わるわけではないことには留意が必要である24。\n\n緊急事態措置の対象となった地域では、都道府県知事が要請・指示の主体となるが、政府が定める基本的対処方針 （特措法 18 条） に沿って要請・指示を行うこととなる25。また、新感染症対策であっても、国民の自由や権利への制限は最低限であるべきであると規定されている26。\n\n2020 年 3 月 14 日に COVID-19 が特措法の対象となると、同法 15 条に基づく政府対策本部が設置され27、各都道府県知事が同法 24 条に依拠して、団体・個人への要請が可能になった。同月には大阪府や東京都、神奈川県、埼玉県、千葉県、山梨県等が外出自粛を要請した28。感染確認者数の増加と社会的危機感の高まりを受け29、2020 年 4 月 7 日から 5 月 25 日にかけて緊急事態宣言が発出された30。緊急事態措置の対象となった都道府県では特措法 45 条に基づく不要不急の外出自粛要請、施設使用制限の要請・指示が可能になった。実際に全ての都道府県で同法 45 条 1 項に基づいた不要不急の外出自粛が要請され、21 都道府県で同法 45 条 2 項に基づき、休業や営業時間短縮要請をはじめとする施設の使用制限が要請され、施設管理者が公表された31。また、5 県ではさらに同法 45 条 3 項に基づく指示及び同法 45 条 4 項に基づく公表が行われた32。緊急事態宣言解除後も、同法 24 条 9 項を根拠として、断続的に外出自粛要請を行った都道府県がある33。また、2020 年 4 月の緊急事態宣言発出後は、解除後も含め、散発的に同法 24 条 9 項を根拠とした休業や営業時間短縮の要請を出している都道府県もある34。また、2020 年末から感染確認者数が 1 日に 3000 人を超える日が続き、重症者数も多いため35、2021 年 1 月 7 日に、1 月 8 日から 2 月 7 日を期間とする緊急事態宣言が発出された36。東京都、神奈川県、千葉県、埼玉県が緊急事態措置の対象とされている37。\n\n\nII. 個人の自由を保障する概念\n\n罰則を伴わないとはいえ、特措法による休業や営業時間短縮要請・指示、外出自粛要請は、国家権力による市民の自由を制限する要請・指示である。国家による介入の回避を重要視する近代立憲主義を基盤とし38、また大日本帝国憲法下での国家権力の強大化を経験した後に制定された日本国憲法の視点からは、市民の自由の制限が重要な論点となりうる。本節では、日本国憲法が保障する個人の自由として、営業の自由及び移動の自由についての判例や学説を検討する。\n\n休業や営業時間短縮の要請・指示は、営業の自由を制限しうる。営業の自由に関連する条文は、憲法 22 条、29 条、13 条である。営業の自由自体を保障する文言は憲法に存在しないが、判例、通説によれば憲法 22 条の職業選択の自由により営業の自由が保障されると考えられている39。また、 22 条及び 29 条に規定される財産権の双方により営業の自由が保障されるとの見解もある40。その上で、憲法 13 条に規定される人格権と関連して営業の自由を位置付けることもできる。薬事法違憲判決は、職業が「個人の人格的価値とも不可分の関連を有する」としており41、学説でも営業の自由と人格的価値の関連が指摘されている42。人格的価値は憲法 13 条から導出できる人格権と関連しており43、営業の自由が人格権の視点からも重要であることを示唆している。\n\n外出自粛要請は、移動の自由を制限しうる。関連する条文は憲法 22 条及び 13 条である。移動の自由は、居住・移転の自由を規定する憲法 22 条に基づき保障されると考えられている44。その上で、移動の自由は人の活動領域を拡大し、人格形成に寄与するとの指摘もあり45、憲法 13 条を基盤とする人格権として移動の自由が捉えられる可能性もある。\n\n\nIII. 個人の自由を制限しうる概念\n\n憲法には個人の自由を保障する概念がある一方で、個人の自由を制限しうる概念も存在する。生命権、生存権・公衆衛生、公共の福祉の脅威となる場合、自由は制限されうる。\n\n第一に、生命権の脅威となる自由は制限されうる。生命権の根拠は憲法 13 条である。日本国憲法における生命権は、1987 年に櫻田が提唱し46、石村47、ウィリアムズ48、小林49が議論を深め、山内が 2000 年に体系化を試みた50。しかし通説では、憲法 13 条の「生命、自由及び幸福追求に対する国民の権利」が幸福追求権を意味するとされ51、判例も憲法 13 条が生命権を規定するとの理解を示しておらず52、生命権については十分議論されてこなかった53。しかし、生命権は以下の二つの理由から、幸福追求権及び人格権とは別個に理解されるべきである。第一に、条文の文理上の解釈である。生命に対する権利、自由に対する権利及び幸福追求に対する権利は並列で表記されているため、生命に対する権利が幸福追求に対する権利に包含されるべきではない54。第二に、権利の性質である。生命の維持は幸福追求権を含むあらゆる権利の前提であり、「もっとも基本的な人権」と考えられるべきである55。生命への権利は、国王の圧政からの解放という近代憲法成立の文脈では、「国家に殺されない権利」が中心的な議論であり、生命権においても主に国家の介入を否定する自由権的な文脈で議論されてきた56。しかし、COVID-19 への対応が必要となる今日においては、国家の積極的な介入を要求する社会権的な視点でも生命権をとらえる必要があり、国家による生命の保護義務も含まれるべきである57。COVID-19 による死者は 2021 年 1 月 10 日現在、日本で 4043 人確認されており58、COVID-19 が生命権の脅威となることを示している59。よって、生命権保障の手段として COVID-19 対策を捉えることができる。\n\n第二に、憲法 25 条の生存権の保障・公衆衛生の保全を目的とした自由の制限は認められうる。日本では 2021 年 1 月時点で、COVID-19 に有効なワクチンは未承認であり、また 2020 年終盤から確認されている変異したウイルスへのワクチンの効果も明らかでない60。よって現状では、「健康で文化的な最低限度の生活を営む権利を有する」とする憲法 25 条を根拠として、ワクチン接種以外の感染症対策が必要とされよう。通説、判例によれば、憲法 25 条に基づく具体的な請求権は認められていない61。従来、憲法 25 条と請求権については、生活保護などの給付請求権について議論されてきたが、通説は給付請求権が認められない理由として、国民の生存権保障のための具体的な方法が憲法では明らかでないため、立法府の判断に委ねられるとする見解62、生存権の内容が抽象的であり、内容を具現化する法律が必要であるとの見解が示されてきた63。しかし、具体的請求権を認めないことは、生存権が憲法に規定されている意味に大きな疑問を生じさせる。また法学や司法は、憲法の視点から生存権を検討すべきであり、立法への過剰な委任は望ましくない64。また、抽象的な規定を具体化するのが法学、司法の役割であると考えられ、憲法規定の抽象性を根拠として具体的請求権が否定されるべきではない65。よって、生存権の内容を法学・司法が具体化し、憲法を基盤とした具体的請求権が認められるべきである。なお、従来では生活保護などの給付請求権が議論されてきたが、生存権保障の方策は給付に限らない。憲法 25 条 2 項は、「国は、すべての生活部面について、社会福祉、社会保障及び公衆衛生の向上及び増進に努めなければならない。」と規定している。よって、「公衆衛生の向上及び増進」のために必要な方策を請求することも、憲法 25 条に基づき可能なはずである。上記の請求がなされた際には、公衆衛生の保持を目的とした個人の自由の制限が正当化されうる。\n\n第三に、憲法 13 条に規定されている「公共の福祉」は、個人の自由を制限する根拠となる。同条は、国民の権利が「公共の福祉に反しない限り、（中略）最大の尊重を必要とする」と規定しており、公共の福祉に適合しない場合、自由・人権が制限されうる。判例は公衆浴場法事件や薬局距離制限事件等を通して、公共の福祉概念に国民の保健・環境衛生が含まれるとしてきた66。また学説でも、他者の権利・利益確保の文脈で、公共の福祉に公衆衛生が含まれると考えられており67、これは妥当であろう。よって、公衆衛生の保全を目的とする COVID-19 対策は公共の福祉に含まれ、個人の自由の制限が正当化されうる。なお日本には、感染力が低いと認識されていたにもかかわらず、公共の福祉の名の下にハンセン病患者の隔離が行われた歴史があり68、公共の福祉と感染症の関係性については慎重な検討が必要である。\n\n\nIV. COVID-19対策への適用\n\n以上では、日本国憲法における個人の自由を保障する概念及び個人の自由を制限しうる概念を紹介した。本節ではそれぞれの概念を COVID-19 対策に適用し、個人の自由が保障されるべきか、もしくは COVID-19 対策のための自由の制限が認められるべきかを検討する。\n\nまず、2021 年 1 月現在の罰則のない要請が憲法上認められるかを検討する。営業の自由及び移動の自由は、居住、移転及び職業選択の自由を規定する憲法 22 条、財産権を規定する 29 条、人格権を規定する 13 条が関連している。これらの人権は公共の福祉の制約を受けるが、権利の性質により制約の程度が異なると考えられている。判例、通説では、精神的自由についてはより厳格な基準で公共の福祉を捉え、経済的自由についてはより緩やかな基準で公共の福祉を捉える、「二重の基準論」が有力になっている69。経済的自由が精神的自由と比較して社会的影響が大きいことに鑑みると、経済的自由に対してより強度な公共の福祉による制約を課すことは妥当である。営業の自由及び移動の自由の根拠となる居住、移転及び職業選択の自由、財産権は経済的自由に含まれると考えられるため70、精神的自由権よりも緩やかな基準で公共の福祉を捉え、公共の福祉による一定程度の自由の制約が許容される。COVID-19 対策は公衆衛生の保全を目的としたものであり、公衆衛生の保全は公共の福祉に適合すると考えられるため、営業の自由及び移動の自由を経済的自由として捉えれば、その制限は正当化される。\n\nなお、営業の自由及び移動の自由を人格権の一部として位置付ければ、公共の福祉がより厳格に捉えられ、COVID-19 対策よりもこれらの自由が優先されるであるとの議論もありうる。しかし、営業の自由及び移動の自由に人格権の側面が認められるとしても、精神的自由である人格権を基盤としてこれらの自由を認めることは困難である。第一に、営業の自由と「人格的価値」との関係性を認めた薬事法違憲判決では、営業の自由と人格的価値としての関連性に言及した後に、職業は「社会的相互関連性が大きい」ため、「公権力による規制の要請がつよ」いとしている71。よって、営業の自由の主な規範的基盤は経済的自由権であり、営業の自由を COVID-19 対策より優先させることは困難である。第二に、移動の自由もその社会的影響を考慮すべきである。確かに従来、個人の移動の社会的な影響は限定的に捉えられてきた。しかし COVID-19 には無症状者が存在し72、感染者が明らかでない。そのため、移動の制限が COVID-19 の感染拡大予防のために重要だと考えられる。このような社会的な影響があることに鑑みれば、COVID-19 対策としての移動の自由の制限は許容される。\n\nその上で、生命権、生存権・公衆衛生の視点からすれば、COVID-19 による死のリスクを減らす方策を国家が採る必要がある。特に生命権は人権の基盤となるため、本質的にその保障が最も重要である。よって、自由が制限されたとしても公衆衛生の保全による生命権、生存権の保障が必要である。検討すべき点として、休業や営業時間短縮の要請・指示及び外出自粛要請が、COVID-19 対策に必要であるのか、という問題が挙げられる。筆者は感染症対策の専門家ではないため、信頼に足る自らの見解を示すことはできない。しかし、2020 年 12 月時点で新型コロナウイルス感染症対策分科会は、主な感染源として飲食の場が挙げられるとの見解を示しており73、飲食店の休業や営業時間短縮の要請・指示には一定の意味があると考えられる。また、人が COVID-19 感染拡大の媒体となるため、移動の自粛要請にも一定の有効性があると考えられる74。\n\n最後に、罰則を伴う措置について検討する。日本国憲法は罰則のある外出制限、休業や営業時間短縮の措置を許容していると考えられる。COVID-19 対策が公共の福祉に適合すれば、罰則を禁止する根拠を見いだすことは困難だからである。とはいえ、憲法が罰則のある休業や営業時間短縮の要請・指示を求めているわけでもない。すなわち、罰則の有無は立法に委ねられている。しかし罰則を導入する際には、行政法における比例原則が適用される必要がある。比例原則の内容として、目的適合性の原則、必要性の原則、狭義の比例性の原則が挙げられる75。よって、罰則は必要最小限で、かつ法益に与える影響が不釣り合いであってはならない。\n\n\nおわりに\n\n本稿は、COVID-19 対策に関わる憲法上の論点を「個人の自由を保障する概念」及び「個人の自由を制限しうる概念」に整理し直した上で、COVID-19 対策が公共の福祉に適合すると捉えられ、特措法に基づく休業や営業時間短縮の要請・指示、外出自粛要請に憲法上の制約はないと論じた。その上で、生命権・生存権の議論を基盤として、国家による積極的な COVID-19 対策が求められると述べた。また、比例原則を考慮する必要はあるものの、憲法は罰則のある措置を許容しているとまとめた。よって、罰則のない特措法に基づく措置は、憲法による要請でなく、立法府の判断により規定されたものである。\n\n最後に今後の検討課題として、2021 年 1 月以降の導入が検討されている罰則の意義と、ポスト・コロナ時代の国家観と憲法を挙げる。第一に、罰則導入の意義を検討する必要がある。罰則導入を検討する一義的な目的は、感染拡大防止のための休業もしくは営業時間の短縮の徹底であると考えられる76。その上で、罰則の社会的な意義についても検討する必要がある。従来の特措法には罰則規定が存在しないが、2020 年 4 月の緊急事態宣言発出以降、営業自粛要請を遵守していないと思われる店舗を私人が攻撃する、「コロナ自警団」や「自粛警察」と呼ばれる現象が起きた77。心理学者の榎本博明は、罰則を課した欧米では、自由の制限への不満の矛先が政府に向かったのに対し、日本では罰則のない自己犠牲を求める要請であったために、不満の矛先が要請を遵守しなかった市民に向かったと述べている78。「コロナ自警団」の現象は、公的な罰則がなくとも社会的な制裁が課されうることを示している。社会的な制裁が横行することは、「正統な物理的暴力行使の独占」が期待・要求される近代国家において望ましくないであろう79。罰則導入により感染拡大防止を徹底できるのか、また社会的制裁を減少させることができるのか、を今後分析する必要がある80。\n\n第二に、ポスト・コロナ時代の国家観と憲法について検討する必要がある。従来日本の憲法学は、大日本帝国憲法下の経験から自由の制限に抑制的な立場をとってきた81。また特措法も、2012 年の成立以降罰則規定が不在であった。これらの前提には、国家の権限強化への警戒感がある82。しかし COVID-19 は、この国家観に変化をもたらす可能性がある。生命権保障のためには国家による積極的な COVID-19 対策が求められる。また、国民が国家の権限強化を求める動きもある。2020 年 6 月に NHK が実施した世論調査では、62% が外出禁止や休業を強制できる法改正が必要であると回答している83。また 2021 年 1 月に NHK が実施した世論調査では、48% が特措法への罰則の明記に賛成と回答しており84、罰則のある措置に肯定的な意見が一定数あることを示している85。世論が実際にどの程度罰則のある措置を望んでいるのかは明らかでない。国家に強力な権限を認めることには全体主義につながるとの懸念があり86、国民が国家による罰則を望む現象が、近代立憲主義の視点から危険視されるのは当然である。しかし未知のウイルスに恐怖を感じ、その克服のために強力な権限を求めるのは、社会の自然な反応ということもできよう。全体主義の歴史に学び、政治による恣意的な権力の集中を避けつつ、科学者の専門知を基盤として、国家が生命権保障のために必要な措置を検討する必要がある。感染症対策における国家の役割、憲法の役割については、今後さらなる議論が求められる。また、COVID-19 は憲法が直面する新たな問題である点も重要である。従来想定されてきた「緊急事態」における「敵」は、人間により構成される国家であり、「敵」の認定には政治的判断が不可避である。その一方で、COVID-19 等感染症対策における「敵」はウイルスであり、科学的な専門知により根拠づけられる87。憲法（学）が必ずしも想定してこなかった新たな、かつ人間社会に与える影響が巨大な「敵」が出現する中で、憲法学が描く国家観を今後再検討する必要がある。\n\nCOVID-19 は、大規模かつ長期化する感染症と向き合うことを迫っており、日本国憲法にとって新たな課題である。新型コロナウイルスを含む新興の人獣共通感染症は増加傾向にあるとの指摘もあり88、今後も日本社会は感染症と向き合う必要がある89。憲法の枠組みに基づき法的な検討を行うとともに、日本社会の特性も鑑みて、有効な感染症対策により生命権を保障する、新たな国家観を構想していく必要がある。",
"appendix": "謝辞\n\n本稿は、国際人権法学会「COVID-19 と人権フォーラム」（2020 年 9 月 19 日）、Tsukuba Global Science Week 2020 Session 6-2 “How Can Constitutions Deal with COVID-19?” （2020 年 9 月 29 日）、第 3 回 COVID-19 と緊急事態法制研究会 （2020 年 10 月 26 日）において発表した原稿をもとに、加筆修正を加えたものである。発表に貴重なコメントをくださった稲正樹博士（元国際基督教大学教授）、新井誠教授（広島大学）、近江美保教授（神奈川大学）、Giorgio Shani 教授（国際基督教大学）、我妻ゆき子教授（筑波大学）、Joelle Grogan 博士（ミドルセックス大学）、それぞれの会議でご質問いただいた先生方に感謝申し上げる。\n\n\nデータ利用可能性\n\n本論文は法学の論文であり、「生データ (raw data) 」は存在しない。書籍や論文として公開されている学説、判例等に基づいている。\n\n\nFootnotes\n\n1 See, Hannah Ritchie, Esteban Ortiz-Ospina, Diana Beltekian, Edouard Mathieu, Joe Hasell, Bobbie Macdonald, Charlie Giattino, and Max Roser, “Policy Responses to the Coronavirus Pandemic,” OurWorldInData.org, accessed on 2 January 2021, https://ourworldindata.org/policy-responses-covid.\n\n2 以下の江藤論文以外に、日本国憲法における「公共の福祉」の概念により、強制力のある COVID-19 対策が可能であるとの議論はあるが （井上達夫「コロナ・ラプソディー― パンデミックが暴く『無責任の体系』」法と哲学 6 号（2020 年） 36-37 頁。Lawrence Repeta, “The Coronavirus and Japan’s Constitution: Article 41 Provides the Government with Sufficient Power to Take Aggressive Action,” The Japan Times, 14 April 2020, https://www.japantimes.co.jp/opinion/2020/04/14/commentary/japan-commentary/coronavirus-japans-constitution/ (accessed on 10 January 2021).）、憲法上の関連する概念を包括的に検討したものでない。\n\n3 江藤祥平「匿名の権力――感染症と憲法」法律時報 92 巻 9 号 （2020 年） 70-77 頁。\n\n4 同論文 70 頁。\n\n5 菅首相は 2021 年 1 月 4 日の記者会見で、罰則を盛り込んだ特措法改正案を 2021 年 1 月に開会する通常国会に提出すると述べた。首相官邸「令和 3 年 1 月 4 日 菅内閣総理大臣記者会見」 https://www.kantei.go.jp/jp/99_suga/statement/2021/0104kaiken.html （2021 年 1 月 4 日、2021 年 1 月 4 日アクセス） 。\n\n6 なお、本稿が対象とするのは 2021 年 1 月現在の特措法に基づく罰則のない措置であるが、罰則が導入されても、特措法の構造が変わらない限り主な COVID-19 対策と憲法をめぐる論点は変わらないと考えられる。\n\n7 感染症法に関する議論は、太田匡彦「新型コロナウイルス感染症にテストされる感染症法 （上） 」法律時報 92 巻 9 号 （2020 年） 85-91 頁、太田匡彦「新型コロナウイルス感染症にテストされる感染症法 （下） 」法律時報 92 巻 11 号 （2020 年） 84-90 頁を参照。\n\n8 新型インフルエンザ等対策研究会『逐条解説 新型インフルエンザ等対策特別措置法』 （中央法規出版、2013 年） 3-6 頁。なお本書籍は、COVID-19 の感染拡大を受け、中央法規出版ウェブサイト内において期間限定で無料公開されている。無料公開してくださった中央法規出版に感謝申し上げる。\n\n9 新型インフルエンザとは、新たに人から人に伝染する能力を有することとなったウイルスを病原体とするインフルエンザを指す。再興型インフルエンザとは、かつて世界規模で流行したが、その後長期間流行しなかったインフルエンザで、再興したものを指す。新感染症とは、人から人に伝染する未知の疾病のうち、以下の三要件を満たすものをいう。第一に、当該疾病にかかった際の病状の程度が重篤であるもの、第二に、当該疾病のまん延が国民の生命、健康に重大な影響を与える恐れがあるもの、第三に、全国的かつ急速なまん延の恐れがあるもの、である。特措法 2 条 1 号、感染症法 6 条 7 項、同条 9 項参照。なお、感染症法は既知の感染症も網羅している点が、特措法との違いである。\n\n10 特措法 1 条。\n\n11 一般社団法人アジア・パシフィック・イニシアティブ『新型コロナ対応民間臨時調査会調査・検証報告書』 （ディスカヴァー・トゥエンティワン、2020 年） 133 頁。\n\n12 同書 133-134 頁。\n\n13 同書 134 頁。感染症法 19 条、20 条、26 条。\n\n14 同書 134 頁。検疫法 13 条 1 項。\n\n15 首相官邸「令和 2 年 2 月 27 日 新型コロナウイルス感染症対策本部 （第 15 回） 」 https://www.kantei.go.jp/jp/98_abe/actions/202002/27corona.html （2020 年 2 月 27 日、2021 年 1 月 2 日アクセス） 。\n\n16 当時の経緯については、一般社団法人アジア・パシフィック・イニシアティブ・前掲注 11 、134-137 頁も参照。\n\n17 新型インフルエンザ等対策研究会・前掲注 8 、8 頁。\n\n18 特措法 15 条、22 条。\n\n19 特措法 32 条。\n\n20 新型インフルエンザ等対策研究会・前掲注 8 、117-118 頁。\n\n21 特措法 45 条 1 ・ 2 項。この「要請」には不利益処分がなく、行政手続法 2 条 1 項 6 号に規定される「行政指導」と考えられる。内閣官房新型コロナウイルス感染症対策推進室長「事務連絡 第 45 条の規定に基づく要請、指示及び公表について」 （令和 2 年 4 月 23 日） https://corona.go.jp/news/pdf/yousei_shiji_0423.pdf （2021 年 1 月10 日アクセス） 。よって、法的義務は課されないと考えられている。参照、髙木光・常岡孝好・須田守『条解行政手続法』 （弘文堂、2017 年） 30 頁。また緊急事態措置の対象となった都道府県知事は、臨時の医療施設の開設のために私有地を使用することができる。特措法 48 ・ 49 条。\n\n22 特措法 45 条 3 項。参照、内閣官房新型コロナウイルス感染症対策推進室長・前掲注 21 。\n\n23 特措法 45 条 4 項。\n\n24 片山は、政府対策本部が設置され、緊急事態宣言が発出されていない際に適用される特措法 24 条は、医師会や看護協会、大学の感染症研究者の協力を得るような事態を想定しており、営業停止などを要請する根拠とはならないとしている。片山善博「連載 128 片山善博の『日本を診る』 『緊急事態宣言』をめぐる法律のとんでもない読み間違い」世界 2020 年 7 月 （934） 号 （2020 年） 105-106 頁。片山の主張するように、政府対策本部が設置され緊急事態宣言が発出されていない時は「身構える段階」であり、緊急事態宣言発出時とは性質が異なる。しかし、同法 24 条に基づく要請は公表の規定がない一方で、緊急事態宣言発出時に適用される同法 45 条に基づく要請・指示は公表を義務付けている。重要なのは、片山も指摘するように、45 条に基づく要請・指示を遵守しない場合に公表されるのではなく、要請・指示が行われた時点で公表される点である。同法 24 条に基づく休業や営業時間短縮の要請が行わなければ、45 条に基づいて休業や営業短縮が行われた場合、突然公表されることになり、不合理である。そのため、24 条によっても休業や営業時間短縮の要請が可能であり、緊急事態宣言により、公表が義務付けられると考える方が自然であろう。\n\n25 都道府県知事が政府の基本的対処方針に基づく「総合調整」 （特措法 20 条 1 項） に従わない場合、政府は「必要な指示」 （同法 33 条 1 項） を出すことができる。なお、安田は緊急事態宣言発出時に着目して、基本的対処方針の役割に言及しているが（安田理恵「日本の新型コロナウイルス感染症対策からみた国、都道府県および住民の関係」法学セミナー788 号 （2020 年） 6-7 頁。）、政府対策本部が設置されている段階であれば、緊急事態宣言が発出されずとも基本的対処方針は同様の役割を果たすと考えられる。\n\n26 特措法 5 条。\n\n27 2020 年 1 月 30 日に閣議決定により新型コロナウイルス感染症対策本部が設置されたが （「新型コロナウイルス感染症対策本部の設置について」 （令和 2 年 1 月 30 日閣議決定） https://www.cas.go.jp/jp/influenza/konkyo_corona.pdf （2021 年 1 月 3 日アクセス） 。） 、同年 3 月 14 日に、特措法に基づく政府対策本部となった。\n\n28 nippon.com 「新型コロナウイルス感染症流行・ 3 月の主な動き」 https://www.nippon.com/ja/japan-data/h00730/ （2020 年 5 月 21 日、2021 年 1 月 4 日アクセス） 。\n\n29 一般社団法人アジア・パシフィック・イニシアティブ・前掲注 11 、141 頁。\n\n30 4 月 7 日に東京、神奈川、埼玉、千葉、大阪、兵庫、福岡の 7 都府県が緊急事態措置の対象となり、4 月 16 日にその対象が全国に拡大した。 5 月 14 日に北海道、東京、神奈川、埼玉、千葉、大阪、京都、兵庫を除く 39 県が緊急事態措置の対象から除外された。 5 月 21 日に大阪、京都、兵庫が対象から除外され、5 月 25 日に北海道、東京、神奈川、埼玉、千葉も除外され、緊急事態宣言が解除された。同書、457-458 頁。\n\n31 内閣官房新型コロナウイルス感染症対策推進室「新型コロナウイルス感染症 緊急事態宣言の実施状況に関する報告」 （令和 2 年 6 月） 3 頁、https://corona.go.jp/news/pdf/kinkyujitaisengen_houkoku0604.pdf （2021 年 1 月 3 日アクセス） 。\n\n32 同報告書、3 頁。\n\n33 例えば東京都は、緊急事態宣言解除後の 2020 年 7 月に不要不急の外出自粛要請を行った。 nippon.com 「新型コロナウイルス感染症流行・ 7 月の主な動き」 https://www.nippon.com/ja/japan-data/h00870/ （2020 年 11 月 19 日、2021 年 1 月 4 日アクセス） 。\n\n34 例えば東京都は緊急事態宣言解除後も休業要請を継続し、段階的に要請を緩和することとした。東京都「新型コロナウイルス感染症を乗り越えるためのロードマップ〜「新しい日常」が定着した社会の構築に向けて〜」 https://www.metro.tokyo.lg.jp/tosei/hodohappyo/press/2020/05/22/documents/11_00_1.pdf （2021 年 1 月 4 日アクセス） 。また大阪府は 2020 年 8 月に、府の指定した対策を講じない接待を伴う飲食店やカラオケ店に休業を要請し、それ以外の飲食店にも営業時間短縮を要請した。 nippon.com ・前掲注 33 。\n\n35 首相官邸・前掲注 5 。\n\n36 内閣官房新型コロナウイルス感染症対策推進室「新型コロナウイルス感染症緊急事態宣言」 https://corona.go.jp/emergency/ （2021 年 1 月 10 日アクセス） 。\n\n37 同ウェブサイト。なお、新型コロナウイルス感染症対策本部は 2021 年 1 月現在も設置されており、緊急事態措置の対象となっていない都道府県知事は特措法 24 条に依拠した要請が可能である。\n\n38 近代立憲主義については、長谷部恭男『憲法講話―― 24 の入門講義』 （有斐閣、2020 年） 1-14 頁を参照。\n\n39 最高裁判所大法廷判決昭和 47 年 11 月 22 日刑集 26 巻 9 号 586 頁。芦部信喜 （高橋和之補訂） 『憲法〔第 7 版〕』 （岩波書店、2019 年） 233 頁。佐藤幸治『日本国憲法論〔第 2 版〕』 （成文堂、2020 年） 335 頁。長谷部恭男『憲法〔第 7 版〕』 （新世社、2018 年） 241 頁。\n\n40 浦部法穂『憲法学教室〔第 3 版〕』 （日本評論社、2016 年） 238-239 頁。渋谷秀樹『憲法〔第 3 版〕』 （有斐閣、2019 年） 295 頁。なお後述の通り、職業選択の自由及び財産権はともに経済的社会権であり、営業の自由の根拠が 22 条のみであっても、22 条及び 29 条であっても、本質的な違いはあまりないと思われる。よって本稿では、採るべき説についての議論は行わない。同様の見解は野中俊彦・中村睦男・高橋和之・高見勝利『憲法I〔第 5 版〕』 （有斐閣、2012 年） 472 頁を参照。\n\n41 最高裁判所大法廷判決昭和 50 年 4 月 30 日民集 29 巻 4 号 572 頁。\n\n42 佐藤・前掲注 39 、335 頁。江藤・前掲注 3 、74 頁。\n\n43 憲法 13 条と人格権の関連については、渋谷・前掲注 40 、183 頁、野中・中村・高橋・高見・前掲注 40 、269-273 頁を参照。\n\n44 浦部・前掲注 40 、243 頁。野中・中村・高橋・高見・前掲注 40 、459 頁。なお渋谷は、憲法 22 条 2 項に規定される「外国に移住する自由」に、外国に一時旅行する自由が含まれるべきであるとの判例に言及しつつ、居住・移転の自由を規定する憲法 22 条 1 項が移動の自由を保障すると述べている。渋谷・前掲注 40 、224-225 頁。\n\n45 浦部・前掲注 40 、243 頁。野中・中村・高橋・高見・前掲注 40 、458 頁。\n\n46 櫻田誉「憲法における生命権の保障-救命救急医療との関連を中心として-」関西大学法学論集 37 巻 2 ・ 3 号 （1987 年） 4 頁。\n\n47 石村修「基本権の体系における生きる権利の意味」法学新報 96 巻 11 ・ 12 号 （1990 年） 98-107 頁。\n\n48 Noel Williams, The Right to Life in Japan (London and New York: Routledge, 1997).\n\n49 小林直樹「人権価値を根底から考える――哲学的人間学の視点から」憲法問題 9 号 （1998 年） 156-159 頁。\n\n50 山内敏弘「基本的人権としての生命権の再構成」杉原泰雄先生古稀記念論文集刊行会編『二一世紀の立憲主義-現代憲法の歴史と課題-』 （頸草書房、2000 年） 325-345 頁。加筆を経て、山内敏弘『人権・主権・平和――生命権からの憲法的省察――』 （日本評論社、2003 年） 2-32 頁にも収録されている。生命権論のその後の展開については、山内敏弘「基本的人権としての生命権の再定位」龍谷法学 53 巻 2 号 （2020 年） 43 頁を参照。\n\n51 芦部・前掲注 39 、120 頁。佐藤・前掲注 39 、196 頁。野中・中村・高橋・高見・前掲注 40 、272 頁。浦部・前掲注 40 、45 頁。\n\n52 判例では、憲法 13 条に基礎付けられる権利・自由として、私生活上の自由 （最高裁判所大法廷判決昭和 44 年 12 月 24 日刑集 23 巻 12 号1625 頁） と人格権 （最高裁判所大法廷判決昭和 61 年 6 月民集 40 巻 4 号 872 頁） が指摘されている。渋谷・前掲注 40 、183-184 頁。\n\n53 山内・前掲注 50 （「基本的人権としての生命権の再定位」） 、1 頁。なお、詳細には論じられていないものの、辻村や渋谷が生命権の議論に触れており、生命権について議論されつつある。辻村みよ子『憲法〔第 6 版〕』 （日本評論社、2018 年） 140 頁。渋谷・前掲注 40 、185-187 頁。\n\n54 山内・前掲注 50 （『人権・主権・平和-生命権からの憲法的省察』） 、4 頁。\n\n55 同書、4 頁。\n\n56 例えば、生田勝義「死刑と生命権 （再論） ――死刑憲法 13 条違憲論は死刑廃止に役立つか――」立命館法学 365 号 （2016 年） 110-141 頁は死刑の観点から生命権を検討している。\n\n57 国家による保護義務を認めることは、国家の不当な介入を招く恐れが大きいとの批判もある。芦部は国家による介入の限定が困難であるとして、日本国憲法の解釈に国家の保護義務を導入することへの懸念を示している。芦部信喜『宗教・人権・憲法学』 （有斐閣、1999 年） 230 頁。しかし、生命の保護が人権保障の基盤であることを考えると、生命保護のための国家による積極的行動は必要であろう。また山内は、近代憲法の思想的基盤であるロックの社会契約論から、国家の市民の保護義務を導き出すことができると述べる。山内・前掲注 50 （「基本的人権としての生命権の再定位」） 、25-26 頁。なお、生命権の議論の先駆者と言える櫻田誉は、日本における救命救急医療体制が不十分であるとの認識から生命権の議論を行っており、COVID-19 対策に関する生命権の議論にも示唆的である。櫻田・前掲注 46 、254-273 頁。\n\n58 厚生労働省「新型コロナウイルス について オープンデータ 死亡者数」 https://www.mhlw.go.jp/content/death_total.csv （2021 年 1 月 11 日アクセス） 。\n\n59 根岸も、日本政府が生命を保護する義務を十分に果たしていないと評価している。 Yota Negishi, “Japan,” Bonavero Institute of Human Rights, Bonavero Report 7/2020: A Human Rights and Rule of Law Assessment of Legislative and Regulatory Responses to the COVID-19 Pandemic across 27 Jurisdictions, 277. ただ、例えば日本における癌による死者は 2018 年に 373,584 人であり （国立がん研究センター 癌情報サービス「最新がん統計」 https://ganjoho.jp/reg_stat/statistics/stat/summary.html （2020 年 7 月 6 日、2021 年 1 月 5 日アクセス。）） 、COVID-19 が他の要因と比較して圧倒的な数の死者の要因となっているわけではないことには留意が必要である。何が生命権の侵害となるかとの見解には、社会における価値判断が必要であろう。本稿は、COVID-19 が感染症であり、一人の感染が他者の生命にも影響を及ぼす可能性がある点、COVID-19 対応のために医療体制が逼迫している点を踏まえ （NHK 「コロナ重症者治療の医師『病床はほぼ満床 年末年始は静かに』」 https://www3.nhk.or.jp/news/special/coronavirus/medical/detail/detail_71.html （2020 年 12 月 28 日、2021 年 1 月 4 日アクセス） 。） 、COVID-19 が生命権への脅威であると論じる。\n\n60 NHK・前掲注 59 。\n\n61 通説は、芦部・前掲注 39 、120 頁、浦部・前掲注 40 、250-251 頁を参照。判例は、憲法 25 条が「すべての国民が健康で文化的な最低限度の生活を営み得るように国政を運営すべきことを国の責務として宣言したにとどまり、直接個々の国民に対して具体的権利を賦与したものではない」とする。最高裁判所大法廷判決昭和 42 年 5 月 24 日民集 21 巻 5 号 1043 頁。\n\n62 浦部・前掲注 40 、251 頁。\n\n63 芦部・前掲注 39 、279 頁。\n\n64 司法が立法の視点を考慮に入れることの問題点については、渋谷・前掲注 40 、278 頁を参照。\n\n65 例えばいわゆる「一票の格差」の問題について最高裁は、投票価値の平等が「他の政策的な目的ないし理由との関連において調和的に実現されるべきもの」とし （最高裁判所大法廷判決 昭和 51 年 4 月 14 日民集 30 巻 3 号 223 頁） 、立法府の役割を認めつつも違憲審査を行ってきた。これまでの主な判例については芦部・前掲注 39 、146-153 頁を参照。また学説でも、投票価値が二対一以上になることは法の下の平等の観点から違憲であるとの見解が示されている。芦部・前掲注 39 、145 頁。生存権も同様に、法学・司法による基準の具体化が望ましいと考えられる。\n\n66 渋谷秀樹「『公共の福祉』とは何か」岡田信弘・笹田栄司・長谷部恭男編『憲法の基底と憲法論――思想・制度・運用――』 （信山社、2015 年） 45 頁。\n\n67 同書、55-56 頁。\n\n68 参照、財団法人日弁連法務研究財団 ハンセン病問題に関する検証会議『ハンセン病問題に関する検証会議 最終報告書』 （2005 年） 129 頁、https://www.mhlw.go.jp/topics/bukyoku/kenkou/hansen/kanren/4a.html （2021 年 1 月 10 日アクセス） 。\n\n69 芦部・前掲注 39 、104-107 頁。最高裁判所大法廷判決昭和 50 年 4 月 30 日民集 29 巻 4 号 572 頁。\n\n70 芦部・前掲注 39 、233-250 頁。\n\n71 最高裁判所大法廷判決昭和 50 年 4 月 30 日民集 29 巻 4 号 572 頁。\n\n72 Yahoo! Japan ニュース「『感染させる人の約半数は無症状。若い人はリアリティを知ってほしい』 尾身会長の緊急メッセージ」 https://news.yahoo.co.jp/articles/0a1ea2579b9116057fec9db92fe50f88638ca603 （2020 年 12 月 31 日、2021 年 1 月 4 日アクセス） 。\n\n73 首相官邸「令和 2 年 12 月 25 日 新型コロナウイルス感染症に関する菅内閣総理大臣記者会見」 https://www.kantei.go.jp/jp/99_suga/statement/2020/1225kaiken.html （2020 年 12 月 25 日、2021 年 1 月 4 日アクセス） 。同分科会は、新型インフルエンザ等対策閣僚会議内の、新型インフルエンザ等対策有識者会議に設置されている。内閣官房「新型インフルエンザ等対策有識者会議の開催について」 （令和 2 年 7 月 3 日一部改正） https://www.cas.go.jp/jp/seisaku/ful/yusikisyakaigi/konkyo.pdf （2021 年 1 月 4 日アクセス） 。\n\n74 本稿では詳細に立ち入らないが、科学的に望ましい対処法が明らかでない場合の対策も重要である。変異した新型コロナウイルスも確認されており、ウイルスの特徴が変化する可能性もあるからである。こうした場合には、国際的に環境問題等に用いられる「予防原則 （precautionary principle） 」を導入することも、生命権を保障するために検討する必要があろう。予防原則とは、「科学的知見が十分に備わっていなくても、ひとたび問題が生じたとき、深刻かつ不可逆的な被害が発生する場合に、何もしないのではなく、必要な対策をとるべきである、とする法原則」である。松本和彦「公法解釈における諸原理・原則の対抗――憲法学から見た比例原則・予防原則・平等原則」公法研究 81 号 （2019 年） 67 頁。予防原則については批判もあるが（参照、西原博史「リスク社会・予防原則・比例原則」ジュリスト 1356 号 （2008 年） 75 頁。） 、生命が人権の基盤であり、一度失われると回復不可能であることを考えると、予防原則を採る必要性がある。感染リスクがないことが立証されるまで、感染リスクとなりうる行為の積極的な抑制を検討する必要があろう。なお、予防原則は後述の比例原則と緊張関係を孕む可能性があり、過剰な自由の制限、罰則を回避しつつ、生命のリスクをいかに軽減するかは今後の検討課題である。\n\n75 高橋明男「比例原則審査の可能性」法律時報 85 巻 2 号 （2013 年） 21 頁。\n\n76 神奈川県知事は 2020 年 12 月に、営業時間短縮の要請に 2 割しか応じていないとの県職員の感触を紹介している。東京新聞「時短営業『 2 割しか応じていない』と危機感 神奈川県・黒岩知事、根拠は『県職員が街を見回った実感』」 https://www.tokyo-np.co.jp/article/75931 （2020年 12 月 22 日、2021 年 1 月 10 日アクセス） 。なお外出制限に関しては、2021 年 1 月 10 日現在、罰則導入は検討されていないようである。\n\n77 参照、鴻上尚史・佐藤直樹『同調圧力:日本社会はなぜ息苦しいのか』 （講談社、2020 年） 128-132 頁。\n\n78 週刊現代「『空気を読む日本人』ほど、なぜか『自粛警察』になってしまう“意外なワケ”」 https://gendai.ismedia.jp/articles/-/78675?page=4 （2020 年 12 月29 日、2021 年 1 月 10 日アクセス） 。日本における同調圧力と「コロナ自警団」については、鴻上・佐藤・前掲注 77 、130 頁参照。\n\n79 Max Weber, “Politics as a Vocation,” in The Vocation of Lectures “Science as a Vocation” “Politics as a Vocation, ” ed. David S. Owen and Tracy B. Strong, trans. Rodney Livingstone (Indianapolis and Cambridge: Hackett Publishing Company, 2004), 33. 原文では本箇所に強調が加えられている。日本語訳は、マックス・ヴェーバー『職業としての政治〔改版〕』 （脇圭平訳、岩波書店、2020 年） 8-9 頁を参考にした。\n\n80 2020 年 5 月の時点で江島は、自粛要請による対策が、政府に強大な権限を与えずとも感染拡大を予防できるか否かを占う試金石になると述べている。 Akiko Ejima, “Japan’s Soft State of Emergency: Social Pressure Instead of Legal Penalty,” in Verfassungsblog on Matters Constitutional, 13 May 2020, https://verfassungsblog.de/japans-soft-state-of-emergency-social-pressure-instead-of-legal-penalty/ (accessed on 10 January 2021). 2021 年 1 月現在では、「コロナ自警団」の事例、休業もしくは営業時間短縮の要請に応じる事業者が不十分である事例から、自粛要請による対策の効果は慎重に判断すべきだろう。\n\n81 大日本帝国憲法では国家緊急権が規定されていた一方で、日本国憲法には同様の規定がないこともその例であろう。参照、高橋和之『立憲主義と日本国憲法〔第 5 版〕』 （有斐閣、2020 年） 、470-471 頁。\n\n82 注 57 も参照。\n\n83 NHK「外出禁止や休業を強制できる法改正必要 62% NHK 世論調査」 https://www3.nhk.or.jp/news/html/20200623/k10012480041000.html （2020 年 6 月 23 日、2021 年 1 月 1 日アクセス） 。また 2020 年 5 月に JNN が実施した世論調査では、56% が罰則規定の導入に賛成している。 TBS NEWS JNN 世論調査「特措法をめぐる法改正について?」 https://news.tbs.co.jp/newsi_sp/yoron/backnumber/20200509/q2-7.html （2020 年 5 月 9-10 日、2021 年 1 月 10 日アクセス） 。\n\n84 NHK「2021 年 1 月 政治意識月例電話調査」 https://www.nhk.or.jp/senkyo/shijiritsu/pdf/aggregate/2021/y202101.pdf （2021 年 1 月 13 日アクセス） 。\n\n85 なお、2020 年 11-12 月に朝日新聞が実施した世論調査では、飲食店の休業指示に従わなかった場合の罰金に賛成したのは 33% に留まる。朝日新聞「休業 従わない飲食店に… 『罰金』 33% 『判断尊重』 62% 本社世論調査」 2021 年 1 月 10 日朝刊 3 面。しかし計 3 回の NHK や JNN による世論調査において半数以上もしくは半数近くが罰則に肯定的な意見を表明しているため、本稿では罰則に肯定的な意見が一定数あると評価した。\n\n86 参照、江藤・前掲注 3 、77 頁。\n\n87 しかし、科学的な知見にも政治的な要素が入り得ることには注意が必要である。\n\n88 勝間靖「新型コロナウイルス感染症 （COVID-19） の感染予防と蔓延防止のための政策\n\n―ベトナム、タイ、ベルギーでの事例を中心として―」WASEDA ONLINE https://yab.yomiuri.co.jp/adv/wol/opinion/20200430.php （2020 年 4 月 30 日、2021 年 1 月 10 日アクセス） 。\n\n89 その要因として、人間による世界各国での森林開発のため、野生動物のウイルスが人間社会に持ち込まれていることが指摘されている。湯本貴和「コロナ危機は生態系からの警告である」世界 2020 年 8 月 （935） 号 （2020 年） 111-112 頁。"
}
|
[
{
"id": "82364",
"date": "07 Apr 2021",
"name": "Hajime Yamamoto",
"expertise": [
"Reviewer Expertise 憲法学"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n本論文は、Covid-19の感染拡大に対応して「新インフルエンザ等対策特別措置法」に基づいて行われた政府による様々な要請や指示を、「憲法の枠組み」で捉えたとき、従来の枠組が不十分だと著者が評価する部分を摘示し、よりよい、と本論文著者が考える憲法学の枠組を提供しようとするものである。\nCovid-19をめぐる問題は、憲法学にとっても最新かつ最重要な諸問題を提起しており、本論文はこのような課題に迅速に応えて執筆されたものである。\n本論文の主張の核心は、憲法の枠組をCovid-19対策で展開されてきた諸措置との関係で捉え直すと、＜個人の人権 vs 公共の福祉＞という二元的対立図式を、憲法上の「個人の自由を保障する概念」と「個人の自由を制限しうる概念」の二つのカテゴリーに再編し、具体的には、個人の人権として位置づけられうる生命権や生存権を、「個人の自由を保障する概念」としてだけではなく、人権制限の契機として作動しうる概念としても位置づけ直すべきだ、とするところにある。こうして具体的には、例えば、Covid-19対策のための諸措置は、生命権保障の手段として位置づけ直されることになる。\n本論文の価値は、著者の考える「憲法の枠組み」がいかなる目的の下に、いかなる役割を担って提出されているか、についての評価によって大きく左右されるのではないか、と考えられる。一方で、著者が位置づけ直そうとする生命権や生存権は、従来の「憲法の枠組み」の中では、生命的価値や公衆衛生的価値としてカウントされており、公共の福祉に吸収されて、殺人罪の処罰や精神病患者の強制入院を憲法上正当化してきた。この点において、本論文の主張は、利益から人権への言葉の言い換えに留まる可能性がある。他方、著者の主張は、例えば、生命権という一つの人権概念が、ある個人の自由権的な権利要求と他者の人権制約をもたらす義務づけ要求を内部に併存させて、一つの人権がベクトルが正反対な多元的な機能を営むものとして再構成させるものである。この点から見ると、人権概念を極めて不明確なもの、あるいは不安定なものとしてしまう、との批判が、従来の憲法学からもたらされる可能性が高い。\n著者の示す実際の政府の諸措置についての合憲性の判定の考え方は、二重の基準や比例原則を援用するオーソドックスな違憲審査の枠組みに落ち着いていて、著者は前半部分で人権概念の大転換を主張しているのにもかかわらず、後半部分における具体的な考察と、従来の憲法学の考え方との違いは、必ずしも大きくない印象がある。\n査読者山元は、従来の近代立憲主義的人権概念を乗り越えようとする著者の基本的スタンスには共感するところが大きい。しかしながら、Covid-19を契機としてそのような試みを行うことは十分理解可能ではあるものの、同じような議論は、例えばテロ対策の文脈でも成り立つように思われる（国民の生命権を保障するための、テロ対策の強化の正当化）。そうだとすると、著者が本論文の問題意識に十分応えるためには、日本の憲法学で歴史的に形成されてきたこれまでのパラダイムの転換という大きな構図を描き、その憲法理論的および実践的意義を説得的に論じる手続がどうしても必要なように思われる。\n関連して、「コロナ自警団」や「自粛警察」の問題は、極めて重要であるが、社会的な制裁が暴力行為に及べば警察による効果的な取り締まりが期待されることは当然であるが、そこには至らない社会的プレッシャーのメカニズムをどのように評価するか、について、著者なりの考察を展開して欲しかった。この点「ゆるやかな規制に対してゆるやかに統制する、ゆるふわ立憲主義」論（曽我部真裕教授）と「市民としての自己拘束」論（江藤祥平教授）が、それぞれ現状の日本を完全に否定しない立場からニュアンスの異なる議論が提出されているところである。著者は、この問題圏についてどのようなアプローチを行うのだろうか。\nこうして、査読者としては、著者のチャレンジングな姿勢を高く評価するとともに、上記の諸論点に関する今後の著者の議論の発展に強く期待したい。\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。 はい\n\n研究設計は適切で学術的価値がありますか。 はい\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。 はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。 はい\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。 はい\n\n結論は結果により妥当な裏付けを得ていますか。 はい",
"responses": [
{
"c_id": "6587",
"date": "21 Apr 2021",
"name": "Hajime Akiyama",
"role": "Author Response",
"response": "山元先生 有益なご指摘をいただき、感謝申し上げます。 第一に、生命権や生存権を「個人の自由を制限しうる概念」と捉えることについて、従来「公共の福祉」の利益と考えられてきた概念を「人権」という言葉に言い換えたにすぎないと指摘される可能性をお示しいただきました。筆者は、まさにこの捉え方の変化にこそ大きな意味があると考えております。従来「人権≒自由」と捉えられてきたように思いますが、自由以外の人権の側面を改めて示すことで、山元先生も言及されているように「従来の近代立憲主義的人権概念を乗り越え」る、新たな人権概念を構想する基盤となると存じます。そのため、「個人の自由を制限しうる概念」を「人権」概念に組み込むことには一定の意味があると考えております。 第二に、人権が個人の自由保障と自由制限双方の正反対な機能を含むと捉えることにより、人権概念が不安定になるとの批判を受ける可能性をご指摘いただきました。筆者は、COVID-19という自然の脅威により、自由を基盤とする従来の人権概念の限界が明らかになっていると考えており、人権の捉え直しが必要であると考えています。そのため、人権概念が不安定になる可能性はありますが、新たな人権概念を検討することで、より包括的な人権概念を構築することができると考えます。 第三に、前半部分で人権概念の大転換を主張しているのにもかかわらず、後半部分における具体的な考察は、従来の憲法学と大きく変わらないのではないか、とのご指摘をいただきました。本論文の主眼は、日本国憲法の条文を基盤として自由と人権の概念を切り離し、人権概念を捉え直すことにありました。そのため、合憲性判定に関する基準や原則については十分に検討できておりません。人権概念の捉え直しにより、これらの基準や原則を捉え直す必要があるかについては慎重な検討が求められるように思いますが、今後の検討課題とさせていただきます。 第四に、COVID-19対策とテロ対策は同様に捉えられるか、との論点をご提示いただきました。「おわりに」にも記述しているとおり、本論文は感染症対策における「敵」が、科学的な専門知により認定される自然であると捉えています。従来は、政治的判断が不可避となる人間集団（国家やテロリストを含む）が「敵」として想定されており、COVID-19対策とテロ対策は本質的に異なると考えます。そして、従来想定されてこなかった自然が新たな「敵」となっているため、新たな人権理解の必要性を論じております。テロ対策の捉え方については、今後検討を重ねて参ります。 第五に、社会的プレッシャーの評価について言及していただきました。この点については、COVID-19対策に法の役割を見出すならば、社会的プレッシャーについては否定的な立場を取らざるを得ません。社会的プレッシャーに法や司法が対応できる余地は限定的だからです。法や司法の意味は、規範が事前に示され、司法による救済の可能性があることだと考えます。社会的プレッシャーについてはこうした法の効果が十分に見込めないため、少なくとも理論的には望ましくありません。とはいえ、曽我部教授、江藤教授の議論にもあるように、日本の社会的現状を踏まえた上で望ましいあり方を模索するのは、極めて重要です。その一方で今後も様々な社会問題が起きる中で、法や司法が十分に役割を果たせる基盤を構築する必要があると感じております。具体的な方法や、その妥当性については大きな論点となりますので、今後の課題とさせてください。 ご指摘いただきました論点につきましては、今後の論文執筆の参考にさせていただきます。 貴重なコメントを頂き、ありがとうございました。"
}
]
},
{
"id": "83082",
"date": "26 Apr 2021",
"name": "Masahiro Sogabe",
"expertise": [
"Reviewer Expertise 憲法"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n本論文は、「COVID-19 対策としての休業や営業時間短縮の要請・指示及び外出自粛要請に、憲法上の制約もしくは要請はあるか」をリサーチクエスチョンとして、憲法学の通説に対する批判も交えつつ、この問いに取り組んでいる。\n本査読者の全般的な評価は、基本的にはすでに査読コメントを残している山元教授と同様であるが、以下の４点について特に指摘しておきたい。\n第１に、筆者は、「公共の福祉」対「個人の人権」という通説的な問題の捉え方に代えて、「個人の自由を保障する概念」対「個人の自由を制限しうる概念」という捉え方を用いるべきだとする。しかし、通説も、「公共の福祉」は抽象的な概念ではなく、具体的な対抗利益を明確にし、その都度の「公共の福祉」の内実を明らかにすべきことを要求しているのであるから、こうした問題設定の修正が何をもたらすのかは明らかではない。\n第２に、筆者は、生存権が具体的な権利であることを強調するが、そこで指摘されている論拠は通説も織り込み済みのものであるはずであり、にもかかわらず通説が抽象的権利説（その内実にも実は注意が必要であるが）にとどまっている理由を乗り越えることができていない。また、本論文の主題との関係で、生存権が具体的権利であるとすることによっていかなる帰結をえようとしているのか、明らかでない。\n第３に、「COVID-19 対策としての休業や営業時間短縮の要請・指示及び外出自粛要請に、憲法上の制約もしくは要請はあるか」というリサーチクエスチョンに対して、一般的な回答を示しているにとどまる。本論文の対象時期においても、法令上の根拠に基づき一定の具体的な対策が展開していたのであるから、それに即した具体論が期待されるところである。\n第４に、冒頭で、COVID-19対策に関して「包括的に検討した」憲法学の論文が少ないとしているが、2020年に限っても、管見の限り下記のようなものが存在する（一部は行政法学者によるものだが。また論文のほか、憲法研究者がメディアの取材に応えた発言も一定数あるだろう）。これらは包括的な検討でないということで考慮されなかった可能性もあるが、絶対数が少ない中、そうした理由で言及をしない理由も乏しいように思われ、先行研究の把握が十分なされたのかどうか不明確である。\n・大林啓吾「感染症リスクと憲法 新型コロナウイルス流行を素材にして」小山剛、新井誠、横大道聡（編）『日常のなかの〈自由と安全〉生活安全をめぐる法・政策・実務』（弘文堂、2020）410頁 ・尾形健「新型コロナと法（第5回）「新型コロナウイルス禍」の福祉国家 : 憲法研究者からみた「新型コロナと法」」法学セミナー790号（2020年） 56頁 ・林知更「法律時評 憲法・非常事態・コロナ」法律時報92巻13号（2020年）1 頁 ・木村草太「休業・休校要請の法的根拠について 特措法24条9項と45条2項の関係（コロナ禍社会における法的諸問題（３））」判例時報2459号（2020年）157頁 ・小山剛「自粛・補償・公表 インフォーマルな規制手法（コロナ禍社会における法的諸問題）」判例時報2460号（2020年）145 頁 ・板垣勝彦「新型コロナウイルス雑感―自粛要請、休業と補償、都市封鎖」横浜法学29巻1号（2020年）185 頁\n\n本研究は明確かつ正確に提示されたものであり、最新の文献を引用していますか。 一部該当\n\n研究設計は適切で学術的価値がありますか。 はい\n\n方法と分析について第三者による再現が可能となるよう十分な詳細が提示されていますか。 はい\n\n（該当する場合は要回答）統計分析および解釈は適切ですか。 対象外（統計を使っていない\n\n結果の基礎となるソースデータはすべて入手可能で再現性を十全に保証していますか。 はい\n\n結論は結果により妥当な裏付けを得ていますか。 はい",
"responses": [
{
"c_id": "7050",
"date": "14 Sep 2021",
"name": "Hajime Akiyama",
"role": "Author Response",
"response": "曽我部先生 重要なコメントをいただき、感謝いたします。 第一に「公共の福祉」と「個人の人権」の分類を、「個人の自由を保障する概念」及び「個人の自由を制限しうる概念」に整理し直す意義についてコメントをいただきました。新たな分類を構想した背景には、「公共の福祉」と「個人の人権」の分類では、人権概念の十全な理解が困難なのではないかとの問題意識があります。人権と自由はほぼ同一視されてきた傾向がありますが、人権を十分に理解するためには、自由権だけでなく、社会権も含めて人権を捉える必要があると考えております。感染症対策との関連では、自由の制限を人権の制約原理と捉えられる公共の福祉でなく、憲法の一義的な価値である人権の一部として位置付けることも可能であるはずです。こうした新たな捉え方により、自由を相対化し、人権のより深い理解を目指したいと考えております。 第二に、具体的権利説への批判を乗り越えることができていないとのご指摘をいただきました。第2版では、抽象的権利説から具体的権利説に投げかけられている批判を踏まえ、具体的権利説の妥当性を論じました。COVID-19対策との関連では、具体的権利説により、営業や移動の自由の制限が感染対策に有効であれば、こうした措置を採ることが生存権の視点から求められる可能性があると考えています。 第三に、本論文を基盤とした具体論の展開についてコメントをいただきました。生命権や生存権の具体的権利説を基盤とすれば、感染拡大が止まらない中、科学的知見に依拠したさらに有効な手段による感染拡大の予防が求められると考えております。しかし、2021年2月の特措法改正により導入された罰則の評価など、十分に検討できていない様々な論点がございますので、今後の研究課題としてまいります。 第四に、先行研究への言及が不十分であるとのご指摘をいただきました。十分に整理できておりませんでしたので、第1版脱稿後に発表された論文も含め勉強させていただき、本論文との関連を検討いたしました。 上記の論点を踏まえ、第2版を執筆いたしました。 貴重なコメントを頂き、ありがとうございました。"
}
]
}
] | 1
|
https://f1000research.com/articles/10-230
|
https://f1000research.com/articles/10-917/v1
|
13 Sep 21
|
{
"type": "Research Article",
"title": "Preventive effect of Nigella sativa on M1/M2 ratio, reducing risk of endothelial dysfunction in cigarette smoked Wistars",
"authors": [
"Meity Ardiana",
"Eka Utami",
"Budi Pikir",
"Anwar Santoso",
"Meity Ardiana",
"Eka Utami",
"Budi Pikir"
],
"abstract": "Background: Smoking is one of the top three causes of cardiovascular disease (CVD). Natural antioxidants including black cumin (Nigella sativa) may inhibit the pathogenesis of initial process of atherosclerosis. The aim of this study was to determine the effect of black cumin (Nigella sativa) in preventing endothelial dysfunction mainly through macrophage M1 / M2 inflammatory response in cigarette smoked male Wistars.\nMethods: In total, 50 Wistar rats were randomly allocated to five experimental groups: two control groups, namely no intervention (K-) and exposure to smoke of 40 cigarettes each day (K+); and three treatment groups: rats given a dose of 0.3 g (P1), 0.6 g (P2) or 1.2 g (P3) black cumin per kilograms bodyweight/ day, respectively, and exposed to smoke of 40 cigarettes each day. After 28 days of cigarette smoke exposure, macrophage M1 / M2 ratio was evaluated by counting total M1 and M2 in ten microscope field of view. Data were analysed by Mann-Whitney test.\nResults: The M1 / M2 ratio on K (-) was 0.9 7 ± 0.9 8 (<1) which means M2 was dominant, while the M1 / M2 ratio on K (+) was of 4.97 ± 3.42 (> 1) which means M1 dominant. There was no significant difference in the number of M1 count in treatment groups P1, P2, P3 (p value = 0.996; 0.170; 0.884, respectively) when compared with K+. Additionally, P2 group has the lower M1 number with the highest significance value when compared to K+. The number of M1 counts on P1 did not differ significantly when compared to P2 with p = 0.121 and P3 with p = 0.936.\nConclusions: In sum, ethanol extract of black cumin prevents endothelial dysfunction by inhibiting increase in macrophages M1 / M2 ratio in rats Wistar exposed to sub-chronic cigarette smoke.",
"keywords": [
"Endothelial dysfunction",
"Nigella sativa",
"black cumin",
"cigarette smoke",
"macrophage."
],
"content": "Editorial note\n\nEditorial Note (16th June 2023): Since publication, concerns have been raised to the Editorial Team regarding the ethical approval and euthanasia procedure used in this research. The Editorial Team requested further detail and an explanation from the authors in March 2023. The authors did not respond to the Editorial Team’s queries after repeated attempts to contact them. Subsequently, the Editorial Team contacted the authors’ institution in May 2023 for an explanation, but a response has not yet been received. The Editorial Team will continue to attempt contact with the institution and will revisit the case in July 2023 if no response is forthcoming.\n\nEditorial Note (8th December 2023): The Editorial Team received a response from the authors in August 2023 regarding the ethical approval for the research. The ethical approval has been validated by the Editorial Team. The Editorial Team are continuing to clarify the euthanasia procedure used in this research with both the authors and their institution.\n\nEditorial Note (26th April 2024): This note is to update readers that we still have not had any correspondence from the authors’ institution since we contacted them first in May 2023. Therefore, there are still concerns remaining regarding the ethical approval and euthanasia procedure used in this research. The F1000 Editorial Team will continue to contact the authors’ institution and the author.\n\n\nIntroduction\n\nEndothelial dysfunction is a leading predictor for atherosclerotic development and coronary heart disease (CHD).1,2 Atherosclerosis is a disease of the blood vessel wall caused by the accumulation of lipids and fibrous tissue in blood vessels, thus progressively narrowing the lumen of blood vessels.3 In 2021, The World Health Organization (WHO) declared that CHD is the number one cause of death in the world which accounts for 17% of the 18 million deaths.4\n\nGlobal data shows that smoking, including second-hand smoke, is one of the top three causes of heart disease in the world and contributed to 7.2 million deaths in 2015.4 Law and Wald (2003) evaluated the association between smoking and CHD which shows a positive correlation between the number of cigarettes smoked per day and relative risk of CHD.5,6 Cigarettes contain seven thousand kinds of chemicals that narrow the arteries and damage the blood vessels which leads to endothelial dysfunction.7\n\nAn evident imbalance between pro-oxidants, which are high due to various components in cigarette smoke, and antioxidants in the body such as superoxide dismutase (SOD), catalase (CAT) and gluthatione peroxidase (GPx) lead to endothelial dysfunction. Endothelial dysfunction is also characterized by a decrease in the endhotelial nitrite oxide synthase (eNOS) enzyme due to oxidative stress. eNOS affects the bioavailability of nitric oxide (NO) which results in decreased antioxidant, anti-inflammatory and anti-thrombotic activity in blood vessels. The decrease in NO causes an increase in endothelial permeability, levels of pro-inflammatory cytokines and the expression of adhesion molecules such as vascular adhesion molecule-1 (VCAM-1). VCAM-1 then increases the adhesion of monocytes and other inflammatory cells to the endothelium. The increase in VCAM-1 triggers the activation and adhesion of macrophages in the endothelium which begins the inflammatory process.1,2,7,8\n\nThe inflammatory cascade involved innate and adaptive immunity in atherosclerosis process.9 Accordingly, macrophage role is tangible. The most essential function of macrophages in the atherogenesis process is the uptake and lipid deposition processes. Oxidized low-density lipoprotein (LDL) is the main lipid form recognized by macrophages through scavenger receptors (SRs) such as CD36 and CD68. These receptors trigger phagocytosis of ox-LDL which in turn increases intracellular cholesterol. Intracellular cholesterol is then metabolized and transported to exogenous recipients such as HDL through efflux proteins, namely ATP- binding cassette (ABC) transporter, ABCA1 and ABCG1.8\n\nMacrophages are known to have several different population forms. Different macrophage populations are grouped based on which certain cytokine activates the macrophages. The first population is a classic population called M1 which is pro-atherogenic. M1 macrophages can be activated via Th1 cytokines such as IFNγ, TNFα, IL-1β, IL-6, IL-8, IL-12p40, and IL-12p35. An alternate anti-inflammatory population is named M2 whose activation is mediated by Th2 cytokines such as IL-3 and IL-4. Macrophages can change into phenotypes M1 to M2 or vice versa depending on specific cytokine signals. This property is known as the plasticity of macrophages. Several studies have shown a change in the ratio of M1 and M2 during the atherogenesis process. The atherogenesis process can be caused not only by an increase in pro-inflammatory macrophages but also a decrease in anti-inflammatory macrophages.8,10 This is supported by research by Chen et al. which shows the polarization of macrophages during the atherogenesis process. M1 macrophages are more dominant in the early phase of atherogenesis and are still asymptomatic. As the atherogenesis process progresses, M2 becomes increasingly dominant when it enters the late symptomatic phase of atherogenesis.11\n\nOn the other hand, a few studies have stated that the low rate in cardiovascular mortality is arguably due to the high level of antioxidants intake.12 Natural antioxidants could be in the form of primary or secondary antioxidants. Primary antioxidants such as SOD, CAT and GPx are antioxidants that prevent the formation of new radical compounds. Secondary antioxidants are used to bind metals that act as pro-oxidants and scavenge free radicals.13,14\n\nOne of the natural antioxidants that is largely used in Asia is black cumin (Nigella sativa). Black cumin has the potential to be used as a prevention for atherosclerotic disease.15,16 Black cumin and its derivative components have radical scavenging potential as well as oxidative stress inhibition capacity by increasing the production of antioxidant, anti-inflammatory and anti-thrombotic agents.17 However, there have been no studies to our knowledge that have studied the effect of Nigella sativa on M1 / M2 inflammatory response in endothelial dysfunction caused by exposure to cigarette smoke. Thus, this research aims to prove the effect of black cumin in preventing endothelial dysfunction through inflammatory response inhibition due to cigarette smoke exposure.\n\n\nMethods\n\nEthical approval for this study has been granted by Faculty of Veterinary Medicine Airlangga University (animal approval no: 2.KE.184.10.201). This study is reported in line with the nimal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines.44\n\nThe study was done from July 2019 to March 2020. Samples were taken from 50 adult healthy male Wistar albino rats certified by Animal Husbandry from Ministry of Agriculture (letter number 524.3/077/35.73.309/2020) with inclusion criteria: 8 weeks of age, male, weight of 150 to 200, non-genetically modified and never received any medical procedure before. The exclusion criteria were female, visually inactive, physically abnormal, dark fur, and genetically modified wistar. Additionally, the drop out criteria were thus those who lost more than 10% of initial body weight, showed change in behaviour, and died during the experimental period. The number of replicated experimental animals based on Lemeshow's formula is a minimum of 10 animals in each group. Lemeshow's formula for estimating the mean of 2 or more unpaired groups is as follows:\n\nInformation:\n\nn = number of replications\n\nσ = estimated standard deviation\n\nZ1-α/2 = standard normal number of standard error related to the level of confidence. If the confidence level is α = 0.05 then Z 1-α/2 = 1.96\n\nZ1-β = standard normal number of standard error related to research strength. If β = 0, 20 then 1-β = Power of test =\n\n0.80 so that Z1-β = 0.84\n\nμ1 = mean of treatment group\n\nμ2 = control group mean\n\nThe calculation results show that μ1 = 53 and μ2 = 41 and σ = 9 are obtained from the following calculations:\n\nn 1 = Number of replication treatments 1\n\nn2 = Number of replication treatments 2\n\nσ = E stimulation standard deviation\n\nSD1 = Standard deviation of treatment results 1\n\nSD2 = Standard deviation of treatment results 2\n\nSo that the calculation obtained:\n\nIn this study, the number of replications used was 9 for each group. Calculations were made for the correction factor of 10% so that 1 animal was added per treatment so that the total sample per treatment was 10. There were five groups in this study, namely K1, K2, P1, P2, and P3, so that the total sample size was 50 individuals.\n\nIn the course of the research, there were several experimental animals that met the drop out criteria. One experimental animal in each group K (+), P1 and P3 died during the study. One experimental animal in each group K(−) and P2 experienced pain. The total number of experimental animals that dropped out was 5, so the remaining experimental animals and continued until the measurement and analysis of variables in each group K(−), K (+), P1, P2, and P3 were @ 9 animals.\n\nAll were caged in groups maintaining to achieve the standard of biosafety level 2 at the Laboratory of the Faculty of Veterinary Medicine, Airlangga University, Indonesia. Microisolator cages were placed in a room with controlled ventilation, half day light and dark cycle, humidity 50% to 60%, and temperature of 22°C to 25°C. The samples received the same feed and drinking water during the study. The feed used was 511 HI-PRO-VITE® (PT. Charoend Pokphand Indonesia) with a moisture content composition of max. 13%; protein 21-23%; fat min. 5%; fiber max. 5%; ash max. 7%; calcium min 0.9%; phosphorus min. 0.6%; aflatoxin max. 50 ppb; total calories 2900-3000 kcal/kg. As an adaptation phase for all groups, only ad libitum water and standard feed were given in the first seven days.\n\nAll efforts were made to ameliorate any suffering of animals by appropriate experiment design and analysis that was robust and genuinely adds to the knowledge base.\n\nAs depicted in Figure 1, rats were simply randomized by numbering 0 to 50 from a number table to assign them to each group. Confounders were not addressed in this experiment. The animals were randomly allocated to the following five groups of ten rats each: (1) negative control group (K-); (2) positive control group exposed to cigarette smoke (K+); (3) black cumin extract treatment group (P1) exposed to cigarette smoke and treated with black cumin extract 0.3g/kgbw/day; (4) black cumin extract treatment group (P2) exposed to cigarette smoke and treated with black cumin extract 0.6g/kgbw/day; (5) black cumin extract treatment group (P3) exposed to cigarette smoke and treated with black cumin extract 1.2g/kg/bw/day. This exposure lasted for 28 days. There was one principal investigator who supervised the conduct and group allocation at all different stages of experiment.\n\nBlack cumin extract was given orally using a gastric probe. Each dose of black cumin extract was dissolved in 1 ml of sodium – carboxymethyl cellulose (Na - CMC). The volume of 1 ml of Na - CMC was adjusted to the normal volume of the rat's stomach, which is 3-5 ml to prevent gastric mucosae’s stress tearing (McConnel, 2008). Cigarette smoke was exposed to the rats by side stream of ventilator pump (CSEM, model Bull), smoked generating chamber, and smoke exposure chamber which connected through silicone tubes as depict in Figure 2.18 A ventilator pump is a controlled positive pressure pump which deliver a constant flow of gas in the respiratory cycle. Unfiltered cigarette Dji Sam Soe® (HM. Sampoerna) containing 39 mg of tar and 2.3 mg of nicotine obtained in the market was used in this study. The cigarette dosage given was adapted from Ali et al., 2012 and Jaldin et al., 2013, namely 40 cigarettes /day (8 cigarettes per administration, 5 times a day). Cigarette exposure was carried out every day (280 cigarettes/week) for 4 weeks (sub chronic).18,19\n\nAfter the 4 weeks, chloroform inhalation as one of euthanasian methods recommended by American Veterinary Medical Association (AVMA) 2013 was performed.20 Subsequently, the aorta was surgically removed from the rats. The histopathological preparations were made using the paraffin method in which tissue was fixed in 10% formalin. Fixed tissues were then cut into sections and then placed in paraffin embedding cassettes. Following this, paraffin blocks were cut at ± 5μm and finally stained.21\n\nImmunohistochemical staining with the streptavidin-biotin complex method was used to determine the expression of M1 and M2 in the rat aorta. The marker used to detect M1 is the CD38 marker while M2 can be specifically detected using the Arginase-1 marker at 24% and the early growth response protein 2 (Egr2) by 70%.20\n\nThe rat aortic tissue was fixed on a glass object and deparaffinized. Rehydration with alcohol was carried out afterwards and then washed with phosphate buffer solution (PBS) and soaked in 3% H2 O2 for 20 minutes. We then added 1% Bovine serum albumin (BSA) in PBS and incubated the samples for 30 minutes at room temperature. Primary antibodies CD38+ (Biolegend 250502) or Egr2 (Abcam ab108399) were then added and subsequently incubated for 30 minutes. Afterwards, the samples were washed using PBS. Secondary antibodies labelled with biotin (Anti Rat IgG Biotin Labeled 31830, Termofischer, Waltham, Massachusetts, USA) were incubated for 10 minutes at room temperature, then washed using PBS.22\n\nOne millilitre of working solution of Strepavidin-Horseradish Peroxidase (SA-HRP SA10001, Termofischer, Waltham, Massachusetts, USA) was added and incubated for 10 minutes at room temperature then washed using PBS. Chromogen DAB (3,3-diaminobenzidine tetrahydrochloride) was added then incubated for 10 minutes at room temperature then washed using PBS and sterile water. The final step was 1 minute counterstaining (hematoxylin and eosin) then covering the samples with a glass cover so that examination under a microscope was possible. M1 and M2 expression in the aorta was observed at 400× magnification in 10 fields of view using a binocular microscope (LB 248). Total number of M1 and M2 expression was counted manually in ten microscope field of view. The M1 / M2 ratio was obtained by dividing the sum of M1 count by the number of M2 count. The M1 / M2 ratio > 1 is M1 dominance, while the M1 / M2 ratio <1 is M2 dominance.22\n\nThe macrophage expression was compared for each group and analysed statistically using the SPSS version 25 (IBM corp, Chicago, USA) using the following tests: (1) Normality test (Saphiro-Wilk test) which aims to test whether the data obtained from each group has a normal distribution, (2) Variant homogeneity test which aims to test whether the variant data obtained between groups is homogeneous, (3) One-way ANOVA test which aims to compare the mean value of more than two groups if the data distribution is normal. If the data distribution is abnormal, the Kruskal-Wallis non-parametric test is used, (4(Post hoc analysis (Tukey HSD) which aims to determine which group is significantly different from the ANOVA test results. The post hoc analysis for the Kruskal-Wallis was the Mann-Whitney test. The post hoc analysis for Brown-Forsythe is the Games-Howell test, and lastly (5) Regression analysis which aims to determine the strength of the correlation between the independent and dependent variables and between the dependent variables.\n\n\nResults\n\nIn total, 45 rats were included in the final analysis.43 The depiction of M1 and M2 macrophage observations in the K- and K+ groups under microscope are represented in Figure 3 and Figure 4. Figure 3 depict CD38+ marked macrophage while Figure 4 depict Egr2 marked macrophage. No picures’ alterations were made when evaluating the M1 and M2 expression.\n\nImmunohistochemical staining of M1 expression by CD38 (white arrow) on (A) Negative control (B) Positive control.\n\nImmunohistochemical staining of M2 expression by Egr-2 (white arrow) on (A) Negative control (B) Positive control.\n\nIn the results of the M1 Mann-Whitney test, the value of p = 0.000 indicates a significant difference between the K(−) and K (+) groups as presented in Table 1 below.\n\nab superscript shows difference between group.\n\nIn the results of the M2 independent t-test, the value of p = 0.0 00 indicates a significant difference between the K(−) and K (+) groups as presented in Table 2 below.\n\nab superscript shows difference between group.\n\nThe M1 / M2 ratio on K(−) was 0.9 7 ± 0.9 8 (<1) which means M2 dominant, while the M1 / M2 ratio on K (+) was of 4.97 ± 3.42 (> 1) which means M1 dominant. The value of the M1/ M2 ratio is summarized in Table 3.\n\nThe M1 / M2 ratio difference test analysis using the Mann-Whitney test showed the value of p = 0.000 which indicates a significant difference between groups as data presented in Table 4.\n\nab superscript shows difference between group.\n\nFigure 5 and Figure 6 show the immunohistochemical results of M1 and M2 macrophages staining in the tunica intima and tunica aortic media of the treatment groups (P1, P2, P3).\n\nImmunohistochemical staining of M1 expression by CD38 (white arrow) on (C) P1 (D) P2 (E) P3.\n\nImmunohistochemical staining of M2 expression by Egr-2 (white arrow) at (C) P1 (D) P2 (E) P3.\n\nIn M1 count as represent in Figure 7, the results of the Brown-Forsythe test showed p = 0.085 conclude that there were no significant differences between treatment groups. The results of the Post Hoc Games-Howell analysis informed that there was no significant difference in the number of M1 count in treatment groups P1, P2, P3 (p value = 0.996; 0.170; 0.884, respectively) when compared with K+. Additionally, P2 group has the lower M1 number with the highest significance value when compared to K+. The number of M1 counts on P1 did not differ significantly when compared to P2 with p = 0.121 and P3 with p = 0.936. The total M1 count was significantly different in P2 when compared to P3 with p = 0.029.\n\nConversely, for M2 count as illustrated in Figure 8, the Kruskal-Wallis test results showed a value of p = 0.000 which indicates a significant difference between groups. The results of the Mann-Whitney analysis showed that the number of aortic M2 count less but not significant at P1 with a value of p = 0.069 and P3 with a value of p = 0.479 when compared to K+. A significant increase in M2 was obtained in P2 with a value of p = 0.000 when compared to K+. The number of M2 counts on P1 is significantly different when compared to P2 with p value = 0.000 and is not significantly different when compared to P3 with p value = 0.3 29. The number of M2 counts is significantly different in P2 when compared to P3 with p value = 0.000.\n\nSubsequently on M1 / M2 ratio scheme as summarized in Table 5, the M1 / M2 ratio for P1 has a value of 9.05 ± 5.76 (> 1) which means M1 is dominant. The M1 / M2 ratio for P2 has a value of 0.42 ± 0.28 (<1) which means M2 is dominant. The M1 / M2 ratio for P3 has a value of 6.22 ± 3.61 (>1) which means M1 dominant.\n\nThe results of the Kruskal-Wallis test showed p value = 0.0 11 which indicates a significant difference between groups. The results of the Mann-Whitney analysis showed that the M1 / M2 ratio is superior significantly in P1 when compared to K+ with a value of p = 0.012. The M1 / M2 ratio for P2 is less when compared to K+ with a value of p = 0.000. The M1 / M2 ratio for P3 increases but is not significant when compared to K+ with a value of p = 0.656. The M1 / M2 ratio for P1 is significantly different when compared to P2 with a value of p = 0.000 and the difference is not significant when compared to P3 with a p = 0.354. The M1/ M2 ratio is significantly different in P2 when compared to P3 with p = 0.000. Data is presented in Table 6 and Figure 9.\n\nabc superscript shows difference between groups (Mann-Whitney test).\n\n\nDiscussion\n\nOne of the tangible factors in developing atherosclerosis through oxidative stress is cigarette smoke. Moreover, the number of cigarette smoked each day is exponentially equal to the increase of oxidative stress level.23 The atomic substances delivering intense reactive oxygen species in cigarette smoke are naturally easy to be absorbed in the human tissue. Consequently, the level of oxidative stress and reactive oxygen species (ROS) increases which then inhibit the endhotelial nitric oxide synthetase (e-NOS) and stimulate VCAM-1 expression.22\n\nReduced level of nitric oxide (NO) is believed to be the key mechanism in the cascade of endothelial dysfunction. Nitric oxide is mainly produced by the assistance of endothelial nitric oxide synthase (e-NOS). Hence, the availability of e-NOS reflect the level of NO in endothelial cells.23 Once endothelial cell is dysfunctional, adenosine coronary flow reserve and acetylcholine response test can be conducted to confirm the functionality of endothelial cell.24\n\nA previous report by Ardiana et al. showed that exposure to cigarette smoke decrease e-NOS level in the aorta.25 A decline in e-NOS concentration led to not only increase in expression of adhesion molecules and vascular tone but also initiate inflammation coagulation cascade.26 As a result, aortic intima-medial is thickening in the early step of atherosclerosis. Ardiana et al. also concluded that 28 days of cigarette smoke is an independent risk factor for atherogenic process through various cascades. Excessive proliferation and apoptosis as compensation mechanism are responsible for vascular intimal media thickening.25 Ardiana et al. found not only an increase of intima-media thickness (IMT) but also structural changes marked by disorganization and vacuolization of smooth muscle cells in the tunica media of the aortic tissue. In addition, increased inflammatory process on the vascular endothelium are closely linked to atherosclerotic process.\n\nMacrophages are one of the immune cells that are closely related to the inflammatory process due to various causes. Macrophages can polarize into M1 subtypes which are pro-inflammatory or M2 which are anti-inflammatory, depending on the signal received.8 Of the various stimuli that can affect the activity of macrophages, cigarette smoke is one of the most dominant stimuli because of its pro-oxidant effects. Macrophage activation and polarization is one of the central mechanisms for the emergence of endothelial dysfunction which later becomes atherosclerosis due to exposure to cigarette smoke.28\n\nThis study suggests that exposure to cigarette smoke stimulated M1 macrophages with CD38 markers and M2 macrophages with Egr-2 markers, with the M1 / M2 ratio being dominant on M1. Research by Eapen et al. supportably found an increase in M1 macrophage accumulation and decreased M2 expression in the alveoli of smoker patients with chronic obstructive pulmonary disease (COPD).29 Yet another study by Dewhurst et al. showed different results where M2 macrophages were more dominant in the alveoli of smokers.30\n\nThese different results explained by Yuan et al. who examined the expression of M1 and M2 macrophages in mice by exposing cigarette smoke with different duration and concentrations. Control group Wistar without cigarette smoke exposure showed basal macrophage expression where M1 was more dominant than M2. The administration of 2% cigarette smoke for 2 days has not shown macrophage polarization in which M1 is still more dominant than M2. On day 6, M2 and its cytokine expression (IL-10, IL-6, TGF-β1 and TGF-β2) were more dominant than M1 and its cytokine expression (TNF-α and IL-12p40). Accordingly, the polarization of macrophages occurs depend on the length of exposure to cigarette smoke. Yuan et al., also found that the higher the concentration of cigarette smoke but with the same duration of exposure may stimulate the polarization towards M2.31\n\nAdditionally, research by Chen et al. showed that M1 activation occurred in the initial inflammatory phase while the M1 activation decreased in further pathological phase.11 To date, no studies have examined the relationship between cigarette smoke exposure including the number of cigarettes and length of exposure to our knowledge. The current study discovered a relationship between exposure to cigarette smoke (40 cigarettes per day for 28 days) and increased M1 and M2 expression with the calculated ratio of M1 / M2 dominant on the M1 compare to control group.\n\nPolarization of macrophages due to exposure to cigarette smoke can go through three different mechanisms, namely through the NF-κB pathway, mitogen-activated protein kinase (MAPK), and Janus kinas (JAK) or signal transducer and activator of transcription (STAT). These pathways are the main routes for the production of various cytokines that affect macrophages. The activation of these pathways is also greatly influenced by the dose and content of the cigarettes used.29\n\nFirstly, the hydroquinone content in cigarette smoke at certain doses is known to inhibit the activation of NF-κB which then reduces the production of pro-inflammatory cytokines such as TNF-α, IL-1β, IL-6, IL-8, TLR2 and TLR4 thus triggering macrophage polarization towards M2. However, low doses of cigarette smoke have the opposite effect.11,33 Secondly, cigarette smoke affect MAPK signals through its acrolein content. A 4-month cigarette smoke exposure can inhibit MAPK activation and reduce pro-inflammatory cytokines TNF-α and IL-12 so that promote more M2 macrophages.34,35 Shorter cigarette smoke exposure has the opposite effect which increases MAPK activation, hence the production of pro-inflammatory cytokines TNF-α and IL-8.36,37 The third pathway affected by exposure to cigarette smoke is the JAK / STAT signal. Cigarette smoke content is known to be able to phosphorylate JAK protein and consequently, activate several STAT proteins. In general, cigarette smoke content increases the activation of STAT3 and STAT6, decreases pro-inflammatory cytokines and increases anti-inflammatory cytokines such as IL-12, IL-10, IL-6 and TGF-β which associated with M2 macrophages. Meanwhile, a decrease in STAT1 activation was associated with an increase in M1 macrophages. To date, no research has looked at the effect of certain cigarette smoke components that predominantly affect the JAK / STAT pathway.29\n\nThe final process of endothelial dysfunction is characterized by macrophages and leucocytes undergoing adhesion, rolling which then enters the sub endothelium to initiate the inflammatory process. The inflammatory process can cause endothelial and subendothelial cell death which is compensated by the excessive proliferation process. Macrophages that enter the sub endothelium can also phagocytose oxidized LDL (oxLDL) and attract other cytokines and leukocytes to form a foam cell that can accumulate and also play a role in atherosclerosis process.38 Interestingly, this study shows black cumin ethanol extract may stimulate macrophage polarization so that there is a change in the M1/ M2 ratio. Studies measuring the effect of giving black cumin to the polarization of macrophages have not been conducted to date. However, research by Dugo et al. can prove the effect of cocoa extract antioxidants on macrophage polarization. Provision of cocoa extract containing several polyphenolic antioxidants has been shown to trigger M1 to M2 macrophage polarization and increase macrophage metabolism through oxidative pathways in in vitro acute leukaemia monocyte cell culture.39\n\nThe polarizing effect of macrophages from M1 to M2 in this study is presumably be due to the mechanism of thymoquinone in black cumin affecting the NF-κB activation pathway. Sethi et al. claimed that thymoquinone at the dose of 10 μM on 4 hours incubation can suppress NF-κB activation in human leukemia myeloid cells and human embryonic kidney cells exposed to TNF- α.33 Suppression of NF-κB activation reduce the production of pro-inflammatory cytokines such as TNF-α, IL-1β, IL-6, IL-8, TLR2 and TLR4 which then stimulate M1 to M2 macrophage polarization.29\n\nThe effect of changing the M1/ M2 ratio due to black cumin administration affected by the dose given. This study shows that M1 was dominant in P1 and P3. However, M2 was surprisingly dominant in P2. This suggests that the macrophage polarization to M2 was effective at 0.6 g/kg of black cumin extract and did not occur at higher doses (1.2 g/kg). The higher dose possibly triggers the pro-inflammatory cytokine IL-1β caused by thymoquinone on black cumin. This is in line with research by Haq et al. which confirmed that the increased dose of black cumin extract from 0.5 μg / ml to 5 μg/ml could increase in vitro IL-1β production in polymorphonuclear leukocytes.41 Likewise, a study by Miliani et al. expressed an increase in IL-1β by leukemia cells exposed to 5 μM thymoquinone.42 High doses of black cumin can increase the production of IL-1β which in turn can increase the activation of NF-κB so that M1 to M2 polarization does not occur. As found in this study, the highest dose of black cumin (1.2 g/kg) showed a high amount of M1 and a low amount of M2.\n\n\nLimitations\n\nThe first limitation of this study was the small number of samples which can increase the likelihood of error and imprecision. Secondly, results from animal models were not duplicated into human models. Another crucial difference is macrophage ratio which is usually much lower in the Wistar rats than in humans. These factors may altered the results’ interpretation of our study. Accordingly, outcomes should be translated within the limitations and context of this study. On the other hand, the homogeneity and high statistical power were the strength of this study.\n\n\nConclusion\n\nIn summary, this research found that exposure to cigarette smoke (40 cigarettes per day for 28 days) was significantly related to M1 and M2 count with the calculated ratio of M1 / M2 dominant on the M1. On the other hand, ethanol extract of black cumin was associated with M1 pro-inflammatory shift to M2 anti-inflammatory macrophage in cigarette smoked Wistar aorta. Hence the preventive effect on endothelial dysfunction in the atherosclerotic process can be suggested.\n\n\nData availability\n\nFigshare: Nigella sativa on M1 / M2 Preventive effect of Nigella sativa in M1 / M2 ratio reducing risk of endothelial dysfunction in cigarette smoked Wistars.\n\nhttps://doi.org/10.6084/m9.figshare.14912442.v1.43\n\nThis project contains the following underlying data:\n\n• DATA PENELITIAN DISERTASI.xlsx\n\n• CD3800000000001.jpg (Macrophag CD38+ antiobodies marker coloured in group K− aortic rats)\n\n• CD3800000000002.jpg (Macrophag CD38+ antiobodies marker coloured in group K+ aortic rats)\n\n• CD3800000000003.jpg (Macrophag CD38+ antiobodies marker coloured in group P1 aortic rats)\n\n• CD3800000000004.jpg (Macrophag CD38+ antiobodies marker coloured in group P2 aortic rats)\n\n• CD3800000000005.jpg (Macrophag CD38+ antiobodies marker coloured in group P3 aortic rats)\n\n• EGR200000000001.jpg (Macrophag M2 Egr2 antiobodies marker coloured in group K− aortic rats)\n\n• EGR200000000002.jpg (Macrophag M2 Egr2 antiobodies marker coloured in group K+ aortic rats)\n\n• EGR200000000003.jpg (Macrophag M2 Egr2 antiobodies marker coloured in group P1 aortic rats)\n\n• EGR200000000004.jpg (Macrophag M2 Egr2 antiobodies marker coloured in group P2 aortic rats)\n\n• EGR200000000005.jpg (Macrophag M2 Egr2 antiobodies marker coloured in group P3 aortic rats)\n\nFigshare: ARRIVE checklist for ‘Preventive effect of Nigella sativa in M1 / M2 ratio reducing risk of endothelial dysfunction in cigarette smoked Wistars’.\n\nhttps://doi.org/10.6084/m9.figshare.15819765.v1.44\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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PubMed Abstract | Publisher Full Text\n\nHristova M, Spiess PC, Kasahara DI, et al.: The tobacco smoke component, acrolein, suppresses innate macrophage responses by direct alkylation of c-jun N-terminal kinase. Am J Respir Cell Mol Biol. 2012; 46(1). PubMed Abstract | Publisher Full Text | Free Full Text\n\nMetcalfe HJ, Lea S, Hughes D, et al.: Effects of cigarette smoke on Toll-like receptor (TLR) activation of chronic obstructive pulmonary disease (COPD) macrophages. Clin Exp Immunol. 2014; 176(3). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoch A, Giembycz M, Stirling RG, et al.: Effect of smoking on MAP kinase-induced modulation of IL-8 in human alveolar macrophages. Eur Respir J. 2004; 23(6). PubMed Abstract | Publisher Full Text\n\nMarumo S, Hoshino Y, Kiyokawa H, et al.: P38 mitogen-activated protein kinase determines the susceptibility to cigarette smoke-induced emphysema in mice. BMC Pulm Med. 2014; 14(1). 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PubMed Abstract | Publisher Full Text\n\nMiliani M, Nouar M, Paris O, et al.: Thymoquinone Potently Enhances the Activities of Classically Activated Macrophages Pulsed with Necrotic Jurkat Cell Lysates and the Production of Antitumor Th1-/M1-Related Cytokines. J Interf Cytokine Res. 2018; 38(12). PubMed Abstract | Publisher Full Text\n\nArdiana M, Santoso A, Pikir BS, et al.: Nigella sativa on M1 / M2 Preventive effect of Nigella sativa in M1 / M2 ratio reducing risk of endothelial dysfunction in cigarette smoked Wistars. figshare. Media. 2021. Publisher Full Text\n\nUtami E, Ardiana M: Author Checklist ARRIVE - Full.pdf. figshare. Media. 2021. Publisher Full Text"
}
|
[
{
"id": "94859",
"date": "27 Sep 2021",
"name": "Nelly Mayulu",
"expertise": [
"Reviewer Expertise Functional Food",
"Natural Product",
"Non-communicable Diseases",
"Food and Nutrition",
"Antioxidants",
"Polyphenols."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study presents the results of the Preventive effect of Nigella sativa on the M1/M2 ratio, reducing the risk of endothelial dysfunction in cigarette-smoked Wistars. Interesting research, but there are some things that I think the researcher needs to explain:\nHow is the extraction process from Black Cumin (Nigella sativa)?\n\nWhat is the nutrient content of the pellets used as standard pellets? e.g. 58.1% carbohydrates, 16.51% crude protein, 0% animal fat, etc\n\nThe researcher/author mentions \"Unfiltered cigarette Dji Sam Soe® (HM. Sampoerna)\" in the Methods-procedure section, have you received permission to mention the brand? or how? please respond to this.\n\nCan researchers provide a dose description that can be used as a reference for clinical trials in humans?\n\nI think some of the things above need to be answered or responded to by researchers/writers through comments. Other than that, I really appreciate the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "126107",
"date": "12 May 2022",
"name": "Reza Mohebbati",
"expertise": [
"Reviewer Expertise Toxicology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript entitled \"Preventive effect of Nigella sativa on M1/M2 ratio, reducing risk of endothelial dysfunction in cigarette smoked Wistars\" was reviewed, and there are several comments for improvement of the manuscript as follow:\nIn the scientific texts, the scientific name for plants must be used. Replace black cumin with Nigella sativa.\n\nAnimals used cigarette smoke passively? Is the protocol true? Is the used smoking protocol generalizable to humans?\n\nIt would be better to evaluate the other white blood cells count and differential.\n\nThe best model for smoking is the guinea pig. It would be better to use this model instead of a rat.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-917
|
https://f1000research.com/articles/10-718/v1
|
02 Aug 21
|
{
"type": "Research Article",
"title": "Sea grapes extract improves blood glucose, total cholesterol, and PGC-1α in rats fed on cholesterol- and fat-enriched diet",
"authors": [
"Mury Kuswari",
"Fahrul Nurkolis",
"Nelly Mayulu",
"Faisal Maulana Ibrahim",
"Nurpudji Astuti Taslim",
"Defny Silvia Wewengkang",
"Nindy Sabrina",
"Ghafur Rasyid Arifin",
"Keren Esther Kristina Mantik",
"Muhammad Rahimi Bahar",
"Najda Rifqiyati",
"Ronald Rompies",
"Piko Satria Augusta",
"Happy Kurnia Permatasari",
"Nelly Mayulu",
"Faisal Maulana Ibrahim",
"Nurpudji Astuti Taslim",
"Defny Silvia Wewengkang",
"Nindy Sabrina",
"Ghafur Rasyid Arifin",
"Keren Esther Kristina Mantik",
"Muhammad Rahimi Bahar",
"Najda Rifqiyati",
"Ronald Rompies",
"Piko Satria Augusta"
],
"abstract": "Background: Sea grapes or Caulerpa racemosa have a lot of phytochemical content, especially unsaturated fatty acids that are beneficial for health. This study aims to evaluate the effects of sea grapes extract on blood glucose levels, total cholesterol-, and Peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1α in male Wistar rats, which were given per-oral (p.o.) cholesterol- and carbohydrates fat-enriched diets (CFED). Methods: Forty male Wistar albino rats weighing between 200 – 250 g were used for this study. Animals were randomly distributed into four groups of ten animals each. Group A served as control (received standard dry pellet diet). Rats in group B were fed on CFED for 4 weeks. Groups C and D were fed on CFED and were administered 150 and 450 mg/kg of sea grapes extract (p.o.), respectively. Results: Group C rats indicated a blood glucose reduction and an increase in PGC-1α serum, in comparison to group D (p<0.05). There were no significant differences between group C and D in blood cholesterol reduction (high dose of the extract did not have significant effects) (p=0.222), and both groups had the same effect in lowering total cholesterol in rats. Conclusion: Sea grapes extract is proven to improve blood glucose, total cholesterol, and PGC-1α levels in rats fed with CFED.",
"keywords": [
"Caulerpa racemosa extract",
"blood glucose",
"total cholesterol",
"PGC-1α",
"functional food"
],
"content": "Introduction\n\nReactive Oxygen Species (ROS) are the amounts of reactive molecules and free radicals derived from oxygen in a molecule (i.e., superoxide, peroxide, hydrogen peroxide, hydroxyl radical, etc.) (Sies & Jones, 2020). Oxygen-based radicals are produced as a byproduct in the mitochondrial electron transport at the aerobic respiration performed by oxidoreductase enzymes and metal-catalyzed oxidation. A recent study has shown that ROS has a role in cell apoptosis that leads to organ dysfunction (Pizzino et al., 2017).\n\nPeroxisome proliferator-activated receptor-gamma coactivator (PGC)-1α is a transcription coactivator that regulates the genes involved in energy metabolism. It is the main regulator of mitochondrial biogenesis (Liang &Ward, 2006). PGC-1α stimulates mitochondrial biogenesis and encourages the remodeling of muscle tissue to a fiber-type composition that is metabolically more oxidative and less glycolytic in nature, and it participates in the regulation of both carbohydrate and lipid metabolism (Puigserver &Spiegelman, 2003; S. Yang et al., 2020).\n\nThe ability of cell defense against ROS has been associated with aging and contributes to the increased oxidative stress state. This condition can disturb the enzyme activity, especially through the reversible oxidative reaction at the thiol functional group at the side chain of the enzyme structures (Birben et al., 2012). This can lead to the alteration of biomolecule structure and integrity, and enzyme dysfunction (Freitas et al., 2016). As a result, insulin resistance and Type 2 Diabetes can development (Facchini et al., 2001; Meigs et al., 2003). Additionally, the effect of aging on changes in liver mass can increase serum Low-Density Lipoprotein (LDL)-cholesterol level, due to the hepatocytes cell death caused by oxidative stress (Anantharaju et al., 2002; Miller, 1984). Hence, effective control of ROS levels is essential. The aging population tends to have a higher prevalence of chronic disease, thus there is a demand for health-improving foods (Park, 2013). The consumption and production of high-antioxidant as functional foods in recent years are popular due to their capability of reducing Reactive Oxygen Species (ROS), as well as having an impact on several aging and chronic related diseases (Park, 2013; Park et al., 2004). However, there are some challenges that are associated with the utilization of functional food. For example, specific functional foods need to be consumed in high concentrations in order to be biologically effective, therefore, this would require the nutritional facts such as the daily dose of the bioactive compound in each serving size to be determined (Kang et al., 2011). Preliminary studies are needed to determine which bioactive compound is the most beneficial, and what is the quantitative-activity relationship between the bioactive compounds contained in functional foods.\n\nSea grapes (Caulerpa racemosa) or lawi-lawi (Indonesia-local terminology) is a species of editable green alga, seaweed in the Caulerpaceae family found in waters surrounding Sulawesi (Pakki et al., 2020). Sea grapes are harvested intensively as they are an important source of macronutrients and micronutrients, especially in East and South-East Asia (grown commercially in ponds and consumed in the Philippines, Indonesia and Vietnam) as a major part of the traditional diet (Chen et al., 2019). Some studies showed that sea grapes contains several bioactive components, such as protein, polysaccharides, polyphenol, flavonoids, and antioxidants (P. Yang et al., 2015; Yep et al., 2019; Taslim & Fahrul, 2021). Moreover, sea grapes have a high antioxidant level, and they have the potential to act as functional food or nutraceuticals (Tanna et al., 2020; Yep et al., 2019; Nurkolis et al., 2021). The extract of sea grapes can reduce glucose level, aspartate aminotransferase (AST), alanine aminotransferase (ATL). Moreover, it appears to have a hepatoprotective activity in diabetic rats (Qudus B Aroyehun et al., 2020). Therefore, this study aims to evaluate the effects of Sea grapes extract on blood glucose levels, total cholesterol, and PGC-1α in male Wistar rats on cholesterol- and fat-enriched diets (CFED).\n\n\nMethods\n\nThis in vivo study was conducted at the pharmacological laboratory, faculty of mathematics and natural sciences, Sam Ratulangi University.\n\n\nCollection and preparation of plant material\n\nFresh sea grapes (Caulerpa racemosa) was collected from the shallow section (5-10 meters from the sea surface) of the Mantehage seawater, North Sulawesi, Indonesia. The botanical identification and authentication were confirmed at the department of pharmacology, faculty of mathematics and natural sciences, Sam Ratulangi University, Indonesia. The specimens were collected for feature references. The sea grapes were rinsed thoroughly with water, air-dried at room temperature and in an 40°C oven, then powdered by an electric mill.\n\n\nPreparation of sea grapes extracts\n\nCrude powder (one kg) was macerated in 96% ethanol for 72 hours with each extraction performed in triplicates, which resulted in 34% yield. The crude extracts were filtered by Whatman 41 filter paper. The total filtrate was concentrated and evaporated at 40°C with a rotary evaporator RV 8 IKA under reduced pressure (100 millibar) for 90 minutes, and evaporated in an 40°C oven to produce a thick extract. The extract was stored in a refrigerator at 10°C until used in the study.\n\n\nAnimal handling and ethical approval\n\nAll experimental rats were kept on standardized free access of feed and ad libitum of water. The study was conducted in the Laboratory of Pharmacology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Makassar, Indonesia. Forty male Wistar albino rats (Rattus norvegicus) (4-5 weeks) weighing between 200 – 250 g were obtained from the Laboratory Animals Farming Makassar, Indonesia, and transported to the research site. The animals were grouped and housed in cages and maintained under standard laboratory conditions (temperature: 27 ± 2oC), with light and dark cycles (12/12 hours). The rats were acclimatized to laboratory conditions for 10 days before the commencement of the experiment. The research protocol (use of experimental animals) refers to the Declaration of Helsinki. The Council for International Organizations of Medical Sciences (CIOMS) has approved the application of ethical health research protocols online (http://sim-epk.keppkn.kemkes.go.id) RSUP Prof. Dr. RD. Kandou, Manado with No. 086/EC/KEPK-KANDOU/VI/2021. Additionally, all experimental procedures were carried out according to the Institutional Animal Care and Usage Committee (ARRIVE guidelines) (Nurkolis et al., 2021).\n\n\nIn vivo studies of sea grapes extracts to evaluate blood glucose, total cholesterol, and PGC-1α levels\n\nCarbohydrates fat-enriched diets (CFED) is a standard mouse food that comes with 1% colic acid, 2% pure cholesterol powder, 20% fat (animal source/pork oil), and 2% corn oil. Additional components are subtly added to the standard CFED and homogenized into a dough with the addition of 1000mL of aqua dest. Small pellets are cut and left to dry at room temperature in sterile conditions. CFED is prepared weekly and stored at 4°C until used to reduce oxidation. CFED consists of carbohydrate (43.57%), coarse protein (12.38%), coarse fiber (4.73%), coarse fat (3.17%), cholesterol (2%), colic acid (1%), animal fat (20%), corn oil (2%), total ash (4.3%), and moisture (6.85%). Compared to a normal diet that contains 58.1% carbohydrates, 16.51% coarse protein, and 0% animal fat, all the other components such as corn oil, cholesterol, and folic acid, were not significantly changed. CFED production guideline was carried out as previously described (Harb et al., 2018).\n\nWistar albino rats were randomly distributed into four groups of ten animals each. Group A served as control (received standard dry pellet diet). Rats in group B were fed on CFED for 4 weeks. Rats in groups C and D were fed on CFED and were given 150 and 450 mg/kg Body Weight (BW) of sea grapes extract, respectively, for 4 weeks. CFED and extract of sea grapes were administered by oral gavage.\n\nThroughout the experiment, all the efforts were made to minimize the pain and distress of the experimental animals. For this purpose after four weeks of extract treatment, rats were kept fasted overnight and given euthanasia under ketamine anesthesia. 2.5 mL of blood samples were collected from the muscle tissue and kept in dry and clean tubes without addition of anticoagulants (Tiger-top tube), to allow clotting at room temperature. The samples were then centrifuged for 20 minutes at 3000 rpm. Finally, the sera were collected for the blood glucose, total cholesterol, and PGC-1α analysis.\n\nBlood glucose and cholesterol levels were assayed using COBAS Integra® 400 plus analyzer (Roche) (See underlying data) (Nurkolis, 2021). Samples were washed with Phosphate Buffered Saline (PBS, pH 7.4) 1% until the liquid runs clear. The samples were centrifuged at 3000 rpm for 20 minutes to obtain pellets and supernatant. The supernatant is taken for the PGC-1α examination (See underlying data) (Nurkolis, 2021). The concentration of PGC-1α was measured by using mouse PGC-1α ELISA Kit (Sunlong Biotech Co., Ltd, # MBS288117).\n\n\nData management and analysis\n\nThe data were statistically analyzed with the use of the MANOVA/Multivariate ANOVA test. The Levene’s test was used to determine which posthoc tests should be conducted. In cases where the Levene’s test p-value was <0.05 Games-Howell test (equal variances not assumed), and for p-value >0.05 Bonferroni test (equal variances assumed) was used. Statistical analyses were performed by using SPPS 26.0 for the Windows version.\n\n\nResults\n\n* Represents p-value <0.05, CI:95%.\n\nThe Levene's Homogeneity test shows that the p-value for glucose and PGC-1α are <0.05, therefore equal variance cannot be assumed, while equal variances can be assumed for cholesterol as the p-value is >0.05.\n\nThe results indicate that blood glucose significantly increased in group B, compared to group A (p < 0.05) (Table 2). Blood glucose significantly decreased in both groups C and D (p < 0.05). The effect of sea grapes administration as much as 150 mg/kg BW is more effective than the sea grapes 450 mg/kg BW, in significantly decreasing blood glucose in rats (p < 0.05).\n\n* Represents p-value <0.05, CI: 95%.\n\nAs expected the rats in group B had significantly increased blood cholesterol levels compared to group A (p < 0.05). In both groups A and B (p < 0.05), blood cholesterol significantly decreased in rats given CFED + sea grapes extract 150 mg/kg BW, and CFED treatment + sea grapes extract 450 mg/kg BW. There was no significant difference between the CFED treatment group + 150 mg/kg BW sea grapes extract, and the CFED treatment group + 450 mg/kg BW sea grapes extract, in reducing blood cholesterol (high dose of the extract did not result in significant effects (p > 0.05)).\n\nGroup B had a significantly decreased PGC-1α serum concentration. PGC-1α serum concentrations significantly increased in group C, as well in group D, compared to groups A and B. The effect of sea grapes administration as much as 150 mg/kg BW is more effective than that of sea grapes 450 mg/kg BW, in the significant increase of PGC-1α serum in rats.\n\n\nDiscussion\n\nThis study showed that the supplementation of sea grapes extract managed to lower blood glucose and serum cholesterol significantly in rats that were given cholesterol- and fat-enriched diets (Figure 1). Although compared to the control group, rats that were given cholesterol- and fat-enriched diets with sea grapes extract had lower levels of blood cholesterol and blood glucose.\n\nThe Results of this study indicate that sea grapes have the capability of reducing blood glucose levels (Table 2). Similarly, Aroyehun et al., have shown that sea grapes have antidiabetic activity. The plasma analysis in this study has also indicated that the sea grapes treated group had a significant decrease (p < 0.05) in their blood glucose levels compared to the untreated diabetic group (Qudus B Aroyehun et al., 2020). Sea grapes extract-treated group demonstrated similar efficacy in lowering blood glucose as Metformin (Qudus B Aroyehun et al., 2020), hence, sea grapes may have an hypoglycaemic effect. A hyperglycaemic state may induce oxidative stress that could be detrimental to insulin-sensitive tissues such as the liver, which may cause damage to the organ (Bugianesi 2005; Manna 2010; Palsamy 2010).\n\nThis study showed that sea grapes reduce hyperlipidemia in rats, however this is not in line with the findings by Aroyehun et al., (Qudus B Aroyehun et al., 2020), which states that sea grapes extract has little to no effect on the cholesterol level of induced diabetic rats. In addition, the effect of lower doses of the extract (150 mg/kg BW) was better in lowering blood cholesterol than higher doses of sea grapes extract (450 mg/kg BW) (Figure 1, Table 3). This can be due to the saturated fatty acids content, especially palmitic acid, which dominates the composition of fatty acids, comprising 80% of the total fat in sea grapes (Qudus B Aroyehun et al., 2020). Studies have shown that palmitate acid may raise total cholesterol levels, specifically LDL-cholesterol levels (Clandinin et al. 2000; Mensink, 2013).\n\n* Represents p-value <0.05, CI: 95%.\n\nLevels of PGC-1α in rats significantly decreased after being given a CFED diet compared to the control group (Figure 1, Table 4). However, PGC-1α levels increased significantly in rats given sea grapes extract, even when compared to the control group. This suggests that PGC-1α, which is one of the major elements in mitochondrial biogenesis, is enhanced by the sea grapes extract. Perhaps the content of flavonoids as well as phenols in sea grapes extract can cause this effect. One study has shown that flavonoid supplementation increases the performance in endurance activities via an increase in expression of PGC-1α as the “master regulator” of biogenesis and skeletal muscle angiogenesis (Khani et al. 2017). In addition, other studies have also shown that antioxidant compounds can upregulate PGC-1α target genes, which not only play a role in preventing oxidative damage, but also reduce mitochondrial ROS levels, ensure mitochondrial integrity during cell differentiation (Beldelli et al. 2014), as well as avoiding the cytotoxic effects of ROS accumulation (St-Pierre et al. 2006).\n\n* Represents p-value <0.05, CI: 95%.\n\n\nConclusion\n\nSea grapes extract is proven to improve blood glucose levels, total cholesterol, and PGC-1α in rats fed with cholesterol- and fat-enriched diets. The results of this study can be used as a reference for clinical trials to further research the beneficial effects of sea grapes for human consumption. However, it is necessary to do the same research with parameters other than blood sugar, cholesterol and pgc-1a, to expand its metabolic scope.\n\n\nData availability\n\nHarvard dataverse: Sea grapes extract effect on blood glucose level (BGL), total cholesterol (TC), and serum PGC-1α concentrations.\n\nDOI: https://doi.org/10.7910/DVN/8IKREA (Nurkolis, 2021).\n\nThe project contains the following underlying data:\n\n• Raw data for the sea grapes extract effect on blood glucose level (BGL), total cholesterol (TC), and serum PGC-1α concentrations.\n\n\nReporting guidelines\n\nHarvard Dataverse: Arrive checklist for Sea grapes extract with blood glucose, total cholesterol, and PGC-1α in rats fed on cholesterol- and fat-enriched diet.\n\nhttps://doi.org/10.7910/DVN/NXF0IW (Nurkolis et al., 2021).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor contributions\n\nM.K and F.N. collated study ideas, designed and experiment, analyzed data, and compiled manuscripts. N.A.T, N. R, N. S, H.K.P, D.S.W and N. M analyzed and interpreted the data and critically revised the manuscript. F. N and F.M.I conducted experiments, analyzed biochemistry, and critically revised the manuscript. N. M, M.R.B, R. R, P.S.A and K.E.K.M, implemented experimental protocols, assisted in statistical analysis, interpreted data, and critically revised manuscripts. All writers read and approve the final manuscript.",
"appendix": "Acknowledgment\n\nWe thank all contributors for their outstanding help in formatting the paper. I would also like to express my gratitude to Prof. Ir. Hardinsyah, MS., Ph.D. (as President of the Federations of Asian Nutrition Societies; President of the Food and Nutrition Society of Indonesia; and Chair of Southeast Asia Probiotics Scientific and Regulatory Experts Network), who has provided comments, suggestions, and input in the research and writing of this paper, as well as the motivation to keep the passion for research during the pandemic.\n\n\nReferences\n\nAnantharaju A, Feller A, Chedid A: Aging Liver. A review. Gerontology. 2002 Nov Dec; 48(6): 343–353. PubMed Abstract | Publisher Full Text\n\nBirben E, Sahiner UM, Sackesen C, et al.: Oxidative stress and antioxidant defense. World Allergy Organ J. 2012; 5(1): 9–19. 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}
|
[
{
"id": "90945",
"date": "20 Aug 2021",
"name": "Carla F. Kairupan",
"expertise": [
"Reviewer Expertise Pathology",
"Moleculer Genetics",
"Herbal Medicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nUpdate Note, 4th February 2022:\nA COI statement has been added detailing a shared affiliation between author and reviewer, which was not declared at the time of the publishing of this report. The COI statement is below.\n-\nThis is an interesting research, in which the treatment with Sea grapes extract clearly improved blood glucose levels, total cholesterol, and PGC-1α in rats. However, it is not the first study that is done on the beneficial effects of Sea grapes extract.\nThe paper is well written and the experimental design is set up well, however, the statistical analysis should be better described.\nThe following points should also be addressed appropriately in the revision.\nThe Laboratory of Pharmacology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University where the study was conducted is not in Makassar.\n\nThe terminology and composition of diets are inconsistent and unclear.\n\nThe area where the blood sample was collected is inappropriate.\n\nThe doses of Sea grapes extract were 150 mg/kg BW and 450 mg/kg BW. How did you decide on these doses? Are there any safety issues?\nThe article may also benefit from an English language edit.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7103",
"date": "13 Sep 2021",
"name": "Fahrul Nurkolis",
"role": "Author Response",
"response": "Dear Dr. Carla F Kairupan, PhD., Thank you for the appreciation and constructive review comments to improve this paper. We have made minor improvements as you mentioned in the review, as follows: 1. The Laboratory of Pharmacology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University where the study was conducted is not in Makassar, it should be a typo and we have changed it to Manado. 2. The terminology and composition of diets are inconsistent and unclear. We've made it clear. 3. The area where the blood sample was collected is inappropriate. We've made that clear, in the tail of the rats. 4. The doses of Sea grapes extract were 150 mg/kg BW and 450 mg/kg BW. How did you decide on these doses? Are there any safety issues? In existing studies, most use 100 mg and 200 mg, therefore the choice of this dose is higher and different from previous studies and 450 is the maximum capacity for a safe rats stomach. Thank you, Greetings, hope you are well!"
}
]
}
] | 1
|
https://f1000research.com/articles/10-718
|
https://f1000research.com/articles/10-916/v1
|
13 Sep 21
|
{
"type": "Research Article",
"title": "Wireless power transfer with transmit diversity",
"authors": [
"Yee-Loo Foo"
],
"abstract": "Background: Wireless power transfer is important for energizing and recharging the Internet-of-Things (IoT) cordlessly. Harnessing energy effectively from radio waves has become a crucial task. It is known that diversities at the transmitting antenna and waves (i.e. simultaneous continuous waves with center frequencies separated apart) can enhance the radio frequency (RF) to direct current (DC) energy conversion. What remains unknown is the extent of which the wave diversity enhances the conversion gain. This study attempts to examine the RF-to-DC conversion gain of applying wave diversity. This paper investigates the effects of wave diversity on the energy conversion efficiency, and contributes the analytical expression that relate the conversion efficiency to the diversity count, i.e. the number of simultaneously transmitted sinewaves. Methods: We adopted a theoretical approach to the problem. First, we derived and presented a theoretical model that incorporated different forms of transmit diversity, i.e. antenna and wave diversities. This model then connected a RF-to-DC energy conversion model resulting from polynomial fitting on circuit simulation results. With the availability of these two models, we determined the theoretical energy conversion gain of simultaneously transmitting multiple sinewaves. Results: The results showed that transmitting multiple sinewaves simultaneously yields diversity gain and higher energy conversion efficiency. Most importantly, the gain and conversion efficiency can now be theoretically quantified. For example, at certain RF power measured at the receiver circuit, the diversity gain of transmitting four sinewaves is 2.6 (as compared to transmitting single sinewave). In fact, both the diversity gain and conversion efficiency increased with the number of simultaneously transmitted sinewaves. In another example, the conversion efficiency of transmitting four sinewaves is 0.1 as compared to 0.075 of two sinewaves. Conclusions: In summary, this paper presents a novel analytical expression for wave diversity in the context of wireless power transfer.",
"keywords": [
"wireless power transfer",
"energy harvesting",
"RF-to-DC energy conversion",
"transmit diversity",
"antenna diversity",
"Internet-of-Things (IoT)"
],
"content": "Introduction\n\nThe Internet-of-Things (IoT) have become omnipresent nowadays, bringing to us some new challenges. To build a robust and resilient IoT network is one of the main challenges. The IoT communication infrastructure must be reliable and trustable. The IoT networks must be resilient against broken links and power outages. Nevertheless, replacing and recharging the device batteries are not only troublesome and impractical, but also nearly impossible in some cases. Wireless power transfer is a solution to this problem.1–3 It can energize and recharge the IoT devices cordlessly. Hence, harnessing energy effectively from radio waves becomes a very important task.2 Figure 1 depicts the concept of wireless power transfer. Wireless energy harvesting is possible even over fading and shadowing channels.4,5 Chen et al.4 have formulated the cumulative distribution function (CDF) and outage probability of the harvested power under these circumstances. On the other hand, Clerckx and Kim5 have assessed the effect of fading on the radio frequency-to-direct current (RF-to-DC) energy conversion, and revealed that fading actually enhanced the conversion efficiency. There are numerous ways of enhancing radio wave energy harvesting, e.g. via transmission over multiple antennas, transmitting multiple sinewaves of different frequencies simultaneously, transmitting specially designed waveforms, etc.5-7 Khan et al.6 have expressed the efficiency of wireless power transfer in terms of the number of transmit antennas. Clerckx and Bayguzina7 have studied the design of energy waveforms that enhanced wireless power transfer to a rectenna, which comprised of an antenna and a diode rectifier. The design involved specifying the amplitudes and phases of the multi-sinewaves in response to the channel condition. The fluctuation in the waveform excited the rectenna circuit. The maximum load current in the circuit was expressed as a function of the numbers of transmit antennas and sinewaves.7 Clerckx and Kim5 have furthered the study based on the similar diode rectenna model, and in addition, a curve-fitting model. Constructed from the data collected from simulations, the curve-fitting model is simpler, resulting in simpler and more tractable analyses. Clerckx and Kim5 evaluated the antenna and phase diversities that resulted in channel fluctuations, similar effect as of fading. They proved that even without using carefully designed energy waveform, which required channel state information (CSI), simple antenna diversity or phase diversity of multi-sinewaves were effective for wireless power transfer. Their findings were supported by the results of experimenting with prototypes. Based on the curve-fitting model, transmitting multi-sinewaves with center frequencies that were equally spaced out did enhance the RF-to-DC conversion efficiency,5 but an analytical quantification on the attained gain remains absent. This study aims to examine the RF-to-DC conversion gain with respect to the wave diversity, and contributes the relevant analysis that expresses the energy conversion efficiency as a function of the antenna diversity and ‘wave diversity’, i.e. the number of transmitted sinewaves.\n\nIn the next section, we describe the communication system model that incorporates transmit diversity. This is followed by the RF-to-DC energy conversion model. Based on the models of transmit diversity and energy conversion, we produce the relevant results and show them in the Results section. This is followed by a Discussion section. Finally, we present the conclusions in the last section.\n\n\nMethods\n\nThis work has met the research ethics requirement and received the university Research Ethics Committee’s approval, with the number EA1772021.\n\nA sender transmits signal x(t), a continuous wave (CW) that has been modulated by symbol s(t), on M antennas at time t. The transmit signal on antenna m is varied by phase φm(t), i.e.\n\nω0 is the carrier frequency. Ε[|s(t)|2]=1. After propagating over the wireless channel, the signal picked up at single receive antenna is\n\nΛ is the path loss, h(t) represents the overall time-varying channel gain.\n\nhm is the amplitude gain from antenna m due to channel fading. Let r(t) = h(t)s(t).\n\nThe effective RF power level at the input of an energy harvester is\n\nAssume that {φm(t)}∀m are uniformly distributed over 2π and are independent, and hm=1 ∀m. It can be shown that\n\n|r(t)|2 is the received signal envelope.\n\nGiven certain expression for s(t), we can determine|r(t)|and thus PRF. In the following, we consider a combination of multiple sinewaves of which the center frequencies are constantly separated apart. Suppose the multisine waveforms are given by\n\nΔw is the inter-carrier frequency spacing. Assume that {φm(t)}∀m are uniformly distributed over 2π and are independent, and hm=1 ∀m.\n\nConsider a special case of M = 1.\n\nTo calculate |r(t)|, let us first consider a simple case of N = 2 sinewaves where n = 1, 2.\n\nIt can be shown that\n\nwhere\n\nWhen M = 1 and N = 3, we find that\n\nBy induction, it can be shown that for M = 1,\n\nTo the best of our knowledge, (14) is a novel expression.\n\nBased on a simulation study on a rectenna circuit and curve fitting on the collected data, Clerckx and Kim5 have shown that the RF-to-DC energy conversion can be represented by a polynomial as follows:\n\nBased on the results from the circuit simulations conducted by Clerckx and Kim,5 when the input was a CW, the coefficients u, v, and w of the polynomial took the following values:\n\nSince PRF=P¯RF|r(t)|2M,\n\nAfter some workings, we have the following expression:\n\nwhere\n\nPDC, 0 is the DC power harvested from P¯RF. Eq. (17) can also be expressed in the following form:\n\netd is the gain from transmit diversity,\n\nThe average harvested DC power,\n\nwhere\n\nThe resultant RF-to-DC conversion efficiency is given by\n\nSubstituting (23) into (21),\n\nThe average RF-to-DC conversion efficiency is thus given by\n\n\nResults\n\nThe following Figures 2 and 3 present the novel results.\n\ne¯td vs. P¯RF for multiple sinewaves.\n\nεavg vs. P¯RF for multiple sinewaves.\n\nThe positive result8 of using multiple sinewaves is demonstrated in the transmit diversity gain (Figure 2) and the actual resultant energy conversion efficiency (Figure 3). From Figures 2 and 3, we see that larger number of sinewaves, with center frequencies being equally spaced out, results in higher RF-to-DC energy conversion, despite using only single transmit antenna (M = 1). This is especially true at low RF input power to the rectenna circuit. For example, at P¯RF=10−7 W, the transmit diversity gain is 2.6 (of 4 sinewaves) as compared to 1.5 (of 2 sinewaves). Nevertheless, the gain starts to diminish as the RF input power becomes higher, as revealed in Figure 2.\n\nFigure 3 shows similar trend of which higher number of sinewaves results in higher conversion efficiency. For example, at P¯RF=3.2×10−6 W, the conversion efficiency is 0.1 (of 4 sinewaves) as compared to 0.075 (of 2 sinewaves).\n\n\nDiscussion\n\nIn this section, we discuss the impacts of the results. By experimenting with prototypes, Clerckx and Kim5 had proven that transmitting multi-sinewaves with center frequencies that were equally spaced out could enhance the RF-to-DC conversion efficiency. Nevertheless, an analytical expression that relates the attained gain to the wave diversity remains absent. The analysis presented in this paper not only fills this gap, but may also benefit the experiments of wireless power transfer that are based on hardware, e.g. using a microwave transmitter to wirelessly power up a LED.3 They can experiment with the antenna diversity and wave diversity that have been theoretically proven effective.\n\nNevertheless, the analysis presented here has not considered the separation distance between the M transmitting antennas. Taking into account of this factor could provide a more comprehensive analysis on the effects of beamforming.1,2 This is especially important in the context of massive wireless power transfer,1 where a large number of IoT devices are targeted.\n\n\nConclusions\n\nWireless power transfer benefits from transmit diversity, be it antenna diversity or wave diversity. The objective of this paper is to express the RF-to-DC energy conversion efficiency as a function of the transmit diversity. Such a mathematical expression was not available previously. This paper contributes an analytical expression that relates the diversity gain and conversion efficiency to the number of simultaneous sinewaves with center frequencies that are equally spaced. Our next step is to investigate the wave diversity gain of beamforming antennas.\n\n\nAuthor contributions\n\nY.-L. Foo designs the research, constructs the computer program, conducts the experiment, reports and discusses the findings.\n\n\nData availability\n\nhttps://doi.org/10.17605/OSF.IO/K9ZNU\n\nOpen Science Framework: Wireless Power Transfer, https://doi.org/10.17605/OSF.IO/39SJV.8\n\nThe project contains the following underlying data:\n\n\n\n- Data.txt\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nLopez OLA, Alves H, Souza RD, et al.: Massive Wireless Energy Transfer: Enabling Sustainable IoT Toward 6G Era. IEEE Internet Things J. 2021; 8(11): 8816–8835. Publisher Full Text\n\nMolefi M, Markus ED, Abu-Mahfouz A: Wireless Power Transfer for IoT Devices-A Review Proc. - 2019 Int. Multidiscip. Inf. Technol. Eng. Conf. IMITEC 2019. 2019; vol. i. Publisher Full Text\n\nChaari MZ, Al-Maadeed S: Wireless Power Transmission for the Internet of Things (IoT). 2020 IEEE Int. Conf. Informatics, IoT, Enabling Technol. ICIoT 2020. 2020; pp. 549–554. Publisher Full Text\n\nChen Y, Zhao N, Alouini MS: Wireless Energy Harvesting Using Signals from Multiple Fading Channels. IEEE Trans. Commun. Nov. 2017; 65(11): 5027–5039. Publisher Full Text\n\nClerckx B, Kim J: On the Beneficial Roles of Fading and Transmit Diversity in Wireless Power Transfer with Nonlinear Energy Harvesting. IEEE Trans. Wirel. Commun. Nov. 2018; 17(11): 7731–7743. Publisher Full Text\n\nKhan TA, Yazdan A, Heath RW: Optimization of power transfer efficiency and energy efficiency for wireless-powered systems with massive MIMO. IEEE Trans. Wirel. Commun. Nov. 2018; 17(11): 7159–7172. Publisher Full Text\n\nClerckx B, Bayguzina E: Waveform Design for Wireless Power Transfer. IEEE Trans. Signal Process. Dec. 2016; 64(23): 6313–6328. Publisher Full Text\n\nFoo Y-L: Wireless Power Transfer. Open Science Framework . Publisher Full Text"
}
|
[
{
"id": "94148",
"date": "21 Sep 2021",
"name": "Onel L. A. López",
"expertise": [
"Reviewer Expertise Wireless communications",
"Wireless power transfer",
"Energy harvesting",
"Internet of Things",
"Positioning systems",
"Cellular systems"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author investigates an interesting research problem and system setting. The aim is at quantifying the diversity gain from multi sinusoidal transmissions, i.e., wave diversity. My major comments are as follows:\nThe main contribution of this work seems to be related to Equation (14). If author adopted a proof by induction, this needs to be properly realized. Please write Equation (14) in a more compact form using summation symbol. Also, the derivation of Equation (14) is only for the case of M=1, what about a general, more practical, case of M>1?\n\nWhy are the introduced phase shifts considered uniformly distributed? This means there is no CSI at the transmitter, or at least it is not exploited. Given that there is vast literature on CSI-free wireless power transfer in the last years, I recommend motivating this assumption better. Since the conversion efficiency depends on |r(t)|2, it would be interesting to see the latter in a plot as a function of N. Currently Section 2 seems completely disconnected from Section 1. What is the main idea behind the discussions/derivations in Section 2?\n\nNumerical results are not currently included for multi-antenna setups.\n\nOther minor comments:\nProofreading is needed. Specifically, adjust Abstract to be in present tense. Correct typos, and grammar issues along the paper.\n\nThe definition of P is missing in Equation (1). After Equation (1), how is y(t) given as a function of xm(t)?\n\nIs the expectation in Equation (4) taken with respect to both waveform and fading randomness? Clarify.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "96552",
"date": "28 Oct 2021",
"name": "Mohamed Zied Chaari",
"expertise": [
"Reviewer Expertise microwave technology",
"RF harvesting energy",
"and wireless power charging."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 structure of the manuscript is well organized, the methods are well described, and the procedures are well conducted. The results are sound and the conclusions are based on the experimental data.\nComments on the manuscript:\nThe abstract must be rewritten. An abstract is a 150- to 250-word paragraph that provides readers with a quick overview of your essay or report and its organization. It should express the wireless power transmission and key points and suggest any implications or applications of the research you discuss in the paper.\n\nThe structure is general idea/reason; aim and goals; materials; methods and procedures; main results; general conclusion.\n\nGood quality, high-resolution figures should be provided.\n\nI have a suggestion to include references 1 and 2 in your work, in order to strengthen the content. The author is working on wireless power transfer with transmit diversity, and these citations give him more idea about our work and can use them for upgrading his work and make a good overview of the WPT.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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/10-916
|
https://f1000research.com/articles/10-914/v1
|
10 Sep 21
|
{
"type": "Case Report",
"title": "Case Report: Syncopal atrioventricular block complicating primary hyperoxaluria type 1",
"authors": [
"Ben Mrad Imtinene",
"Kamoun Sofien",
"Ben Mrad Melek",
"Zairi Ihsen",
"Oumaya Zeineb",
"Ben Fatma Lilia",
"Mami Ikram",
"Kaaroud Hayet",
"Khadija Mzoughi",
"Kraiem Sondos",
"Kamoun Sofien",
"Zairi Ihsen",
"Oumaya Zeineb",
"Ben Fatma Lilia",
"Mami Ikram",
"Kaaroud Hayet",
"Khadija Mzoughi",
"Kraiem Sondos"
],
"abstract": "Primary hyperoxaluria (PH) type 1 is a rare hereditary metabolic disorder resulting in accumulation of calcium oxalate in several organs, including the heart. Cardiac oxalosis in PH is poorly described in the medical literature. We report the case of a 42-year-old woman diagnosed with primary hyperoxaluria type 1 and end-stage renal failure who presented with syncope related to a paroxysmal third-degree atrioventricular block. The patient benefited from the implantation of a dual chamber pacemaker with a good outcome. Conduction blocks in case of primary hyperoxaluria type 1 are exceptional; in fact, less than five reports have previously been published in the medical literature. With this case, we would like to highlight the need for regular and careful monitoring of cardiac status in patients treated for primary oxalosis, especially when renal function is impaired.",
"keywords": [
"atrioventricular block",
"primary hyperoxaluria",
"syncope",
"end-stage renal failure",
"heart block"
],
"content": "Introduction\n\nPrimary hyperoxaluria (PH) type 1 is a scarce hereditary metabolic malady in which an increased production of oxalic acid results in hyperoxalemia and an accumulation of calcium oxalate in different body organs, including the heart.1 Oxalosis involving the myocardium can lead to congestive heart failure, arrhythmias and conduction disturbances.2 We report the case of a 42-year-old-woman followed for PH over 15 years who was admitted to our cardiology department for a paroxysmal syncopal atrioventricular block (AVB). Heart block in patients with primary oxalosis is exceptional, indeed less than eight reports have been previously reported in the medical literature.\n\n\nCase report\n\nA 42-year-old Tunisian housewife was referred eighteen months ago to our cardiology department for repetitive episodes of syncope over two weeks. The patient had PH1 diagnosed at the age of 27 by a genetic study that revealed a c.33-34insC mutation; she had a grandfather with the same disease. Over time, she developed progressive renal failure, and five years earlier, she had undergone a left partial nephrectomy for nephrocalcinosis. Nevertheless, she developed total chronic renal failure and had recently begun hemodialysis via a left humerocephlic fistula.\n\nUpon admission in March 2020, physical examination showed a mucocutaneous pallor. Blood pressure was 100/60mmHg, and heart rate was 70/min. Cardiac auscultation found a 2/6-degree systolic aortic murmur. She had no signs of heart failure. Electrocardiogram (EKG) performed in the emergency room showed a regular sinus rhythm at 75 beats per minute (bpm), a complete left bundle branch block (LBBB), and a first-degree AVB (Figure 1). Laboratory tests showed a normochromic normocytic anemia at 5.9 g/dl, urea level at 37.7 mmol/l, creatinine level at 1771 micromol/l, a normal potassium serum level at 4.3 mEq/l, and a low calcium serum level at 2.08 mmol/l.\n\nThe patient’s plasma oxalate level was 98.5 umol/L. Urinary crystallographic exam showed the presence of calcium oxalate crystals in the urine of characteristic icosahedral shape (Figure 2). Plain abdominal X-ray showed images of nephrocalcinosis of the left kidney (Figure 3).\n\nDuring monitoring in the intensive care unit, the patient presented a further episode of syncope with an EKG (Figure 4) showing a prolonged ventricular asystole (Figure 4A) with second degree AVB 2/1 (Figure 4B) and a ventricular rate of 55 bpm followed by a complete AVB (Figure 4C) with a ventricular rate of 50 bpm. First, the patient received an isoprenaline infusion (1 mL/hour =0.5 microgram/kg/minute) under EKG control, but the heart rate did not accelerate. Within minutes, repeated episodes of syncope imposed the urgent placement of a temporary cardiac pacing lead. Transthoracic echocardiography showed increased left ventricular mass index and diastolic dysfunction. The patient was implanted with a dual-chamber pacemaker (Figure 5) with a good outcome. The patient was discharged three days later.\n\nAfter one-year follow-up in April 2020, no episodes of syncope were reported. The patient is still waiting for a kidney transplant.\n\n\nDiscussion\n\nPrimary hyperoxaluria type 1 (PH1) is an autosomal recessive inherited metabolic disorder related to the deficiency of alanine glyoxylate aminotransferase, a peroxisomal liver enzyme that allows the transformation of glyoxylate into glycine.1 This deficiency leads to oxalate overproduction by the liver, followed by urine filtration and complexation with calcium to form massive calcium-oxalate nephrolithiasis potentially leading to chronic renal failure (nephrocalcinosis).1 Once end-stage renal failure develops, calcium oxalate is deposited in other organs because of high plasma oxalate concentrations, which exceed the saturation threshold for calcium oxalate.1\n\nCardiac involvement in PH is rarely described; medical literature is limited to case reports and small case series. Mookadam and colleagues, from the team of the Mayo Clinic Rochester, published in 2010, is the first and only systematic study describing cardiac abnormalities in PH. They reviewed a dataset of 33 patients with primary hyperoxaluria.2 The mean age at the time of cardiac manifestation was 40 years.2 Cardiac anomalies are associated with an alteration in renal function and appear to correlate with the plasma oxalate level.2 Of the patients with cardiac findings, 78% had a history of end-stage renal failure.2 In our case, the oxalate plasma level was much higher. Mookadam, also describes this finding in his study.2 The plasma oxalate level was 79.4 μmol/L in those with cardiac findings, compared to 7.3 μmol/L in those without.2\n\nConduction deficits and heart block have previously been reported in patients with primary oxalosis.3–7 Massie et al.,4 reported the first case of cardiac electrophysiologic abnormalities due to oxalate infiltration in a 27-year-old man. In that case, oxalate was described to infiltrate the sinoatrial node and to approach the atrioventricular node leading to numerous electrophysiological abnormalities. This finding is also shared by other authors.5–7 Conduction blocks are reported in 13.2% of patients in the Mayo Clinic study.2\n\nMyocardial invasive transjugular biopsy remains the gold standard for the diagnosis of cardiac involvement; but it is not routinely used and does pose a definable risk.2\n\nTwo reports in the literature have performed a histologic study of the conduction system, they showed extensive crystal deposits all around the sinoatrial node, atrial myocardium, atrial preferential pathways, common bundle, and both bundle branches associated to secondary degenerative and fibrotic changes.3,4 In addition, the arteries of the atrioventricular and sino-atrial nodes exhibited mural crystals with a narrowing of the lumens.3\n\nAlthough ventricular pacing may avoid death from complete heart block, it is improbable to prolong life expectancy in oxalosis patients once visceral involvement becomes important.4 Dialysis is supposed to temporarily remove oxalate, but it cannot compensate for the excessive oxalate production rate, thus making it difficult to excrete calcium oxalate in the urine and eventually increasing the blood oxalate level.8\n\nLarge left ventricular mass index, impaired left ventricular and right ventricular function, left atrium enlargement, diastolic dysfunction, increased wall thickness suggestive of myocardial dissemination, and rhythm abnormalities are probably due to calcium oxalate deposits in cardiac tissue.2\n\nWhile kidney transplantation corrects kidney failure, liver transplantation is the only solution for definitive correction of the metabolic defect in PH 1. Combined hepatorenal transplantation is the only therapeutic alternative to dialysis,1 which, unfortunately, is not yet practiced in Tunisia. Cardiac manifestations can be fatal; however, they are reversed after successful liver transplantation.9\n\nThe case, which we have presented here, has been limited by the short follow up of the patient. However, it demonstrates that in front of any syncopal signs, particularly in patients with primary hyperoxaluria, monitoring in a cardiological resuscitation unit can be lifesaving.\n\n\nConclusion\n\nOxalate deposits in cardiac tissue compromise prognoses as they can lead to potentially fatal complications. This case demonstrates the need for regular and careful monitoring of cardiac status in patients treated for primary oxalosis, especially when renal function is impaired. Because oxalate cannot be sufficiently removed by hemodialysis, early hepato-renal transplantation is required to improve the chances of survival in these patients.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of the patient’s clinical details and clinical images was obtained.",
"appendix": "References\n\nCochat P, Hulton SA, Acquaviva C, et al.: Primary hyperoxaluria Type 1: indications for screening and guidance for diagnosis and treatment. Nephrol Dial Transplant. 2012 May; 27(5): 1729–36. PubMed Abstract | Publisher Full Text\n\nMookadam F, Smith T, Jiamsripong P, et al.: Cardiac abnormalities in primary hyperoxaluria. Circ J. 2010 Nov; 74(11): 2403–9. Epub 2010 Sep 29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nColtart DJ, Hudson RE: Primary oxalosis of the heart: a cause of heart block. Br Heart J. 1971 Mar; 33(2): 315–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMassie BM, Bharati S, Scheinman MM, et al.: Primary oxalosis with pan-conduction cardiac disease: electrophysiologic and anatomic correlation. Circulation. 1981 Oct; 64(4): 845–52. PubMed Abstract | Publisher Full Text\n\nTonkin AM, Mond HG, Mathew TH, et al.: Primary oxalosis with myocardial involvement and heart block. Med J Aust. 1976 Jun 5; 1(23): 873–4. PubMed Abstract\n\nWest RR, Salyer WR, Hutchins GM: Adult-onset primary oxalosis with complete heart block. Johns Hopkins Med J. 1973 Oct; 133(4): 195–200. PubMed Abstract\n\nQuan KJ, Biblo LA: Type I primary hyperoxaluria: an unusual presentation of ventricular tachycardia. Cardiol Rev. 2003 Nov-Dec; 11(6): 318–9. PubMed Abstract | Publisher Full Text\n\nSalyer WR, Keren D: Oxalosis as a complication of chronic renal failure. Kidney Int. 1973 Jul; 4(1): 61–6. PubMed Abstract | Publisher Full Text\n\nDetry O, Honoré P, DeRoover A, et al.: Reversal of oxalosis cardiomyopathy after combined liver and kidney transplantation. Transpl Int. 2002 Jan; 15(1): 50–52. Epub 2002 Jan 18. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "94212",
"date": "28 Sep 2021",
"name": "Meriem Drissa",
"expertise": [
"Reviewer Expertise General cardiology",
"rhythmology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, well-written manuscript. The article highlights the importance of cardiac monitoring in patients treated for primary oxalosis, especially when renal function is impaired. The manuscript respects the CARE case reports guidelines. The patient's case is well reported with good quality figures. The discussion part of the article is very well done and is exhaustive. The conclusion is consistent with the case presented.\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": "101142",
"date": "13 Dec 2021",
"name": "Khawla Kammoun",
"expertise": [
"Reviewer Expertise Nephrology",
"Dialysis"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think this is a nice paper. It is about a case of end stage renal failure due to primary hyperoxaluria treated with haemodialysis who developed an atrioventricular block treated with a dual chamber pacemaker.\nIt highlights a severe cardiac complication which threatens the patient's vital prognosis.\nThis complication is rarely described in literature - a cardiac infiltration by oxalate crystals.\nThe paper has some English structure errors which need review and correcting: 'hereditary metabolic malady' ⇒ I think it is better to say hereditary metabolic disease 'Less than eight reports have been previously reported' ⇒ less than eight cases…….. 'upon admission' ⇒ on admission 'mucocutaneous pallor' ⇒ yellowish skin 'cardiac anomalies' ⇒ cardiac abnormalities 'In our case, the plasma oxalate level was much higher.' ⇒ In our case, the plasma oxalate level was very high.\nWe suggest to review the paper by an English expert\n\nComments on review questions added below by peer review team:\nQ. Is the background of the case’s history and progression described in sufficient detail? A. Partly\nComments: *oxalosis history : renal stone?, age of onset of renal stone, renal failure, parent consanguinity? cause of nephrectomy (In the best of our knowledge: nephrocalcinosis is not an indication for nephrectomy) verify if nephrectomy was performed for pyonephrosis ,infection problem?\n\nQ. Are enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? A. Partly\nComments: We suggest describing haemodialysis regimen (dialysis number session/week, duration session etc…)\n\nQ. Is sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? A. Partly\nComments: *We suggest to to summarize the literature case report ( less than eight) in a table *I am not agree with the proposed Strategy for the treatment of Chronic kidney disease in case of oxalosis *W suggest to discuss and give some recommendation for evaluation following initial diagnosis to screen heart abnormalities *I purpose to view the strategy described in reference n 1 and I suggest some other references such: Lorenzo V, Torres A, Salido E. Primary hyperoxaluria. Nefrologia. 2014 May 21;34(3):398-412. Milliner DS, Harris PC, Cogal AG, Lieske JC. Primary Hyperoxaluria Type 1. 2002 Jun 19 [updated 2017 Nov 30]. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Mirzaa G, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2021. PMID: 20301460.\n\nQ. Is the case presented with sufficient detail to be useful for other practitioners? A. Yes\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": []
}
] | 1
|
https://f1000research.com/articles/10-914
|
https://f1000research.com/articles/10-913/v1
|
10 Sep 21
|
{
"type": "Research Article",
"title": "Clinical trial research on COVID-19 in Germany – a systematic analysis",
"authors": [
"Julian Hirt",
"Abeelan Rasadurai",
"Matthias Briel",
"Pascal Düblin",
"Perrine Janiaud",
"Lars G. Hemkens",
"Julian Hirt",
"Abeelan Rasadurai",
"Matthias Briel",
"Pascal Düblin",
"Perrine Janiaud"
],
"abstract": "Background: In 2020, the COVID-19 pandemic led to an unprecedented volume of almost 3,000 clinical trials registered worldwide. We aimed to describe the COVID-19 clinical trial research agenda in Germany during the first year of the pandemic. Methods: We identified randomized clinical trials assessing interventions to treat or prevent COVID-19 that were registered in 2020 and recruited or planned to recruit participants in Germany. We requested recruitment information from trial investigators as of April 2021. Results: In 2020, 65 trials were completely (n=27) or partially (n=38) conducted in Germany. Most trials investigated interventions to treat COVID-19 (86.2%; 56/65), in hospitalized patients (67.7%; 44/65), with industry funding (53.8%; 35/65). Few trials were completed (21.5%; 14/65). Overall, 187,179 participants were planned to be recruited (20,696 in Germany), with a median number of 106 German participants per trial (IQR 40 to 345). From the planned German participants, 13.4% were recruited (median 15 per trial (IQR 0 to 44). Conclusions: The overall German contribution to the worldwide COVID-19 clinical trial research agenda was modest. Few trials delivered urgently needed evidence. Most trials did not meet recruitment goals. Evaluation and international comparison of the challenges for conducting clinical trials in Germany is needed.",
"keywords": [
"COVID-19",
"SARS-CoV-2",
"Randomized clinical trials",
"Germany"
],
"content": "Introduction\n\nThe COVID-19 pandemic has led to an unprecedented volume and speed in the international clinical research agenda. Almost 700 clinical trials were registered worldwide in the first 100 days, which planned to recruit almost 400,000 participants to assess interventions to treat or prevent COVID-19.1 However, this research agenda has been tainted by a multitude of small trials with 50 from the 700 trials aimed to include more than 1,000 participants.1 Nevertheless, there were remarkable efforts to conduct large adaptive pragmatic trials directly informing therapeutic decisions in COVID-19 patients: the UK Randomised Evaluation of COVid-19 thERapY (RECOVERY) trial recruited 10,000 patients in two months,2 the established Randomised, Embedded, Multifactorial Adaptive Platform trial for Community-Acquired Pneumonia (REMAP-CAP) was rapidly adapted to COVID-19,3 and the COVID-19 Solidarity Trial for COVID-19 Treatments (SOLIDARITY) sponsored by the World Health Organization (WHO), was conducted in six months.4 In the first 100 days, China, the US, Spain and France, had the largest share of the initiated trials, with many planned as international collaborations.1 Germany contributed to large-scale international studies such as REMAP-CAP5 and WHO-SOLIDARITY,6 and the German Federal Ministry for Education and Research (BMBF) provided 1.6 billion € for COVID-19-related research.7\n\nThe aim of this study was to describe the German contribution to the worldwide COVID-19 clinical trial agenda, including all randomized clinical trials (RCTs) with German participants, that were registered during the first year of the pandemic.\n\n\nMethods\n\nWe searched the COVID-evidence database to identify RCTs in international trial registries (ClinicalTrials.gov; WHO International Clinical Trials Registry Platform). Additionally, we manually searched the German Clinical Trials Register (DRKS). For all eligible registered trials, we searched corresponding publication results and preprints in the Living OVerview of Evidence platform for COVID-19 (L·OVE), Cochrane COVID-19 Study Register, MEDLINE/PubMed, and Google Scholar using the trial registry number (last search 1 April 2021, see extended data8).\n\nWe included all planned, ongoing, or completed RCTs assessing interventions to treat or prevent COVID-19, registered in 2020, that recruited or planned to recruit at least one participant in Germany.\n\nOne author (JH) conducted the searches and screened the trials for eligibility and a second author (PJ or LGH) was consulted in cases where eligibility was unclear. Four authors (JH, PJ, AR, MB) extracted data on trial characteristics (status, duration, design, population, intervention and control, recruiting countries, actual/planned trial size, funding) and published results.\n\nTrials with industrial/commercial sponsors were classified as industry-funded, those with public/non-commercial sponsors as public-funded, and trials with public/non-commercial sponsors with collaborators from industry as publicly funded with industry contribution. Trials were also classified as completely (i.e., national trials) or partially (i.e., international) conducted in Germany. Details on the extraction process are provided as extended data.8\n\nWe identified contact details of corresponding investigators for all eligible trials using registry information and web search. For each trial, we asked investigators via email about the current trial status, inclusion date of the first patient, number of patients recruited in Germany, and any published results (prior to April 2021, see extended data8). For trials completely conducted in Germany with public funding, we further asked (i) if they were aware of other trials with public funding that we have not identified and (ii) to confirm the extracted information on their trial (see extended data8). We received replies from 60% (39 out of 65) of all eligible trials. This complemented the data contained in registries or publications and provided full information on actual and target sample size in Germany for 34 trials (52.3%).\n\nCOVID-evidence is a living database that is continuously being updated.9,10 Registry entries retrieved weekly from ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform are automatically pre-screened for eligibility using basic filters to identify RCTs. Unclear and identified RCT entries are then manually screened to verify eligibility.\n\nIn August 2021, the RCT filter of COVID-evidence was updated. The data presented herein are based on the COVID-evidence processes (including RCT filter and automatic pre-screening) as of April 2021. For transparency and exhaustiveness, we updated our search in the COVID-evidence database in August 2021 with the use of the most recent processes and post-hoc identified trials.\n\nWe report medians with interquartile ranges (IQRs) if not stated otherwise. For all analyses, we used R (version 4.1).\n\n\nResults\n\nIn 2020, 65 RCTs were planned to investigate treatments or preventive interventions for COVID-19 with participants from Germany (Table 1 and extended data8). They aimed to include a median of 300 participants per trial (IQR, 174 to 830) internationally, including 106 in Germany (IQR, 40 to 345, Table 2).\n\nAbbreviations: IQR = interquartile range; N/n = number.\n\nNotes: * The number of trials corresponds to trials with full recruitment information; ** For the 13 trials that provided recruitment information and announced a completion date by April 2021 (timepoint of the recruitment status assessment), the median proportion of target sample size was 13.6% (IQR, 0.6 to 24.0%, range 0 to 113%).\n\nAbbreviations: IQR = interquartile range; N = number.\n\nNotes: * The number of trials corresponds to trials with full recruitment information; ** Five trials had public funding with industry contribution and are not considered in this table.\n\nAfter a peak with 18 registrations in April 2020, one to nine trials were registered each month. As of 21 May 2021, 35 were ongoing (53.8%), six not yet recruiting (9.2%), nine terminated early (13.8%), 14 (21.5%) completed, and one withdrew and will never recruit (1.5%).\n\nOur results also indicate that 17 trials (26.2%) had published results; 15 were partially conducted in Germany, 15 were explored COVID-19 therapies and 12 were industry-funded. From those 17 trials with published results, 12 trials had results published as peer-reviewed articles or preprints, and five trials had published results exclusively as press release or in the registry. Results were reported by 11 trials, while six stated interim results (Table 3).\n\nFrom the 65 trials, 56 investigated COVID-19 therapies (86.2%) with a total planned sample size of 33,540 participants internationally (median 256 per trial [IQR, 172 to 450]); seven (12.5%) planned to recruit more than 1,000 participants.\n\nDrugs and biologicals (e.g., convalescent plasma) were investigated in 48 of 65 trials (73.8%). The spectrum of treatments was wide, including antivirals (n = 10, 20.8%, e.g., remdesivir n = 4), monoclonal antibodies (n = 8, 16.7%, e.g., tocilizumab n = 3), convalescent plasma (n = 6, 2.5%), hydroxychloroquine (n = 5, 10.4%), and kinase inhibitors (n = 4, 8.3%, e.g., baricitinib n = 1).\n\nAll trials assessing interventions to prevent COVID-19 were vaccine trials (13.8%; 9 from 65). They were considerably larger than therapy trials with a total planned sample size of 153,639 participants (median 2,520 per trial [IQR, 1,200 to 34,000]); seven of the nine vaccine trials (77.7%) planned to include over 1,000 participants. From the 187,179 planned participants in the 65 trials, 82.1% were healthy participants planned to be recruited in vaccine trials.\n\nNone of the trials investigated non-pharmaceutical interventions to prevent the pandemic spread, such as social distancing or behavioral interventions.\n\nHospitalized patients were recruited in 44 (67.7%), outpatients in 14 (21.5%), and both inpatients and outpatients in seven (10.8%) trials. No trial was conducted in nursing homes, kindergarten, childcare, or schools (Table 1 and extended data8). Adolescents (12 years and older) were included in five trials partially conducted in Germany, however, trials that included children below the age of 12 did not exist.\n\nMost trials were double blinded (n = 36, 55.4%) and used a two-arm parallel group design (n = 54, 83.1%). From the 11 trials that had an adaptive design (17.0%), five re-estimated the target sample size.\n\nFrom the 65 trials, 35 (53.8%) were industry-funded, 25 (38.5%) publicly funded, and five (7.7%) publicly funded with industry contribution. None of the publicly funded trials assessed a vaccine (Table 4). In these 65 trials, 38 were partially conducted in Germany (58.5%), which planned to recruit 172,782 participants across all included countries (median 402 per trial [IQR, 210 to 967]). Additionally, there were 27 trials completely conducted in Germany (41.5%) that planned to recruit 14,397 participants (median 200 per trial [IQR, 103 to 500]) in 125 German study centers (median 1.5 centers per trial [IQR, 1 to 8.8]).\n\nFrom the 38 trials partially conducted in Germany, nine (23.7%) planned to recruit over 1,000 participants compared with five from 27 (18.5%) of the trials that were completely conducted in Germany.\n\nThe median number of planned participants from Germany was 106, while the median recruited was actually 15 participants per trial (IQR, 0 to 44), corresponding to a median proportion of 13.4% of the Germany-specific target sample size recruited per trial (IQR, 0 to 29.2%, range 0 to 113%). This proportion was almost identical (13.6%) in the 13 trials that announced a completion date by April 2021 and provided recruitment information (Table 2). Two of these 13 (15.4%) reached their target sample size (i.e., at least 99%; Figure 1).\n\nNotes: The figure illustrates the length of the trials with their start and end date of conduct, sorted by start date and colored by status (based on trial registration details or investigators’ request). The darker part of the bars illustrates the proportion of the target sample size in Germany that was actually recruited within each trial with the corresponding proportion (percentages reported next to the bar). The dashed vertical line corresponds to the timepoint of the recruitment status assessment, April 2021. Trials can be declared as “completed” with or without reaching their target sample size. “Terminated” trials end without reaching their intended goals and started recruiting but are not considered “complete”. “Withdrawn” trials will never start or recruit patients. * Trials that were partially conducted in Germany: the proportion of target sample size focus only on German participants and does not reflect the international recruitment accrual; $ End date was not available and was arbitrarily set at 1 June 2022.\n\nFrom the 65 trials, 11 (16.9%) have not yet been recruiting or, although they had planned to, will never recruit participants in Germany.\n\nThe trials with recruitment information from the investigator survey were more often completely conducted in Germany (74.1% vs. 36.8% partially conducted in Germany), more often publicly funded (80% vs. 34.3% industry-funded), and more often registered in the first half of 2020 (64.3% vs. 31.8% second half of 2020; see extended data8).\n\nThe search in COVID-evidence in August 2021 identified three additional small trials aiming to include 64 to 130 patients. Two were registered late December 2021, and two have been completed, however none of the results are available. For details see extended data.8\n\n\nDiscussion\n\nThis systematic analysis of the clinical trial research agenda on COVID-19 in Germany showed that from the almost 3,000 trials registered worldwide in 2020, only 65 trials planned to include participants in Germany.\n\nApproximately 20,696 participants from Germany were planned to be included in COVID-19 clinical trials, of which 10,613 patients would be treated for this disease. The typical COVID-19 trial with a German contribution aimed to include 106 persons in Germany, however achieved to recruit a fraction (13.4%, or 15 persons per trial). This estimate did not change when we considered trials which planned to be completed at the timepoint of our recruitment assessment in April 2021. While precise information was not available for all trials, it can be estimated that under 3,000 individuals have been included in COVID-19 RCTs in Germany (13.4% of the 20,696 German participants planned in 55 of 65 trials). In trials for COVID-19 treatments, the estimated total participants were approximately 1,500 (13.5% of 10,613 participants in 48 of 56 treatment trials). This is a small fraction of the approximately 155,000 COVID-19 hospitalizations reported during 2020 in Germany.11 These data indicate that in Germany about 1 out of 100 hospitalized patients participated in a trial to investigate potential COVID-19 therapies, while in the United Kingdom, 1 out of 6 hospitalized patients for COVID-19 took part in the RECOVERY trial.12\n\nIt was also unexpected that despite the very prominent and successful position of Germany in research and development of highly effective vaccines, more German participants have not contributed to the overall vaccine research agenda.\n\nThere was a considerable public investment in clinical research for COVID-19. The German Federal Ministry of Education and Research (BMBF) spent 1.6 billion € for research projects related to COVID-19, a large part being allocated to vaccine development.7 The RECOVERY trial reported the cost per patient at £250, corresponding to a total of approximately 1 million Euro for a trial with 3,000 persons.13 As illustrated in Figure 1, the planned number of participants in Germany has been reached in three of the completed, and none of the early terminated trials. Moreover, 2 out of the 13 trials that announced a completion date by April 2021 reached their target sample size. The proportions of already recruited participants in the ongoing trials agree with the overall interpretation, and do not exclude delayed recruitment, which is further corroborated by the six not yet recruiting trials. Decisions for early termination may very well indicate reasonable and well-founded strategic decisions to avoid wasting research resources, however it may also reflect recruitment difficulties or other challenges. An overestimation of eligible participants or prejudiced views by recruiters and participants on trial interventions are common reasons for low recruitment.14 However, the massive impact of the COVID-19 pandemic on health care systems and clinical research institutions has challenged trial recruitment as well.15,16 Most countries do not have the long-established and effective clinical trial infrastructure and academic environments such as the UK, where the feasibility of rapid setup and implementation of massive clinical trials has been impressively demonstrated. The RECOVERY trial was planned in two days, included more than 10,000 patients with the first patient enrolled after nine days, and discovered the first mortality-lowering treatment for COVID-19 in two months.2 The highly pragmatic and embedded-in-usual-care study design were major drivers of this unprecedented successful clinical research.\n\nAs the reasons that might have led to successful or unsuccessful recruitment in the German trials were not assessed in this study, further research is needed to understand the recruitment challenges, and how they can be mitigated to facilitate recruitment success for clinical trials in Germany in situations where decision-relevant evidence is urgently needed. A careful comparison of the German research environment for clinical trial research with international circumstances seems warranted.\n\nThe focus of the trial research in Germany was similar to the worldwide trial landscape with a strong weight on exploring treatment with drugs and biologicals.1 Our results indicate that there were no RCTs registered in 2020 assessing strategies to control the pandemic spread, social distancing, or behavioral interventions although those have been strictly applied in Germany. There was also no German contribution with RCTs conducted in nursing homes, kindergarten, childcare, or schools although the role of these settings was under considerable discussion. Conversely, there are international examples of RCTs aiming to determine the best strategies for preventing virus transmission. Many trials in the US, for example, were planned to investigate how tailored programs to increase adherence to preventive measures would affect transmission rates.17–19 Another US randomized trial included almost 20 million people to assess how digital information may affect local case rates.20 Different testing strategies to ensure safe gatherings at mass events have also been investigated in Spain,21 France22 and Norway.23 In case of facing future pandemics with similar challenges, such research would be highly important to develop evidence-based public health interventions and to improve policy-making in Germany.\n\nThis study has several limitations. First, our sample depended on accurate trial registrations and reports in the biomedical literature. We cannot exclude those trials conducted in Germany that have not been identified, for example because they were not registered, the registry data gave no indication of a German contribution, or the registry entry was delayed. Nevertheless, searching the Germany-specific registry DRKS did not yield any additional trials. The use of the most recent version of COVID-evidence in August 2021 resulted in just one more trial not previously captured by the filter, and two additional studies registered very late (28 and 30 December 2020) not previously captured due to time lags in registries. While these three studies are not included in the recruitment analysis, they have similar characteristics to the other trials and would not impact our overall interpretation. Second, although we obtained information for more than half of all included trials in an investigator request, we still had incomplete data on the actual recruitment in Germany with imbalances related to some trial characteristics. For example, we had recruitment information for 34.3% of the industry-funded trials compared to 80% of the publicly-funded trials. However, it is unlikely that the other trials have substantially higher recruitment and completion rates, and that missing recruitment information significantly affected our results. Even a five-fold higher recruitment rate in these remaining trials would not change the overall picture: which is that most trials have not been successfully recruited. Finally, the estimation of a target sample size might not be applicable for the few trials with an adaptive design, since sample size (and other methodological trial characteristics) may change over time. Therefore, our analysis related to adaptive designs should be seen contextualized within the trial progress. However, the median reported target sample size for trials with and without adaptive designs was similar.\n\n\nConclusions\n\nThe overall German contribution to the worldwide clinical trial research agenda for COVID-19 has been relatively modest. While few excellent examples of successful individual trial recruitment exist, most trials were not able to meet their goals and did not deliver the much needed evidence. A close evaluation and international comparison of the challenges and barriers for conducting clinical trials in Germany is urgently needed.\n\n\nData availability\n\nOpen Science Framework (OSF): COVID-evidence: A living database of trials on interventions for COVID-19/Clinical trial research on COVID-19 in Germany – a systematic analysis.\n\nDOI: https://doi.org/10.17605/OSF.IO/CD6RQ.8\n\nThe supplement file contains the following extended data:\n\n- Data sources and search strategy\n\n- Email template/Recruitment information request\n\n- Email template/Data confirmation request\n\n- PRISMA flow diagram for trial identification\n\n- Table 1 a. Characteristics of randomized COVID-19 trials planned to be conducted in Germany\n\n- Table 1 b. Trial characteristics and recruitment details\n\n- Characteristics of trials identified post-hoc\n\nOpen Science Framework (OSF): COVID-evidence: A living database of trials on interventions for COVID-19.\n\nDOI: https://doi.org/10.17605/OSF.IO/GEHFX.9\n\nThe project contains the following extended data:\n\n- COVID-evidence protocol\n\n\nReporting guideline\n\nOpen Science Framework (OSF): PRISMA checklist for ‘Clinical trial research on COVID-19 in Germany – a systematic analysis.\n\nDOI: https://doi.org/10.17605/OSF.IO/CD6RQ.8\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication)\n\n\nAuthor contributions\n\nJH performed conceptualization, formal analysis, investigation, methodology, project administration, validation, visualization, original draft preparation, and review & editing of the article. AR and MB conducted investigation, validation, and review & editing of the article. PD conducted data curation and review & editing of the article. PJ performed conceptualization, formal analysis, investigation, methodology, project administration, supervision, validation, visualization, original draft preparation, and review & editing of the article. LGH was involved in conceptualization, funding acquisition, methodology, project administration, resources, supervision, validation, visualization, original draft preparation, and review & editing of the article.\n\n\nEthical approval\n\nNot required, this article does not contain any personal medical information about any identifiable living individuals.",
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Reference Source\n\nNorwegian Institute of Public Health: Antigen Rapid Test Screening to Prevent SARS-CoV-2 Transmission (COVID-19) at Mass Gathering Events.: NCT04898127.2021. Accessed June 28, 2021.Reference Source\n\nGoldman JD, Lye DCB, Hui DS, et al.: Remdesivir for 5 or 10 Days in Patients with Severe Covid-19. N Engl J Med. 2020; 383(19):1827–1837. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpinner CD, Gottlieb RL, et al.: Effect of Remdesivir vs Standard Care on Clinical Status at 11 Days in Patients With Moderate COVID-19: A Randomized Clinical Trial. JAMA. 2020; 324(11):1048–1057. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBeigel JH, Tomashek KM, Dodd LE, et al.: Remdesivir for the Treatment of Covid-19 - Final Report. N Engl J Med. 2020; 383(19):1813–1826. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVlaar APJ, de Bruin S, Busch M, et al.: Anti-C5a antibody IFX-1 (vilobelimab) treatment versus best supportive care for patients with severe COVID-19 (PANAMO): an exploratory, open-label, phase 2 randomised controlled trial. Lancet Rheumatol. 2020; 2(12):e764–e773. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosas IO, Bräu N, Waters M, et al.: Tocilizumab in Hospitalized Patients with Severe Covid-19 Pneumonia. N Engl J Med. 2021; 384(16):1503–1516. Publisher Full Text\n\nLescure F-X, Honda H, Fowler RA, et al.: Sarilumab in patients admitted to hospital with severe or critical COVID-19: a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Respir Med. 2021; 9(5):522–532. Publisher Full Text\n\nAxfors C, Schmitt AM, Janiaud P, et al.: Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials. Nat Commun. 2021; 12: 2349. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAngus DC, Derde L, Al-Beidh F, et al.: Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial. JAMA. 2020; 324(13):1317–1329. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGordon AC, Mouncey PR, Al-Beidh F, et al.: Interleukin-6 Receptor Antagonists in Critically Ill Patients with Covid-19. N Engl J Med. 2021; 384(16):1491–1502. Publisher Full Text\n\nZarychanski R: Therapeutic Anticoagulation in Critically Ill Patients with Covid-19 – Preliminary Report: The REMAP-CAP, ACTIV-4a, and ATTACC Investigators.Preprint 2021. Accessed July 12, 2021.Publisher Full Text\n\nREMAP-CAP: Equivalency Of Tocilizumab And Sarilumab2021. Accessed May 28, 2021.Reference Source\n\nREMAP-CAP. PRESS RELEASE: International Trial of SARS-CoV-2 Convalescent Plasma Pauses Enrollment of Critically Ill COVID-19 Patients: PRESS RELEASE REMAP-CAP2021. Accessed May 28, 2021.Reference Source\n\nNovartis: Novartis provides update on RUXCOVID study of ruxolitinib for hospitalized patients with COVID-192020. Accessed May 28, 2021.Reference Source\n\nMulligan MJ, Lyke KE, Kitchin N, et al.: Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults. Nature. 2020; 586(7830):589–593. PubMed Abstract | Publisher Full Text\n\nPolack FP, Thomas SJ, Kitchin N, et al.: Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N Engl J Med. 2020; 383(27):2603–2615. Publisher Full Text\n\nWalsh EE, Frenck RW, Falsey AR, et al.: Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates. N Engl J Med. 2020; 383(25):2439–2450. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbivax: Abivax Follows DSMB Recommendation to Stop the Phase 2b/3 miR-AGE Covid-19 Clinical Trial Due to Lack of Efficacy2021. Reference Source\n\nNovartis: Novartis provides update on CAN-COVID trial in hospitalized patients with COVID-19 pneumonia and cytokine release syndrome (CRS)2020. Accessed May 28, 2021.Reference Source\n\nEli Lilly and Company: Lilly and Incyte announce results from the Phase 3 COV-BARRIER study of baricitinib in hospitalized COVID-19 patients.2021. Accessed May 28, 2021.Reference Source\n\nKremsner P, Mann P, Bosch J, et al.: Phase 1 Assessment of the Safety and Immunogenicity of an mRNA- Lipid Nanoparticle Vaccine Candidate Against SARS-CoV-2 in Human Volunteers: Preprint.2020. Accessed July 12, 2021.Publisher Full Text\n\nLundgren JD, Grund B, Barkauskas CE, et al.: A Neutralizing Monoclonal Antibody for Hospitalized Patients with Covid-19. N Engl J Med. 2021; 384(10):905–914. Publisher Full Text\n\nSupady A, Weber E, Rieder M, et al.: Cytokine adsorption in patients with severe COVID-19 pneumonia requiring extracorporeal membrane oxygenation (CYCOV): a single centre, open-label, randomised, controlled trial. Lancet Respir Med. 2021. Article in Press. Publisher Full Text\n\nKörper S, Weiss M, Zickler D, et al.: High Dose Convalescent Plasma in COVID-19: Results from the Randomized Trial CAPSID: Preprint.2021. Accessed July 12, 2021.Publisher Full Text"
}
|
[
{
"id": "124218",
"date": "11 Mar 2022",
"name": "Anthony De Soyza",
"expertise": [
"Reviewer Expertise Research background Respiratory medicine",
"Clinical Trials",
"COVID 19"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting and candid report by Hirt, Hemkens and colleagues highlighting limited successes in recruitment into COVID-19 research during the specified time using trial registrations in 2020 in Germany.\nIt highlights that recruitment was rarely satisfactory with a median rate of recruitment vs target of ~13%. The median number of planned participants from Germany was 106, while the median recruited was actually 15 participants per trial (IQR, 0 to 44). The manuscript displays data on the recruitment rates of studies identified by multiple methods and covers a broad range of COVID facing approaches including devices (ECMO), anti virals and anti- inflammatory therapies.\nThe work has many commendable features but there are some limitations that could be more fully discussed.\nFirstly the registration period may not relate to actual study opening. It is therefore unclear how many studies were impacted by either slow start up and/or rapid closure. The hydroxychloroquine studies noted, for example, may well be explained by the rapid success of RECOVERY reporting lack of benefit meaning early closure. These data may be included within the manuscript but are not easy to identify - some of the explanatory text is more identifiable in this matter in the discussion.\nThe poor recruitment and attempts to understand why is important as solutions to resolving poor recruitment within a pandemic are complex. The UK experience note din the discussion had a number of factors contributing to “success” ranging from “infrastructure “commented upon by the authors. This relates to an expectation research is part of normal clinical practice and there is specific funding into most organisations to deliver upon this via in England the National Institute for Health Research (NIHR) Comprehensive research network (CRN).\nWhat is not well described in this paper is the differences in approvals/ site selection/ national imperatives and process for dealing with competing studies in Germany. The trials infrastructure in Germany is not discussed (who decides which sites take on which studies and what resource if any is funded nationally? What is the incentive to do pragmatic non-commercial studies vs fee paying low volume complex industry studies? One cannot therefore develop an understanding of why there were such differences in experiences within Germany (some studies did hit targets as reported herein) and why there are differences between countries.\nThese all need to be discussed/ dissected to understand how coordination of research efforts was/ was not a root cause of the poor recruitment as opposed to lack of staff capacity/selecting small volume high intensity trials vs low intensity pragmatic trials.\nThe authors may wish to clarify the tables/ figures where figure 1 notes trials 1-34 but does not directly link them to the preceding tables. It would be useful to understand why some of the studies hitting target were different to those not.\nOther issues relate to ongoing open studies that are limited to Germany only - there can be investigator led reticence to close down failing studies – if these studies are still failing to recruit and are closed down then recruitment success to studies overall will fall further as a % of studies hitting target. This limitation should be noted\nThe authors may wish to note Cunliffe et al (2020) How achievable are COVID-19 clinical trial recruitment targets? A UK observational cohort study and trials registry analysis - PubMed (nih.gov) an analysis of clinical trials feasibility in the UK showing that there was likely an over commitment within the UK that needed national coordination to prioritise the most important studies.1\n\nThe UK National Institute for Health research (NIHR) developed and rapidly implemented an Urgent Public health (UPH) Panel. It pulled in very broad expertise and linked with governmental advisory panels from therapeutics and vaccines plus trials infrastructure delivery & methodology experts to help focus efforts on selecting and then delivering studies. This huge body of work involved reviewing 1000s of studies thrice weekly for much of 2020 to drill down a focus; 95 were listed of which the initial 5 included RECOVERY and PRINCIPLE studies (listed from Jan 2020-Mach 2020). See Urgent Public Health COVID-19 Studies | NIHR.\nThere are very many challenges in delivering research successfully even more so in the middle of a pandemic. The authors should be commended on writing the first chapter in Germanys’ book on this. The authors identify the success was below ideal. The challenges are now to identify where improvements can be made to ensure in the future, Germany can harness the potential to deliver research more rapidly.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "179772",
"date": "21 Dec 2023",
"name": "Waldemar Siemens",
"expertise": [
"Reviewer Expertise Meta-research",
"meta-analysis",
"GRADE"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 analysis on clinical trial research on COVID-19 in Germany for which the authors searched the trial registries and well-known platforms like (L-OVE) and the Cochrane COVID-19 Study Register. The data is shown in a descriptive way and underline the modest contribution of Germany regarding RCTs on COVID-19. I have only some minor comments. The authors could elaborate more on the funding structure and trials infrastructure in Germany to give the reader more context knowledge (e.g., background and/or discussion). I also would encourage the authors to justify in the background why the analysis focused on Germany, why not on Switzerland or another country? In general, I agree with the way the results are shown and the corresponding conclusion.\n\nMinor comments:\nAbstract:\nPlease add databases you searched.\nBackground:\n\nPlease justify why RCTs in Germany were analyzed.\n\nYou could give more information on the funding structure and trial infrastructure in Germany.\nMethods:\n\n“Four authors (JH, PJ, AR, MB) extracted data on trial characteristics” – no double extraction, correct?\nResults:\n“Most trials were double blinded” - Who was exactly blinded? Had you a closer look or did you just extract if the expression 'double blind' was used?\nTable 1:\nSometimes there is a number after the decimal point and sometimes not. Please be consistent.\nDiscussion:\nYou could give more information on the funding structure and trial infrastructure in Germany to enhance the understanding of the results for the reader.\n\nDo authors plan to re-assess the data in 2023? (all trials should have finished recruiting then).\n\nYou mention some valid implications for research. Do you also have recommendations or implications for practice? E.g., trialists, funding bodies. Or implications for (meta-)researchers how?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-913
|
https://f1000research.com/articles/10-911/v1
|
10 Sep 21
|
{
"type": "Research Article",
"title": "Optimised deep neural network model to predict asthma exacerbation based on personalised weather triggers",
"authors": [
"Radiah Haque",
"Sin-Ban Ho",
"Ian Chai",
"Adina Abdullah",
"Radiah Haque",
"Ian Chai",
"Adina Abdullah"
],
"abstract": "Background – Recently, there have been attempts to develop mHealth applications for asthma self-management. However, there is a lack of applications that can offer accurate predictions of asthma exacerbation using the weather triggers and demographic characteristics to give tailored response to users. This paper proposes an optimised Deep Neural Network Regression (DNNR) model to predict asthma exacerbation based on personalised weather triggers. Methods – With the aim of integrating weather, demography, and asthma tracking, an mHealth application was developed where users conduct the Asthma Control Test (ACT) to identify the chances of their asthma exacerbation. The asthma dataset consists of panel data from 10 users that includes 1010 ACT scores as the target output. Moreover, the dataset contains 10 input features which include five weather features (temperature, humidity, air-pressure, UV-index, wind-speed) and five demography features (age, gender, outdoor-job, outdoor-activities, location). Results – Using the DNNR model on the asthma dataset, a score of 0.83 was achieved with Mean Absolute Error (MAE)=1.44 and Mean Squared Error (MSE)=3.62. It was recognised that, for effective asthma self-management, the prediction errors must be in the acceptable loss range (error<0.5). Therefore, an optimisation process was proposed to reduce the error rates and increase the accuracy by applying standardisation and fragmented-grid-search. Consequently, the optimised-DNNR model (with 2 hidden-layers and 50 hidden-nodes) using the Adam optimiser achieved a 94% accuracy with MAE=0.20 and MSE=0.09. Conclusions – This study is the first of its kind that recognises the potentials of DNNR to identify the correlation patterns among asthma, weather, and demographic variables. The optimised-DNNR model provides predictions with a significantly higher accuracy rate than the existing predictive models and using less computing time. Thus, the optimisation process is useful to build an enhanced model that can be integrated into the asthma self-management for mHealth application.",
"keywords": [
"Machine learning",
"deep neural network",
"personalisation",
"asthma self-management"
],
"content": "Introduction\n\nAsthma is a chronic lung disease that affects people of all age groups around the world.1 Asthma exacerbation causes asthma attacks, and the frequency of asthma attacks depends on the exposure to asthma triggers.2 Weather is a common triggering factor of asthma exacerbation.3 Studies show that weather triggers, such as temperature, humidity, air pressure, and wind, cause asthma attacks.4–6 Weather impact is specific to individual asthmatic patients due to their lung performance, which varies among patients. This depends on their demographic characteristics, such as age and gender.7 Geographical location is also a factor because the association between weather triggers and asthma is inconsistent in different climate regions.4\n\nAlthough asthma cannot be cured, avoiding exposure to weather triggers through asthma self-management can minimise the risk of asthma exacerbation.8 Recently, there have been attempts to develop mHealth applications to assist asthma self-management. However, until now, no application for effective asthma self-management exists that has been widely adopted by users or integrated into primary asthma care records.2 This is because there is a lack of solutions that can offer accurate predictions of asthma exacerbation based on personalised weather triggers and provide tailored feedback to users.\n\nDeep Neural Network (DNN) is a type of neural network algorithm with multiple hidden layers and several nodes.9 In recent years, DNN has been significantly utilised in the health informatics research domain for forecasting and pattern recognition.10–13 This is because DNN models tend to learn more effectively and have better performance in providing accurate predictions (especially through optimisation) than traditional Machine Learning (ML) algorithms.14 Nevertheless, the application of ML and DNN in weather-based healthcare is still in its infancy. In fact, to the best of the authors’ knowledge, none of the existing research has applied DNN to predict asthma exacerbation based on demography and weather. Therefore, the main contribution of the work in this paper is to apply DNN and propose an optimisation process to predict asthma exacerbation based on personalised weather triggers with low error and high accuracy. The findings will be helpful for developing mHealth solutions with personalisation for effective asthma self-management.\n\n\nMethods\n\nWith the aim of integrating weather, demography, and asthma tracking, an mHealth application, namely Weather Asthma (WEA), was developed for this study.15 The WEA is an android-based application that collects user demography and monitors daily weather forecasts in individual users’ location to identify the potential weather triggers. Consequently, both demography and weather data are selected as input features in the asthma dataset.\n\nThe WEA application also allows users to conduct the Asthma Control Test (ACT).16 The ACT is a self-administered survey which is considered the standard assessment for monitoring chronic asthma and recommended by the Global Initiative for Asthma.17 The ACT score is selected as the target output for prediction because it helps identify the severity and chances of asthma exacerbation.16\n\nData was collected through the WEA application from ten participants with asthma over a period of one-year. Participants conducted ACTs by regularly answering five multiple-choice questions, which include four asthma symptom-related questions and one asthma self-evaluate question. Each question is scored between 1-5. Once the ACT was submitted, a timestamp was formed with the participant’s demography and the weather information of that day and time at their location. This timestamp, along with the total ACT score, are stored in the database, as seen in Table 1. All participants consented to the data collection and the ethical approval was obtained from the Multimedia University Research Ethics Committee (EA1532021).\n\nThe first step of data pre-processing is identifying the missing data in the dataset through a heatmap, illustrated in Figure 1, which visualises the locations of missing values. Fortunately, the selected dataset does not contain any missing or NaN values.\n\nThe second step is dropping irrelevant features including “User ID” and “Timestamp”. “Smoking habit” is also dropped because its correlation coefficient value with the target variable “ACT score” in the heatmap is close to zero. Table 2 represents the final dataset, which consists of 1010 records with ten input features and one output variable. Figure 2 shows the ACT scores’ distribution, which ranges from 12 to 21. Figure 3 illustrates a scatterplot and countplot for weather features, where a strong correlation can be observed between the weather features and “ACT score”.\n\nThe third step is converting the categorical variables in the dataset to numeric representations using the label encoder. The fourth step is splitting the dataset into training (707 samples) and testing (303 samples) datasets.\n\nDNN can be modelled with various ML techniques, such as regression and classification.18 Regression is responsible for modelling and characterising the relationship between the input features and the target output. Regression is applied to predict numerical values.19 Hence, regression is used in this study to predict the ACT score, which is a numerical value.\n\nConsequently, a DNN Regression (DNNR) model is applied on the dataset. In DNNR, the hidden layers are located between the input layer and the output layer, as seen in Figure 4. The hidden layers apply weights to input values and direct them via an activation function for the output values.20 The activation function assists in deriving distinguishing features that are required for the prediction.10 This is particularly helpful to model the asthma dataset which contains multiple types of input features. The Rectified Linear Unit (ReLU) activation function is used because it provides nonlinear transformations for deep modelling.9\n\nThe following are the main equations used for prediction using the DNNR model:\n\nwhere x is the input features, y^ is the predicted values, w is the input weights, b is the bias (a constant number used for adjustment), e is the internal elements in the hidden layers, f(e) is the activation function, m is the number of input features, and j is a constant number between [0, m].\n\nEvaluating the DNNR model is essential to determine its prediction error and accuracy, which can be achieved through Mean Absolute Error (MAE), Mean Squared Error (MSE), and Explained Variance Score (EVS). The MAE sums up the absolute difference between the actual and the predicted values. The MSE sums up the squared differences between the actual and the predicted values. The EVS computes the variance score which determines the accuracy of nonlinear regression models.9 The following equations calculate the MAE, MSE and EVS of the DNNR model:\n\nwhere y is the actual output values, y^ is the predicted values, n is the number of records in the dataset, v is the biased variance, and i is a constant number between [0, n].\n\nOptimising the DNNR model is crucial for prediction with low error, high accuracy, and less computing time. This can be achieved by applying essential optimisation methods which include data scaling and parameter tuning. For data scaling, standardisation is used because it is beneficial for enhancing the performance of the DNNR model and its optimisation.9 This happens by rescaling the input and the output values using the following equations:\n\nwhere s is the input/output variables, s′ is the standardised input/output values, μ is the mean of the input/output values, σ is the standard deviation of the input/output values, n is the number of records in the dataset, and i is a constant number between [0, n].\n\nThe DNNR parameters include hidden layers, nodes at each hidden layer, batch size, epochs, weight initialiser, loss function, and optimiser. Grid-search is an optimisation algorithm which automates the trial procedure of tuning these parameters and selecting their best values.21 Nevertheless, tuning a large number of parameters and their search values using grid-search leads to excessive computational time and power. In this study, the fragmented-grid-search method is used where parameters are tuned independently in parallel, hence taking less computing time for optimisation. Figure 5 demonstrates the optimisation algorithm and Figure 6 illustrates the overall optimisation process.\n\n\nResults\n\nUsing the DNNR model on the dataset, a score of 0.83 is achieved with MAE = 1.44 and MSE = 3.62. Table 3 shows 5 predicted values against their actual values and Figure 7 contains the residual visualisation. It can be seen that the differences between the predicted and the actual values vary up to ±15. While this might seem an acceptable prediction error for some datasets, in the case of the asthma dataset, this amount of loss is unacceptable. This is because the range of the ACT score can only be from 5 to 25, where scores of 5 to 15 are categorised as “poorly-controlled asthma”, 16 to 19 as “not well-controlled asthma”, and 20 to 25 as “well-controlled asthma”.17\n\nIn the last row of Table 3, with the actual value of 19 (not well-controlled), the predicted value is 20 (well-controlled), which gives a contradictory prediction result. This can be a serious problem while providing tailored feedback to asthmatic patients, resulting in an insufficiently effective asthma self-management solution. For an optimised model, the acceptable loss range needs to be less than ±0.5. For example, with the actual value of 19, the prediction value can be at most 19.4≃19 (with maximum +0.4 loss) or at least 18.6≃19 (with maximum −0.4 loss). Therefore, an optimised-DNNR model is built to reduce the prediction error and increase the overall accuracy.\n\nFor the optimised-DNNR model, two hidden layers are used with 50 nodes at each hidden layer. Adaptive Moment Estimation (Adam) is used as the optimiser, which is helpful for optimising the learning and convergence rates during model training.13 Table 4 summarises the optimum parameter values obtained using fragmented-grid-search and the total tuning time. Figure 8 shows the loss rate of the training and the testing datasets swiftly decreased using the ReLU activation function.\n\nUsing the optimised-DNNR model on the dataset, a score of 0.91 was achieved with a total accuracy of around 94%. The MAE and the MSE rates are 0.20 and 0.09 respectively, which are in the acceptable loss range (error < 0.5). Figure 9 illustrates the residual plot of the optimised-DNNR model which shows a strong correlation between the predicted and the actual values. Figure 10 confirms that the optimised-DNNR model provides predictions within the loss range ±0.5.\n\n\nDiscussion and conclusion\n\nRecent popularity of mHealth and DNN enabled developing solutions to collect data from asthmatic patients and provide accurate predictive alerts. Although several studies support the association between weather and asthma, there is a lack of solutions for effective asthma self-management that can predict asthma exacerbation based on personalised weather triggers. This is due to three problems:\n\n\n\n1. Limited availability of real-time weather data that can link weather triggers with demography and asthma severity for individual asthmatic patients. This study obtained the dataset from the WEA application which comprises relevant input features (weather and demography) and target output (asthma severity).\n\n2. Existence of nonlinear relationships in the asthma dataset due to multiple types of input features and interconnected correlations. This study applied DNN for modelling the dataset, which effectively handles nonlinearity by using the ReLU activation function.\n\n3. Lack of accurate predictive models and precautionary frameworks for effective asthma self-management. This study built an optimised model that provides accurate predictions of asthma exacerbation with errors in the acceptable loss range (error < 0.5).\n\nThe experimental results reveal that the standardisation technique improves the stability of the DNNR model, which enhances the performance of the optimisation algorithm and the optimiser. Furthermore, the fragmented-grid-search method is able to tune several parameters with much less computing time (≈26 minutes) than the standard grid-search used in previous studies (e.g. ≈4.3 hours for tuning 2 parameters22). Moreover, model training takes less than one minute due to the Adam optimiser, which helps the model converge efficiently. Overall, the optimised-DNNR model provides predictions with a significantly higher accuracy rate (94%) than the existing ML models in the literature for predicting asthma exacerbation (e.g. 87% with naïve Bayes,2 85% through logistic regression,8 and 84% using random forest23).\n\nConsequently, the optimisation process helps build an enhanced model for effective asthma self-management. Subsequently, the optimised model will be integrated into the WEA application for predicting asthma exacerbation based on personalised weather triggers and providing tailored feedback to users. The main limitation of this study is that the data was collected from a limited number of users and in one climate region. In future, more users from different climate regions will be considered for testing the generalisation capability of the proposed model.\n\nRH and SBH conducted the research, analysed the data, and wrote the paper. IC and AA improved and edited the paper. All authors have approved the final version.",
"appendix": "Acknowledgements\n\nThe authors would like to thank all the participants of this study, who dedicated their time and effort to use the Weather Asthma application and conduct the Asthma Control Tests.\n\n\nSoftware and data availability\n\nZenodo. Dataset and source code for the research paper titled: “Optimised deep neural network model to predict asthma exacerbation based on personalised weather triggers”. DOI: https://doi.org/10.5281/zenodo.5271780.24\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).\n\n\nReferences\n\nSeo S, Kho H, Kim K: Predicting asthma attacks: Effects of indoor pm concentrations on peak expiratory flow rates of asthmatic children. Chest. 2020; 157(6): A8. Publisher Full Text\n\nTsang KCH, Pinnock H, Wilson AM, et al.: Application of machine learning to support self-management of asthma with mHealth. Proc. 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Montreal, QC, Canada; 2020, pp. 5673–5677.\n\nBodaghkhani E, Mahdavian M, MacLellan C, et al.: Effects of meteorological factors on hospitalizations in adult patients with asthma: A systematic review. Canadian Resp J. 2019; 9: 1–11. Publisher Full Text\n\nRazavi-Termeh S, Sadeghi-Niaraki A, Choi S: Asthma-prone areas modeling using a machine learning model. Sci Rep. 2021; 11(1). Publisher Full Text\n\nSharma A, Saini S, Chhabra P, et al.: Air pollution and weather as the determinants of acute attacks of asthma: Spatiotemporal approach. Indian J Public Health . 2020; 64(2): 124–129. PubMed Abstract | Publisher Full Text\n\nPoole J, Barnes CS, Demain JG, et al.: Impact of weather and climate change with indoor and outdoor air quality in asthma: A work group report of the AAAAI environmental exposure and respiratory health committee. J Allergy Clin Immunol . 2019; 143(5): 1702–1710. 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Publisher Full Text\n\nKoshimizu H, Kojima R, Kario K, et al.: Prediction of blood pressure variability using deep neural networks. Int J Med Informatics. 2020; 136: 104067. Publisher Full Text\n\nSuresha H, Parthasarathy S: Alzheimer Disease Detection Based on Deep Neural Network with Rectified Adam Optimization Technique using MRI Analysis. Computers and Communications (ICAECC): Third International Conference on Advances in Electronics. 2020; 1–6. Publisher Full Text\n\nPandey S, Janghel R: Recent deep learning techniques, challenges and its applications for medical healthcare system: A review. Neural Processing Letters. 2019; 50(2): 1907–1935. Publisher Full Text\n\nHo SB, Haque R, Chai I, et al.: Integrating mobile devices with cohort analysis into personalised weather-based healthcare. Lecture Notes Computer Sci. 2020; 12496: 606–618. Publisher Full Text\n\nHaque R, Ho SB, Chai I, et al.: Intelligent health informatics with personalisation in weather-based healthcare using machine learning. Lecture Notes Data Engineering Communications Technologies. 2021; 72: 29–40. Publisher Full Text\n\nGlobal Initiative for Asthma: Global strategy for asthma management and prevention. Accessed May 23, 2021. Reference Source\n\nSubasi A: Practical Machine Learning for Data Analysis using Python. Academic Press; 2020; pp. 91–202.\n\nManasa J, Gupta R, Narahari NS: Machine learning based predicting house prices using regression techniques. Proc. 2nd International Conference on Innovative Mechanisms for Industry Applications (ICIMIA), Bangalore, India. 2020, pp. 624–630. Publisher Full Text\n\nDeepAI Hidden Layer. Accessed May 23, 2021. Reference Source\n\nErten G, Keser S, Yavuz M: Grid search optimised artificial neural network for open stope stability prediction. Int J Mining, Reclamation Environment. 2021. Publisher Full Text\n\nLiashchynskyi P, Liashchynskyi P: Grid search, random search, genetic algorithm: A big comparison for NAS. ArXiv abs . 1912; 06059: 2019.\n\nKocsis O, Arvanitis G, Lalos A, et al.: Assessing machine learning algorithms for self-management of asthma. E-Health Bioengineering Conf (EHB). 2017; 571–574. Publisher Full Text\n\n1191402606: 1191402606/Optimised-deep-neural-network-model: Dataset and source code (v1.0.0). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "95806",
"date": "07 Oct 2021",
"name": "Mark Elshaw",
"expertise": [
"Reviewer Expertise Machine learning and robotics."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 an interesting paper, which is timely. There is suitable use of deep learning, however there is a need to consider whether the problem is big data. It is good that there is some consideration of preprocessing. The paper follows a clear scientific process. There is a need to clearly outline why this paper is novel and to offer greater discussion of the future direction of the project.\nThere is some indication of the performance achieved, but I would have liked to see greater statistical analysis. There is a need for consideration of the state of the art and how the approach in this paper compares with the state of the art.\nOverall a very well written and well presented paper that would benefit a little from greater analysis of the achievements. The analysis that you might consider using is the f-score, false positive and false negatives, and the use of ROC curves. The developed approach would be of clear benefit to asthma patients.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "94416",
"date": "22 Oct 2021",
"name": "Meei Hao Hoo",
"expertise": [
"Reviewer Expertise usability engineering",
"persuasive design and data mining."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe novelty of this study is to improve the accuracy of prediction of asthma by using optimised deep neural network and this gives a contribution to enhance the current model in terms of accuracy and computational performance. Most decisions in the research work are justifiable with supported of references made to the previous related works. Main results are explained in regards to the use of optimizer in building the model.\nIn overall, the paper has a good-structured layout. However, the content in the method section can be improved to give a good flow of understanding. Either way to have an overall methodology of the study that describing the steps taken in the methods, or the arrangement and/or explanation in the methods follow the optimization process as in Figure 6.\nSuggest also to include relevant works to support the choice of ADAM optimizer in the study as compared with other optimizers, as well as the used of ReLU activation function over Mish (for example) and others in order to build strong arguments.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "95805",
"date": "02 Nov 2021",
"name": "Kwan-Yong Sim",
"expertise": [
"Reviewer Expertise Data science",
"software testing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe main contribution of the paper is to identify the correlation patterns among asthma, weather, and demographic variables. Optimization of the DNNR model by applying standardization and fragmented grid search successfully reduced the error rate below 0.5 required for effective asthma self-management.\nOverall the paper is technically sound and made clear contributions to asthma self-management and improving the stability of the DNNR model proposed.\nThe authors should include the following discussion to make the paper more cohesive:\nAs the study was conducted based on limited data collected from 10 users, the author should discuss the potential impact if a larger dataset is being used, including from different climate regions or different demographics.\n\n\"smoking habit\" was mentioned as one of the features in data pre-processing. The author should explain what other features were included the data set (if any) and why they were included in the first place.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-911
|
https://f1000research.com/articles/10-680/v1
|
28 Jul 21
|
{
"type": "Case Report",
"title": "Case Report: Cerebral venous thrombosis revealing celiac disease",
"authors": [
"Romdhane Wiem",
"Arfa Sondess",
"Chelly Jihene",
"Jomaa Olfa",
"Hammami Sonia",
"Hmida Karima",
"El Arbi Fatma",
"Berriche Olfa",
"Arfa Sondess",
"Chelly Jihene",
"Jomaa Olfa",
"Hammami Sonia",
"Hmida Karima",
"El Arbi Fatma",
"Berriche Olfa"
],
"abstract": "Celiac disease (CD) is an autoimmune enteropathy resulting from intolerance of an individual genetically predisposed to gluten. It has a large clinical polymorphism ranging from a classic digestive clinical presentation due to the malabsorption syndrome to extra-intestinal symptoms. Among the hematologic abnormalities, venous thromboembolic disease (VTE) has been reported, and they are most often located in the abdomen or lower limbs, but the cerebral localization was exceptionally described. We report a case of CD revealed by cerebral thrombophlebitis. A 44-year-old patient with no medical history and no drug intake, presented with hemiplegia followed by a status epilepticus in a context of apyrexia, initially hospitalized in intensive care. Magnetic imaging resonance displayed a cerebral venous thrombosis of the sigmoid sinus requiring anticoagulant treatment, then transferred to our department for the etiological investigation. On questioning, the patient reported chronic diarrhea and weight loss with no other associated symptoms. The examination revealed an underweight patient with pale conjunctiva, improvement of her deficit symptoms, and no other abnormalities. Laboratory tests noted biological signs of malabsorption. The thrombophilia assessment revealed a protein C deficiency with a slight increase in anticardiolipin antibodies and anti-Beta 2 glycoprotein 1 antibodies. Immunological tests noted positives anti-transglutaminase and IgA anti-endomysium antibodies. Duodenal biopsy demonstrated villous atrophy. After ruling out the other causes of VTE, the diagnosis of cerebral venous thrombosis secondary to CD was retained. Early diagnosis and treatment of CD improves the quality-of-life for patients and may spare them various long-term or even fatal complications.",
"keywords": [
"Celiac disease",
"venous thromboembolic disease",
"malabsorption syndrome",
"Hypercoagulability."
],
"content": "Introduction\n\nCeliac disease (CD) is an autoimmune enteropathy resulting from intolerance of an individual genetically predisposed to gluten. It affects 0.6–1.0% of the world population.1 It has a large clinical polymorphism ranging from a classic digestive clinical presentation due to the malabsorption syndrome; diarrhea and abdominal pain; to extra-intestinal symptoms.2 It requires lifelong adherence to a gluten-free diet.\n\nAmong the hematologic abnormalities, venous thromboembolic disease (VTE) has been reported in the literature, with a 25% higher risk in patients with CD compared with the general population.3 VTE is most often located in the abdomen or lower limbs, but the cerebral localization has been exceptionally described.4\n\nHere, we report a case of CD revealed by cerebral venous thrombosis discovered while exploring a status epilepticus. This presentation has not been reported previously in the literature.\n\n\nCase report\n\nA 44-year-old Tunisian female patient, housewife, with no medical history and no drug intake, presented with hemiplegia followed by a status epilepticus in a context of apyrexia, initially hospitalized in intensive care. Neuroimaging displayed a cerebral venous thrombosis of the superior sagittal sinus (Figure 1) requiring anticoagulant treatment (low-molecular -weight -heparin 100 IU/kg × 2/24 h followed by Warfarin for 6 months. After treatment, the patient was transferred to our department of Internal Medicine for the etiological investigation.\n\nCerebral CT scan (A, B: axial plane, C: Sagittal plane) showing a venous thrombosis of superior sagittal sinus (A, C) and a left temporoparietal porencephalic cyst (B).\n\nOn examination, the patient reported chronic diarrhea and weight loss with no other associated symptoms. Physical examination revealed an underweight patient (BMI:16.9) with pale conjunctiva, improvement of hemiparesis, and no other abnormalities. Laboratory tests noted biological signs of malabsorption. [(Hemoglobin: 10 g/dl (normal range > 12 g/dl), Albumin: 17.9 g/L, cholesterol: 2.8 mmol/l (normal range < 5,1 mmol/l).]\n\nThrombophilia assessment revealed a protein C deficiency 57% (normal range: 70-120%), a slight increase in anticardiolipin antibodies 11 IU/ml (normal range <7 UI/ml) and anti-Beta 2 glycoprotein 1 antibodies 18 IU/ml (normal range < 8 IU/ml) with normal levels of protein S, antithrombin III and homocysteinemia, and negative factor V Leiden. Immunological tests noted positive anti-transglutaminase >50 IU/ml (normal range < 8 U/ml) and anti-endomysium antibodies at 0.6 g/L (normal range < 0.2 g/L).\n\nFrom examination and laboratory results, VTE was diagnosed and CD as the cause was suspected. Duodenal biopsy demonstrated villous atrophy, meaning that the diagnosis of CD could be retained after ruling out the other causes of VTE as the neoplastic aetiologies; gynaecologic examination didn’t show a lesion, neither chest radiography or colonoscopy.\n\nThe outcome of the patient was deemed favorable with anticoagulant therapy (low-molecular weight Heparin followed by Warfarin for 6 months without bleeding complications), combined with a gluten-free diet during the follow-ups over a period of 3-years in our outpatient consultation.\n\n\nDiscussion\n\nCD is defined as a chronic immune-mediated small intestinal enteropathy caused by gluten intolerance in genetically predisposed individuals.5 The activation of both the innate and adaptive response of the immune system, following the ingestions of gluten leads to damage to the proximal mucosa of the small intestine, resulting in the malabsorption of nutrients and the appearance of extra-intestinal manifestations.\n\nCD is a systemic disorder, with different forms of clinical manifestations, from a classic digestive clinical presentation to extra-intestinal symptoms. The intestinal form of CD is more commonly found in the pediatric population6 and rarely in adults. It includes diarrhea, which is a common presenting sign, in addition to malabsorption symptoms.\n\nNevertheless, extra-intestinal manifestations are being increasingly recognized, most likely due to better awareness of atypical presentations. They can include chronic fatigue, anemia, osteoporosis, recurrent aphthous stomatitis, elevated liver enzymes, joint or muscle pain, epilepsy, peripheral neuropathy, and infertility7 Therefore, it is reported that extra-intestinal manifestations may appear before the diagnosis of CD, as shown in our case.\n\nIt has been recognized that chronic inflammation is also an independent risk factor for VTE as the consequence of inflammatory cytokines and oxidative stress on the coagulation cascade is demonstrated.8\n\nOur patient presented a deficiency of protein C; which has been reported in previous studies related to CD, results in the over activity of coagulation factors V and VIII thus increasing the risk for thrombotic events.9 We noted also a slight increase in anticardiolipin antibodies and anti-Beta 2 glycoprotein 1 antibodies, as shown in several studies where a higher prevalence of autoantibodies among patients with CD, including anti-phospholipid antibodies (see review of studies in9). It is possible that these anti-phospholipid antibodies might also contribute to hypercoagulability.\n\nA thrombosis assessment should be considered in patients with CD as the risk factors for thrombosis can be acquired in CD by a vitamin deficiency or antiphospholipid antibodies. These factors must be investigated, corrected, and even thromboembolic prophylaxis should be initiated.\n\nVTE as a presentation of CD is unusual and rarely reported, especially since this thrombosis is located in the cerebrum. The seriousness of these manifestations show that malabsorption syndrome should be systematically investigated to explore any symptoms due to systemic complications of malabsorption, for early diagnosis and better prognosis. Furthermore, a long diagnostic delay may increase the risk of poor clinical response.10\n\nIn fact, other central nervous system manifestations were reported more associated to CD than cerebral thrombosis, including cerebellar ataxia, peripheral neuropathy, seizures, headache, cognitive impairment, and psychiatric symptoms.11\n\nEarly diagnosis and treatment of CD improves the quality-of-life for patients and may spare them various long-term or even fatal complications like thromboembolic diseases.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of the clinical details and associated images was obtained from the patient.",
"appendix": "References\n\nBiagi F, Klersy C, Balduzzi D, et al.: Are we not over-estimating the prevalence of celiac disease in the general population? Ann Med. 2010; 42: 557–561. PubMed Abstract | Publisher Full Text\n\nHalfdanarson TR, Litzow MR, Murray JA: Hematologic manifestations of celiac disease. Blood. 2007; 109(2): 412–421. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUngprasert P, Wijarnpreecha K, Tanratana P: Risk of venous thromboembolism in patients with celiac disease: a systematic review and meta-analysis. J Gastroenterol Hepatol. 2016; 31: 1240–1245. PubMed Abstract | Publisher Full Text\n\nBouziane M, Arous S, Habbal R: Cerebral venous thrombosis as a rare thromboembolic complication of celiac disease: a case report. Eur Heart J Case Rep. 2020; 4(5): 1–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHusby S, Koletzko S, Korponay-Szabó IR, et al.: European Society for Pediatric Gastroenterology, Hepatology, and Nutrition guidelines for the diagnosis of coeliac disease. J Pediatr Gastroenterol Nutr. 2012 Jan; 54(1): 136–160. PubMed Abstract | Publisher Full Text\n\nVivas S, Ruiz de Morales JM, Fernandez M, et al.: Age-related clinical, serological, and histopathological features of celiac disease. Am J Gastroenterol. 2008 Sep; 103(9): 2360–2365; quiz 2366.80. PubMed Abstract | Publisher Full Text\n\nKayar Y, Dertli R, Sürmeli N, et al.: Extraintestinal Manifestations Associated with Celiac Disease. East J Med. 2019; 24(4): 478–483. PubMed Abstract | Publisher Full Text\n\nSamad F, Ruf W: Inflammation, obesity, and thrombosis. Blood. 2013; 122: 3415–3422. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPrevitali E, Bucciarelli P, Passamonti SM, et al.: Risk factors for venous and arterial thrombosis. Blood Transfus. 2011; 9(2): 120–138. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFuchs V, Kurppa K, Huhtala H, et al.: Delayed celiac disease diagnosis predisposes to reduced quality of life and incremental use of health care services and medicines: A prospective nationwide study. United European Gastroenterol J. 2018 May; 6(4): 567–575. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPennisi M, Bramanti A, Cantone M, et al.: Neurophysiology of the “Celiac Brain”: Disentangling Gut-Brain Connections. Front Neurosci. 2017; 11: 498. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "92258",
"date": "23 Aug 2021",
"name": "Juha Taavela",
"expertise": [
"Reviewer Expertise Celiac disease",
"gluten sensitivity"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 found celiac disease in a patient with venous thromboembolism. I especially like the conclusion that early diagnosis of CD is needed which is an important topic in CD (Popp et al., 2019). The case report is interesting, however, I have some comments:\nThe link between celiac disease and VTE is unknown. The authors suggest in the discussion that a thrombosis assessment should be considered in CD patients. Such a conclusion cannot be drawn from a couple of case reports. And the suggestion of thromboembolic prophylaxis is also not supported by such small data. I believe the situation is similar as in IBD, in which the acute phase causes a risk for VTE (Grainge et al, 2010). However, celiac disease is a much easier disease to treat than some IBDs, and such acute situations in the ER are not seen in CD. This must be changed in the discussion.\n\nAnother thing to discuss is that is the cause of protein C deficiency, coagulation factors and anti-phospholipid antibodies CD or just the fulminant diarrhea and nutrition deficiency?\n\nAs a minor remark the article should also mention that a significant proportion of celiacs are nowadays found while screening in-at risk groups such as Graves disease, type 1 diabetes etc (2). And these patients are without any symptoms but they benefit from treatment (Kurppa et al., 2014).\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": []
},
{
"id": "91588",
"date": "27 Aug 2021",
"name": "Bouomrani Salem",
"expertise": [
"Reviewer Expertise Autoimmune diseases",
"Internal Medicine",
"Thrombophilias"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present an original case report of cerebral venous thrombosis occurring in a patient with celiac disease and discuss the causal link between these two pathologies. Indeed, thromboembolic complications are part of the possible extra-intestinal manifestations of this disease with several cases and different locations reported.\nThe authors insist on the fact that the revealing character, as well as the status epilepticus, is the element which makes the originality of their observation.\nSome modifications are necessary before the indexing of this manuscript:\nKeywords: add \"cerebral venous thrombosis\" to the list of keywords\n\nIntroduction: remove the last sentence \"This presentation has not been reported previously in the literature.\" and replace it with \"this clinical situation remains exceptional and unusual during CD\". Indeed, several cases of cerebral venous thrombosis as the first manifestation of CD have been reported in the literature, some of which are associated with convulsive seizures or epilepsy. Seizures are nonspecific and can simply be a consequence of cerebral thrombosis. This possibility must be mentioned.\n\nCase report: the assessment of thrombophilia is incomplete. The other tests should be noted (if they were performed): prothrombin G20210A mutation (Factor II Mutation)? Tumor markers? Anti nuclear antibodies? Lupus anticoagulant?\n\nDiscussion:\nThe causal link between CVT and CD must be well discussed and the possible mechanisms of hypercoagulability during this disease well explained i.e. deficiencies in B12, folate and vitamin K, persistent chronic inflammation, hyperhomocysteinemia, the presence of anti-phospholipids antibodies, fibrinolysis abnormalities, endothelial dysfunction, thrombocytosis, etc.\nThe presence of antiphospholipid antibodies in this patient should also be discussed: simple positivity of these autoantibodies already reported during CD, or an authentic antiphospholipid syndrome associated with CD (venous thrombosis + positive anticardiolipin antibodies and anti-Beta 2 glycoprotein 1 antibodies). The association of these two autoimmune diseases remains a possible eventuality! 1 Is the control of these autoantibodies carried out at 12 weeks?\nThe possible origin of protein C deficiency must also be discussed: a real thrombophilia? protein loss through diarrhea? or the received anticoagulant treatment (Warfarin)?\n\nBibliography: the list of bibliographic references is not well selected. Indeed, to support the discussion, the cases reporting CVT and CD, in particular the inaugural forms and associated with epilepsy, may be cited and used in the discussion: [refs 2-6]\nLikewise, the very latest update on thromboembolic and cardiovascular complications associated with CD should be cited in the list of bibliographic references and used to discuss the different possible mechanisms of thrombogenesis during this disease 7.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-680
|
https://f1000research.com/articles/10-909/v1
|
10 Sep 21
|
{
"type": "Research Article",
"title": "Developing and validating a prediction model for frequent attenders at a Swedish emergency department using an electronic medical record system, a retrospective observational study",
"authors": [
"Lis Abazi",
"Elin Lindqvist",
"Gunnar Edman",
"Magnus Norberg",
"Jan Bergman",
"Ingmar Zachrisson",
"Sune Forsberg",
"Elin Lindqvist",
"Gunnar Edman",
"Magnus Norberg",
"Jan Bergman",
"Ingmar Zachrisson",
"Sune Forsberg"
],
"abstract": "Background: Frequent attenders (FA) account for a significant number of emergency department (ED) visits but to date there is no prediction model to identify patients at risk of becoming a FA. The aim of this research was to identify and describe FA using readily available data provided by electronic medical records and create a prediction model to identify future FA Method: Adults ≥18 years that visited the ED during 2015 were included. Patients with ≥4 visits were defined as FA, and patients with ≤3 visits were placed in the control group. Numerous variables were analyzed and differences between the groups compared. Logistic regression analysis was used to determine the predictor variables and the model validated using Receiver Operating Characteristic (ROC) on an independent sample. Results: 6635 patients were included in developing the model: 15.3 (n=1012) were classified as FA and 15.4 (n=1011) as the control group. Variables associated with at risk of becoming a FA were the following: age above 60 years OR 1.52 [CI 1.27 – 1.82], ED arrival by ambulance or helicopter OR 1.31 [CI 1.08 – 1.58], sheltered living OR 3.82 [CI 2.37 – 6.17], previous contact with psychiatric department OR 1.52 [CI 1.23 – 1.89], 10 outpatient care visits or more OR 4.81 [CI 3.81 – 6.08] and 10 outpatient care physician visits or more OR 3.94 [CI 3.25 – 4.78]. The ROC in the validation set had an area under the curve of 0.85 [CI 0.84 – 0.86].\nConclusion:\nData from electronic medical record software can be used to create and validate the risk of becoming a FA in the ED. We found that age over 60 years, ED arrival by ambulance or helicopter, sheltered living, previous contact with psychiatric departments, and frequent visits at outpatient care together predict the risk of becoming a FA.",
"keywords": [
"Emergency department",
"Frequent attenders"
],
"content": "Introduction\n\nSeveral reports and studies report a steadily increasing demand for services at emergency departments (ED).1–4 A small percentage of patients (1-8%) account for a large percentage of ED visits per year (8.5-28%).1,4-6 These patients, who are commonly referred to as “frequent attenders” (FA) are defined by the number of their visits and definitions range from 3-12 ED visits per year.1,4 Although this patient group was identified and described decades ago,7 to date there are no effective interventions that reduce the frequency of their ED visits.6\n\nFA consist of a heterogenic group of patients. Their demographics, their diseases, and their social conditions vary significantly. Thus, the group is not easily described.8 While it is claimed that some FA visit the ED for non-emergency care, several studies reveal FA are a vulnerable group with a verifiably increased risk of mortality.9 Previous studies have described FA as somewhat older and more likely to seek ED care in non-daytime hours than non-FA.5,10,11 Poverty, homelessness, chronic disease, mental disorders, and drug and alcohol misuse are characteristics more often associated with FA than with non-FA.8,10,12,13\n\nA general assumption is that health care services do not sufficiently meet the medical and social needs of FA.1,4,6 Given this situation, plus the increasing pressure on limited ED resources from frequent attendance, a solution is needed that can address the needs of this group and the demands on the health care system.1,4,6,10,11,13,14 Numerous attempts have been made to solve this problem. These attempts include interventions such as case management, patient education, management care plans, social interventions, and health care centres. However, these attempts have not had a major effect in reducing the number of ED visits by FA.4,6,12 One explanation for this failure may be that these interventions are only initiated after ED patients are identified as FA. Possibly the interventions might be more successful if patients were identified as likely FA earlier in the identification phase.\n\nFurthermore, very little scientific data exist on FA in Swedish emergency departments and the few publication that exist on frequent attendance focus on primary health care.15 The Swedish health care and social system differs significantly from many of those countries studying FA (e.g. USA, United Kingdom etc.) and therefore it is of interest to investigate if the experiences of FA are similar in a Swedish emergency department compared to that reported internationally.\n\nThe aim of this study was to identify and characterise FA and to create and validate a prediction model to find FA by using electronic medical record software in an emergency department in Sweden.\n\n\nMethods\n\nThe Stockholm Regional Ethics Review Board approved this research (D. nr 2017/1695-31/2). There was no requirement to obtain patient consent set by the ethical committee.\n\nThe patients in the study were adults (≥18 years) who had visited the ED at Norrtälje Hospital, Sweden, during 2015. The patients’ initial visit during 2015 was used for inclusion and therefore labelled the “inclusion visit” [Figure 1]. This visit, which was used for patient selection only, was not included in the analysis. A study period of 12 months was chosen for each included patient. This individual 12-month observational period was defined by tracking a 12-month period before and after the inclusion visit in such a way that a maximum number of visits were included during a 12-month period [Figure 1]. Patients with four or more ED visits during this 12-month period were identified as FA and patients with three or fewer ED visits were identified as controls. The first visit (at the beginning of the 12-month observational period) was labelled the “first visit”, the second visit was labelled the “second visit”, etc. The purpose of this inclusion process was to observe and compare each individual patient in the same way instead of basing the observational period on calendar time only. The cut of value of four visits or more was chosen prospectively based on previous studies.\n\nThis is a retrospective observational register study. The medical record system – Take Care (TC) at Norrtälje Hospital (Sweden) – was used to identify patients. We identified patients by their personal identity numbers (encrypted before the analysis). The data variables from the first visit were age, gender, number of ED visits in the 12-month observational period, number of outpatient care visits, sheltered living (care facility or not), and enrolment at a health care centre. The data variables from the first visit and (if applicable) from the second visit were ED visit date and time, ED transport, triage priority, main complaint, ED care unit (medicine/surgery/orthopaedic), medication number/type, and ICD-10 diagnosis at discharge (if hospitalised).\n\nPhysical findings recorded for the patients were blood pressure (mmHg), heart rate (beats per minute/bpm), temperature (°C), peripheral oxygen saturation (%), height (cm), weight (kg). Laboratory statistics recorded for the patients were haemoglobin g/L (Hb), thrombocyte particle concentration ×109/L (TPK), leukocyte particle concentration ×1012/L (LPK), creatinine (μmol/L), glucose (mmol/L), C-reactive protein (mg/L) (CRP), sodium (mmol/L), potassium (mmol/L), bilirubin (μmole/L), aspartate aminotransferase (μkat/L) (ASAT), alanine aminotransferase (μkat/L) (ALAT), alkaline phosphatase (μkat/L) (ALP), lactate dehydrogenase (μkat/L) (LD), albumin (g/L). Information on previous contact with psychiatric departments and death within one year following the first visit was also collected.\n\nThese data were chosen because they were easily available to extract from the electronic medical record software and were thought to be clinically relevant in the light of previous studies.\n\nThe Norrtälje Municipality is approximately seventy kilometres from Stockholm, Sweden. The Municipality has a total area of 6030.42 km2 with a population of 61 864 inhabitants (2019). One-third of the Municipality's inhabitants (20 721 inhabitants, 2018) live in the central town. The surrounding rural area is sparsely inhabited. The Municipality is a somewhat deprived socioeconomic area (compared to many other areas in Sweden). The average yearly income and the average education level are below national averages.16,17 Norrtälje Hospital is a small hospital that serves the Municipality and its environs. The Hospital, which has specialist clinics and four wards with 96 beds, is integrated with local primary health care in a way that the both the hospital and the primary health care are within the same organisation with the same management and board. The health care is publicly funded, requires no health insurance and the nearest next emergency department which also is of a higher level, is 60 km away. Attendance to the emergency department does not require referral and can be done at the initiative of the patient. The emergency department treats approximately 20 000 patients yearly.\n\nThe Statistical Package for Social Sciences, SPSS Version 25.0 (IBM SPSS Statistics, RRID:SCR_019096) was used for the statistical analysis. The data was randomly split into two equally large samples where the first was used for analysis (training set) and the second for validation (validation set).\n\nAll variables were summarized using standard descriptive statistics such as frequency, mean and standard deviation. Group differences between the categorical variables (e.g., gender, weekday of the first visit, death within one year after the first visit) were analysed using Pearson's chi-square method. Group differences between the continuous variables (e.g., age) were analysed using Student's t-test for independent groups. The significance level in all analyses was 5 % (two-tailed). If a variable was severely skewed (skewness above 1.5 as for length of hospital stay and for the number of pharmaceutical drugs), a non-parametric Mann-Whitney U test was conducted. The model was created using logistic regression analysis on complete cases on the training set on the relationships between group (FA – “Yes”/”No”) and the identified risk variables. After the model was defined, a predicted risk score for each patient was recorded in both the training set and the validation set. The risk score of the training set and validation set was then used in a Receiver Operating Characteristic (ROC) analysis comparing these two and the sensitivity and specificity determined.\n\n\nResults\n\nIn total 13,193 patients were included in the study and randomly split into two groups of 6635 patients (training set) and 6558 patients (validation set). In the training set 15.3% (n = 1012) were classified as FA and 15.4% (n = 1011) were placed in the control group as non-FA. Significant differences between the two groups were found in the following variables: age, sheltered living, number of outpatient care visits, number of outpatient care physician visits, ED arrival by ambulance or helicopter, triage priority, weekday of the first visit, length of hospital stay, previous contact with a psychiatric department, and one-year survival after the first visit [Table 1]. No significant differences were found between gender and time of visit [Table 1].\n\nOn average, FA compared to non-FA were older (65.3 years vs 54.5 years), made more outpatient care visits (27.2 visits vs 9.0 visits) and more physician visits (15.5 visits vs 4.9 visits), and had a lower survival rate within one year after the first visit (75.5% survival rate vs 92.2% survival rate). The ED arrival rate by ambulance or helicopter was higher for the FA than for the non-FA (28.3% of arrivals vs 17.5% of arrivals). The FA also had a higher triage priority and made more visits on a weekday (74.8% of visits vs 71.1% of visits). FA also had longer lengths of hospital stays (7.9 days vs 1.1 days) and had a higher rate of previous contact with psychiatric departments (21.8% of contacts vs 10.7% of contacts).\n\nGroup comparisons of laboratory and physical findings revealed significant patient group differences in creatinine, potassium, haemoglobin, and glucose [Extended data – Table 1]. Significant differences were found between the groups for systolic blood pressure, saturation and thrombocytes, but these differences, although significant, applied to only a few patients. Approximately 50 % of the laboratory findings and approximately 20 % of the physical findings were missing in the entire study population. We were therefore unable to use these variables in the analysis. Therefore, they are only briefly presented in the supplementary material [Extended data – Table 1].\n\nMultivariable logistic regression found the following variables posed a risk to patients of becoming a FA [Figure 2]; age above 60 years OR 1.52 [CI 1.27 – 1.82], ED arrival by ambulance or helicopter on the first visit OR 1.31 [CI 1.08 – 1.58], sheltered living OR 3.82 [CI 2.37 – 6.17], previous contact with psychiatric department OR 1.52 [CI 1.23 – 1.89], 10 outpatient care visits or more in the observational period OR 4.81 [CI 3.81 – 6.08], 10 outpatient care physician visits or more in the observational period OR 3.94 [CI 3.25 – 4.78].\n\nData from the multivariable logistic regression was used to perform a ROC curve analysis which resulted in an AUC of 0.841 [CI 0.828-0.854] for the training set and an AUC of 0.849 [CI 0.836-0.861] for the validation set [Figure 3] indicating a good model. The ROC curve was then used to find the optimal cut of value and resulted in a sensitivity of 44.5% and a specificity of 91.9% with a positive predictive value of 44.5% and negative predictive value of 91.9%.\n\n\nDiscussion\n\nTo our knowledge this is the first time readily available electronic medical record data has been used to identify and characterize FA and to create a FA prediction model. Our study shows that these data, which can be obtained technologically using electronic medical record software, can be used to predict ED patients’ risk of becoming FA.\n\nWe found that the variables that most closely correlated with FA status were the following: age above 60 years, ED arrival by ambulance or helicopter, sheltered living, previous contact with psychiatric department, 10 or more outpatient care visits and 10 or more outpatient care visits at physician. This model resulted in an AUC of 0.849 [CI 0.836-0.861] when validated in an independent sample.\n\nThe sensitivity and specificity of the model can be adjusted according to the needs the purpose of the model. In our case we aim to use the model for early identification of potential FA and target them with an intervention with low risk of harm. In such case false negative cases are of less importance. However, too many false cases will result in extra work and make the intervention more difficult to accomplish. Furthermore, it is of importance that we correctly identify enough future FA, so an intervention makes a clinical difference. Therefore, we finally settled with a sensitivity of 44.5% and a specificity of 91.9%. Although the sensitivity is low and many FA will be missed, there will be enough correctly identified for an intervention without including too many false positive.\n\nMany studies have described ED FA as a heterogenous group.9 Studies also associate older age, poorer physical and mental health, and greater social vulnerability with these patients.8–13 These studies are performed in health care and social systems that differ from the Swedish. Still, our study confirms these findings. We found that the FA (compared to the control group) were older, were in a worse physical health state, had a higher mortality rate, arrived at the ED more often by ambulance or helicopter, had more deranged blood sample values and physical parameters, had been in contact with the psychiatric department more often, and had been hospitalized for more days.\n\nIn confirmation of other research, we found that the FA are recurrent visitors at most health care system levels.18 We found very high usage of outpatient care among the FA – 27 vs 9 outpatient care visits/year – and the highest OR for frequent attendance. With this descriptive model of FA, we can better identify them at early ED visits, provide better care for them by combining hospital and outpatient care resources, and perhaps reduce the number of their ED visits.\n\nSeveral interventions have been tested that are designed to address the needs of FA. These interventions have had little success.6 The most promising intervention is perhaps “case management,” which has sometimes reduced the number of ED visits. We think the results from our study may be used to identify FA at early care stages and easier randomize FA to comparable interventions.\n\nWe acknowledge there is a difficulty in generalizing our findings (certainly beyond Sweden's national boundaries) because we use data only from one small Swedish hospital. In any case, it is challenging to draw generalizations in an international dimension regarding FA and to make comparisons among FA studies. Health care/social systems, emergency care, and populations vary greatly – country to country.19–21 The burden of disease (both physical and mental) in the ED also differ among countries.22 Nonetheless we believe that our method and findings can be of interest to the scientific community and add to the general knowledge.\n\nOur study sample was drawn from ED patients only at Norrtälje Hospital during a relatively brief time period (one year) which makes the results difficult to generalize. Nonetheless we believe that our method and findings can be of interest to the scientific community and add to the general knowledge. We may also have underestimated the number of FA as patients in the control group may have sought emergency health care at another caregiver which we would have missed. The nearest emergency department is 60 km away and requires therefore a certain effort from the patient to visit. We therefore estimate this to be a smaller group and not conflict significantly with the results. Furthermore, the definition of when a patient does his or her first visit at the ED is also very difficult to define. Our analysis was based on this first visit with the ambition of finding FA as early as possible. Even though we cannot say that we have correctly identified the first ED visit for the patients, we still believe our model of defining the first visit is a better way of finding FA at an earlier stage compared to only looking at a calendar year.\n\n\nConclusion\n\nOur research finds that frequent attendance at the ED may be predicted by the following variables: age above 60 years, ED arrival by ambulance or helicopter, sheltered living, previous contact with psychiatric department, 10 or more outpatient care visits and 10 or more outpatient care visits at physician. These patient variables collectively observed in the first ED visit resulted in a good model with an AUC of 0.849 [CI 0,836-0,861] in the validation sample.\n\n\nData availability statement\n\nWe want to do our utmost to contribute to the scientific community by sharing data and being transparent. We are however unable to give our raw underlying data fully and unconditionally to anyone as we have asked and received permission to this data with condition of it being used for our publication purpose only and presented in an aggregated form. Moreover, our raw data contains several detailed variables and although the data is pseudonymized, if combined with other databases we see a risk of individuals being identified.\n\nWe therefore need to restrict our data sharing. However, if request is made for our data for scientific purpose in line with our research question, we commit to providing our raw data. This is done by a contacting the corresponding author at lis.abazi@.ki.se and a reply will be given at the latest within a month.\n\nOpen Science Framework: Developing and validating a prediction model for frequent attenders at a Swedish emergency department using an electronic medical record system, a retrospective observational study. https://doi.org/10.17605/OSF.IO/BK6S4.23\n\nThis project contains the following underlying data:\n\n• Extended data table 1.docx (supplemental table with laboratory results)\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\nLaCalle E, Rabin E: Frequent users of emergency departments: the myths, the data, and the policy implications. Ann Emerg Med. 2010; 56(1): 42–8. [published Online First: 2010/03/30]. PubMed Abstract | Publisher Full Text\n\nPines JM, Hilton JA, Weber EJ, et al.: International perspectives on emergency department crowding. Acad Emerg Med. 2011; 18(12): 1358–70. [published Online First: 2011/12/16]. PubMed Abstract | Publisher Full Text\n\nWilliams ER, Guthrie E, Mackway-Jones K, et al.: Psychiatric status, somatisation, and health care utilization of frequent attenders at the emergency department: a comparison with routine attenders. J Psychosom Res. 2001; 50(3): 161–7. [published Online First: 2001/04/24]. PubMed Abstract | Publisher Full Text\n\nOlsson M: Akutmottagningens mångbesökare: hur kan vården förbättras?. Stockholm: Forum för kunskap och gemensam utveckling, Stockholms läns landsting; 2006.\n\nMoore L, Deehan A, Seed P, et al.: Characteristics of frequent attenders in an emergency department: analysis of 1-year attendance data. Emerg Med J. 2009; 26(4): 263–7. [published Online First: 2009/03/25]. PubMed Abstract | Publisher Full Text\n\nSoril LJ, Leggett LE, Lorenzetti DL, et al.: Reducing frequent visits to the emergency department: a systematic review of interventions. PLoS One. 2015; 10(4): e0123660. [published Online First: 2015/04/16]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndren KG, Rosenqvist U: Heavy users of an emergency department: psycho-social and medical characteristics, other health care contacts and the effect of a hospital social worker intervention. Soc Sci Med. 1985; 21(7): 761–70. [published Online First: 1985/01/01]. PubMed Abstract | Publisher Full Text\n\nJacob R, Wong ML, Hayhurst C, et al.: Designing services for frequent attenders to the emergency department: a characterisation of this population to inform service design. Clin Med (Lond). 2016; 16(4): 325–9. [published Online First: 2016/08/03]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoe J, Kirkland S, Ospina MB, et al.: Mortality, admission rates and outpatient use among frequent users of emergency departments: a systematic review. Emerg Med J. 2016; 33(3): 230–6. [published Online First: 2015/05/09]. PubMed Abstract | Publisher Full Text\n\nBoh C, Li H, Finkelstein E, et al.: Factors Contributing to Inappropriate Visits of Frequent Attenders and Their Economic Effects at an Emergency Department in Singapore. Acad Emerg Med. 2015; 22(9): 1025–33. [published Online First: 2015/08/19]. PubMed Abstract | Publisher Full Text\n\nLocker TE, Baston S, Mason SM, et al.: Defining frequent use of an urban emergency department. Emerg Med J. 2007; 24(6): 398–401. [published Online First: 2007/05/22]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPhillips GA, Brophy DS, Weiland TJ, et al.: The effect of multidisciplinary case management on selected outcomes for frequent attenders at an emergency department. Med J Aust. 2006; 184(12): 602–6. [published Online First: 2006/06/29]. PubMed Abstract | Publisher Full Text\n\nWooden MD, Air TM, Schrader GD, et al.: Frequent attenders with mental disorders at a general hospital emergency department. Emerg Med Australas. 2009; 21(3): 191–5. [published Online First: 2009/06/17]. PubMed Abstract | Publisher Full Text\n\nSkinner J, Carter L, Haxton C: Case management of patients who frequently present to a Scottish emergency department. Emerg Med J. 2009; 26(2): 103–5. [published Online First: 2009/01/24]. PubMed Abstract | Publisher Full Text\n\nStrombom Y, Magnusson P, Karlsson J, et al.: Health-related quality of life among frequent attenders in Swedish primary care: a cross-sectional observational study. BMJ open. 2019; 9(7): e026855. [published Online First: 2019/08/02]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIncome and tax statistics: Statistics Sweden: [cited 2019 2019-06-19]; accessed 2019-06-19 2019.Reference Source\n\nEducational attainment of the population: Statistics Sweden: [cited 2019 2019-06-19]; accessed 2019-06-19 2019.Reference Source\n\nHansagi H, Olsson M, Sjoberg S, et al.: Frequent use of the hospital emergency department is indicative of high use of other health care services. Ann Emerg Med. 2001; 37(6): 561–7. [published Online First: 2001/06/01]. PubMed Abstract | Publisher Full Text\n\nSchutte S, Acevedo PNM, Flahault A: Health systems around the world - a comparison of existing health system rankings. J Glob Health. 2018; 8(1): 010407. [published Online First: 2018/03/23]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRidic G, Gleason S, Ridic O: Comparisons of health care systems in the United States, Germany and Canada. Materia socio-medica. 2012; 24(2): 112–20. [published Online First: 2012/01/01]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnell A, Willis M: International comparison of health care systems using resource profiles. Bull World Health Organ. 2000; 78(6): 770–8. [published Online First: 2000/08/05]. PubMed Abstract | Free Full Text\n\nGlobal, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980-2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet. 2018; 392(10159): 1736–88. [published Online First: 2018/11/30]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbazi L: Developing and validating a prediction model for frequent attenders at a Swedish emergency department using an electronic medical record system, a retrospective observational study.2021, May 18. Publisher Full Text"
}
|
[
{
"id": "270992",
"date": "21 May 2024",
"name": "Jason Scott",
"expertise": [
"Reviewer Expertise Health and social care quality including specifically frequent use of emergency care services."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review this study. In its current form I cannot recommend indexing, specifically that it appears to be nearly a decade out of date in both the data used and the use of literature. More detailed comments are below:\n1. Literature used is outdated and not comprehensive. One example is the first sentence of the introduction, which refers to a (current) increasing demand for ED, yet cites studies published in 2001, 2006, 2010 and 2011.\n\n2. The problem of outdated literature continues with the statement that there are no effective interventions. This is highly contested; causes of frequent use are highly complex and people who frequently use services are heterogeneous, which likely contributes to mixed evidence around effectiveness. Take for instance people who frequently use ED due to poor mental health, a recent review by Gabet et al (2023) identified several interventions with promising evidence around effectiveness. Many other reviews since 2015 have similar results, though some highly anticipated interventions (Eg. hotspotting) have then shown to be ineffective (Finkelstein et al., 2020). The authors need to update the entire introduction and discussion using contemporary literature and with greater critical engagement of the wider evidence base, including the increasing qualitative evidence base around frequent use of other services that the authors themselves found contribute to ED use (Eg. ambulance services; Evans et al., 2024 – I disclose being a co-author so feel welcome to identify other relevant literature).\n\n3. Regardless of the issues around the literature, the premise that earlier identification of people at risk of becoming a frequent attender is valid and does not need changing.\n\n4. The data used in the study are from 2015, which is nearly a decade old. A lot has happened since then that has changed health systems throughout the world. Could the authors please comment on whether the data (and thus the study) is still relevant.\n\n5. The index visit was categorised as the first visit during the study period. Was any consideration given as to whether some of the patients may have been either long-standing or relatively new frequent attenders prior to the study period and how this was factored into the analysis. For instance, it may be that most people recruited into the study in month 1 were longer-standing frequent attenders, and subsequent months may have been newer frequent attenders, thus examining two different groups of people (we know there are almost certainly differences in characteristics between the groups).\n\n6. Frequent attenders were split into a training set and validation set. Were any analyses conducted to confirm that the two groups were similar, or was there a reliance on randomisation? It would also be helpful to describe, in the methods, how they were randomised.\n\n7. The authors state this is the first time routine data have been used to create a prediction model; this is absolutely not the case. Authors need to examine more recent literature on the topic. Notably, given my previous comment (5) around index visits, Chiu et al identified that the greatest predictor of frequent use was being a past frequent user.\n\n8. A comment in the discussion says that existing studies were conducted in health systems not comparable to the Swedish health system. It would be helpful if the authors could explain and unpick the differences.\nReferences Chiu, Y. M. et al (2023 [ref - 1]). Machine learning to improve frequent emergency department use prediction: a retrospective cohort study. Scientific Reports, 13(1), 1981.\nEvans, B. A. et al (2024 [ref - 2]). Experiences and views of people who frequently call emergency ambulance services: A qualitative study of UK service users. Health Expectations, 27(1), e13856.\nFinkelstein, A. et al (2020 [ref - 3]). Health care hotspotting—a randomized, controlled trial. New England Journal of Medicine, 382(2), 152-162.\nGabet, M. et al (2023 [ref - 4]). Effectiveness of emergency department based interventions for frequent users with mental health issues: A systematic review. The American Journal of Emergency Medicine, 74, 1-8.\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?\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? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-909
|
https://f1000research.com/articles/10-908/v1
|
09 Sep 21
|
{
"type": "Research Article",
"title": "Exploratory graph analysis of the network data of the Ethereum blockchain",
"authors": [
"Timothy Tzen Vun Yap",
"Ting Fong Ho",
"Hu Ng",
"Vik Tor Goh",
"Ting Fong Ho",
"Hu Ng",
"Vik Tor Goh"
],
"abstract": "Background: This research uses exploratory graph analysis to analyze the transaction data of the Ethereum network. This is achieved through network visualization and mathematical and statistical modelling of the network data. Methods: The dataset used in this study was extracted from the Ethereum in the BigQuery public dataset, specifically selected transactions in July 2019. The transactions were firstly modelled as network graphs and then visualized using the Kamada-Kawai and force-directed graphs layouts. Further modelling was explored with classical random graph and network block, with emphasis on network cohesion, hierarchical clustering and community membership. Results: Looking at the network visualization and hierarchical clustering of the data, the network shows 170 clusters, the largest having 135 members. Through random graph modelling the optimum number of clusters is shown to be 95. Referring to the generated dendrograms, notable large transactions center around the DRINK token, the Maximine Exchange, the Upbit2 Exchange and the IDEX Exchange, identified through public disclosure of their Ethereum addresses. The network graphs tend to go towards the DRINK smart contract and the Maximine Exchange, indicating deposit actions, while it is the opposite for the IDEX Exchange. Further analysis also shows a different number of communities than the expected number. Falling short of the expected 170 clusters, the model is not able to capture additional mechanism that may be present at the density and social interaction distribution level of the network. On the other hand, network block modelling shows only four major clusters out of the 170 expected clusters, an indication that the model is not able to capture the network sufficiently. Conclusions: The study was able to capture and model the interconnectedness of the system with its notion of elements, in this case, the transactions on the network.",
"keywords": [
"Ethereum",
"graph analysis",
"blockchain",
"network modelling"
],
"content": "Introduction\n\nA blockchain is a distributed and replicated data structure in which a linked chain of digital information known as a block, is stored as a public database or ledger. Each of the blocks in the chain may contain zero or more records of transactions or exchanges. If another exchange happens on the network, a copy of the transaction is added to the record of every member on the network.1\n\nBlockchain has several characteristics that make it so compelling. Firstly, blockchain is immutable. It cannot be corrupted, changed, or altered.2 A blockchain is also decentralized if it is a public one. There is no governing authority overseeing the network. In addition, information on the blockchain is cryptographically hashed, thus preserving privacy and integrity of the data that is stored.2 Ethereum is an open-source blockchain, known for its decentralized smart contract platform. It is programmable and allows for the fabrication and distribution of decentralized applications (DApps).3\n\nThis research investigates the transaction data of the Ethereum network, through a graph analysis approach. This is achieved through network visualization and mathematical and statistical modelling of the network data. The work presented here provides a targeted analysis of the Ethereum network, capturing the interconnectedness of the system with its notion of elements, in this case, the transactions on the network.\n\nSmall-world models were proposed by Watts et al.4 These creators were interested in the way that numerous networks in the genuine work show significant levels of clustering, yet with the little distance between most vertices. They recommended rather starting with a network graph with a cross-section structure, and afterward arbitrarily 'reworking' a little the level of the edges. Assuming we have many N vertices that are instigated on an intermittent style, each of the vertex joins its neighbors to their respective side.4\n\nBarabási et al. proposed a preferential attachment model for modeling networks.5 The more associated a vertex is, the more probable it is to get new connections. A vertex with a further extent has a more grounded capacity to get joins added to the network.6\n\nExponential random graph models (ERGMs) have relations to generalized linear models. However, the appropriate specification and fitting of exponential random graph models can be more unobtrusive than that of a standard generalized linear model. Furthermore, a significant part of the standard inferential foundation accessible for generalized linear models, based upon asymptotic approximations to fitting chi-square distributions, is not in the consideration for exponential random graph models.7\n\nStochastic block models (SBM) are a class of models in the statistical data analysis of the network or graph data, and they can be utilized to find or comprehend the structure and the latent of a network graph for clustering. This model will in general deliver a graph containing networks, subsets described by being associated with edge densities.7\n\nDataset\n\nThe dataset of transaction records of Ethereum was taken from the BigQuery public dataset (Ethereum in BigQuery).8 The attributes from_address and to_address will be used as nodes (vertices) and the relationship between them will be the edges of the nodes in this study. The attributes and their descriptions are shown in Table 1. In this exploratory study, only arbitrarily selected 1000 contiguous rows of transactions in July 2019 are considered.15\n\nSoftware for analysis\n\nThe analysis is performed in R version 4.0.2, utilising the igraph R package for network analysis. The source code used can be found at Zenodo.16\n\nNetwork graph\n\nA graph G=VE is a set of E of links (edges), a set V of nodes (vertices), and where components of E are unordered pairs uv of distinct vertices u,v∈V . The number of vertices Nv=Vand the number of edgesNe=V are also called the order and size of the graph G, respectively.7\n\nVisualizing the network\n\nTo visualize a large network having over 1000 vertex and edge attributes, few methods exist. Kamada, et al. proposed a technique to draw general graphs.9 This technique tends to be broadly utilized in the network structures that are managed by the system. The mathematical displacement between the node in the drawing can be identified by graph-theoretic displacement. The spring algorithm proposed by Kamada, et al. has good properties such as symmetric drawings, edge crossing with a relatively small number of edges, and isomorphic graphs with almost congruent drawings.9\n\nThe DrL method provides two-dimensional visualizations of exceptionally huge theoretical chart structures.10 The graph is drawn employing a force-directed algorithm based on recreated strengthening. This clustering is utilized to create a coarsened graph (less vertex) which is at that point redrawn. This handle is rehashed until an adequately small graph is produced.10\n\nCharactering network cohesion\n\nOne way to deal with characterizing the network cohesion of a specific network graph is through the identification of the subgraph of interest. The standard case is that of finished subgraphs and henceforth are subgroups of vertices that are completely strong, as in all vertices inside the subgroup are associated by edges. Large groups of subgraphs are considered rare in practice because they need the required network graph itself to be dense.7\n\ndⅇnH=EHVHVH−1∕2 is the general formula of the density of a subgraph H=VHEH, that the recurrence of acknowledged edges is comparative with possible edges, in an undirected graph G which has no self-loops and various edges. In the situation that if G is a directed graph, VHVH−1 will be replaced with the denominator of the equation above. The value of zero and one in denH is to justify how near the subgraph H is to be becoming a clique in the network.7\n\nIn graph clustering, the relative frequency also can be one of the methods to defining a cluster. The standard use of the term clustering coefficient normally means the quantityclTG=3τΔGτ3G , where τΔG is the number of triangles in the graph G, and τ3G is the number of connected triples. The value of clTG is the transitivity of the graph and is also referred to as the fraction of transitive triples A graph G is fully connected if each node is reachable from all other nodes, and that a graph’s connected component is a maximally connected subgraph.7\n\nHierarchical clustering\n\nVarious methods have been proposed for clustering, varying in essentially by the way they assess the nature of the proposed clustering and quality of the enhancement brought about by the algorithms.11 These strategies adopt a greedy strategy to looking through the states of all potential partitions C, through altering progressive applicant partitions iteratively.\n\nOne of the most popular measures is modularity.10 Let C=C1…Ck as a given candidate partition and define fij=fijC to be the fraction of edges in the original network that connect vertices in C1 with vertices in Cj. The modularity of C is the value modC=∑k=1kfkkC−fkk∗2, where fkk∗ is the expected value of fkk under some model of random edge assignment.10\n\nClassical random graph modelling\n\nGraph modelling refers to a collection ℙθG,G∈g:θ∈ω, where g is a collection of possible graphs, ℙθ is a probability distribution on g, and θ is a vector of parameters, ranging over possible values in ω. A collection g and a uniform probability ℙ· over g is usually used to refer to a random graph model.7 Erdos et al. established a series of the seminal paper on the classical theory of random graph models.8 Erdos et al.’s model specifies a collection of gNv,Ne of all graph G=VE with V=Nv and E=Ne, and assigns probability ℙG=NNe−1 to each G∈gNv,Ne, where N=Nv2 is the total number of distinct vertex pairs.8\n\nNetwork block models\n\nIn a random graph, G, let G=VE. The graph can be categorized into one of Q classes. Each element of the block model for a particular graph can be specified as each element of the adjacency matrix Y, labelled as q and r of vertices i and j, respectively, with a probability of Bernoulli random variable. Snijders, et al. introduced a parametric limit of the form.13\n\n\nResults and discussions\n\nThe network graph (Figure 1) shows a total number of 170 clusters among 1000 rows of data. The top three clusters inside the network graph consist of the size of 135 vertices, followed by 55 vertices, and 39 vertices. There are 103 clusters having a pair of vertices, that is the smallest cluster size in this network.\n\nThe Kamada-Kawai layout uses a combination of spring model and the technique local minimization of global energy.15 The graph is shown in Figure 2.\n\nClauset proposed a fast and greedy approach to optimization through an agglomerative type of hierarchical clustering algorithm.11 Figure 3 shows the outputs from the clustering, while Figure 4 shows the dendogram from the clustering. The clusters are the same as the ones shown from the network graph (Figure 1). There are also many two-member communities in this network, which may indicate disposable addresses after single use.\n\nLooking into the clusters, Figures 5 and 6 show the membership of the largest cluster, with 135 addresses. We notice that all the addresses point toward address 0x0089659f609933d16a5cd6c2be1a5dca1abe24ad. Looking at the Ethereum blockchain Explorer, Etherscan,14 the address belongs to the DrinkChain (DRINK) token.\n\nFigures 7 and 8 show the membership of the second-largest cluster which contains a total number of 55 addresses. Members of the clusters point toward the address 0x8e766f57f7d16ca50b4a0b90b88f6468a09b0439.\n\nThis address belongs to the token, Maximine Coin (MXM).\n\nFigures 9 and 10 show a cluster with 39 addresses, they all point to the address 0xBA826fEc90CEFdf6706858E5FbaFcb27A290Fbe0.\n\nThis address belongs to Upbit2, a digital asset exchange in South Korea. This cluster is most probably showing withdrawals as the network graphs are pointing out from the center.\n\nFigures 11 and 12 show a cluster with 20 addresses, they all point to the address 0x2a0c0DBEcC7E4D658f48E01e3fA353F44050c208.\n\nThis address belongs to IDEX, a decentralized exchange.\n\nFrom hierarchical clustering, it is shown there are 170 communities.\n\nTo examine this further, network modelling was considered. In this case, two assumptions were made. The first one, the same order of vertex and size, 800 and 1000 respectively, was maintained. The second is the same as the first, but with a fixed degree of sequence.\n\nIn random graph modelling, Monte Carlo methods were used to generate approximations quickly over 1000 trials. For each of the trials, community detection was employed. Figure 13 shows the number of communities. It is shown both assumptions detected 24 and 95 communities, respectively. This is nowhere close to the actual 170 number of communities. There could be additional mechanism at work which complicate the density and the social interaction distribution in modeling the network.\n\nFigure 14 shows the integrated conditional likelihood (ICL), with its corresponding classes Q. It is shown that the fitted model has 4 classes, which suggests a suitable latitude of 4 for this model.\n\nTo investigate further, we estimated the posterior probability of each of the class members. We noticed that the evidence for the class membership assignment shows a very strong relationship between vertices with a maximum posterior probability of 99%. From the reorganized adjacency matrix (Figure 15), 0.57894737 and 0.38596491 will be the larger proportions and the rest the smaller class proportions.\n\nFigure 16 shows the visual summary of the class connection probabilities and the concordance of the 4 classes. Falling short of the expected 170 clusters, the modelling effort was not able to capture additional mechanism that may be present at the density and social interaction distribution level of the network.\n\n\nConclusions\n\nThe paper presented a targeted analysis of the Ethereum network, capturing the interconnectedness of the system with its notion of elements, in this case, the transactions on the network. The study takes into account only selected transactions in July 2019, which may not be generally representative of the Ethereum network. This will be addressed in future work.\n\n\nData availability\n\nZenodo: Extracted Ethereum transactions for July 2019 from the Ethereum in BigQuery public dataset. https://doi.org/10.5281/zenodo.5263166.15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAnalysis code available from: https://github.com/tzenvun/exploratory-network-eth.\n\nArchived analysis code as at time of publication: https://doi.org/10.5281/zenodo.5336085.16\n\nLicense: GNU General Public License v3.0.",
"appendix": "References\n\nReiff N: 2020, February 1. Reference Source\n\nAnwar H: 6 key blockchain features you need to know about. 101blockchians. 2018, May 24. Reference Source\n\nFrankenfield J: Ethereum.2020, June 27; Retrieved from Investopedia. Reference Source\n\nWatts DJ: Collective dynamics of 'small-world' networks.1998; 440–442.\n\nBarabási AL, Albert R: Emergence of scaling in random networks. science. 1999; 286(5439), 509–512. Publisher Full Text\n\nJain AK, Murty MN, Flynn PJ: Data clustering: a review. ACM computing surveys (CSUR) . 1999; 31(3): 264–323. Publisher Full Text\n\nKolaczyk ED, Csárdi G: Statistical analysis of network data with R . New York: Springer; 2014.\n\nGoogle Cloud: 2021, June 28; Retrieved from Ethereum in BigQuery - a Public Dataset for smart contract analytics. Reference Source\n\nKamada T, Kawai S: An algorithm for drawing general undirected graphs. Information processing. 1989.\n\nMartin SB: Dr.L: Distributed Recursive (Graph) Layout. Computer software. 2007.\n\nClauset A: Finding local community structure in networks. Physical review E. 2005; 72(2): 026132. PubMed Abstract | Publisher Full Text\n\nErdos P, Rényi A: On the evolution of random graphs. Publ. Math. Inst. Hung. Acad. Sci . 1960; 5(1): 17–60. Publisher Full Text\n\nSnijders TA, Pattison PE, Robins GL, et al.: New specifications for exponential random graph models. Sociological Methodol . 2006; 36(1): 99–153. Publisher Full Text\n\nEtherscan: 2021, June 28. Retrieved from Etherscan. Reference Source\n\nYap, Timothy TV, Ho: Extracted Ethereum transactions for July 2019 from the Ethereum in BigQuery public dataset [Data set]. Zenodo. 2021. Publisher Full Text\n\ntzenvun: tzenvun/exploratory-network-eth: First release (v1.0.0). Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "121271",
"date": "04 Mar 2022",
"name": "Barbara Guidi",
"expertise": [
"Reviewer Expertise Blockchain",
"Peer to Peer Systems",
"Social Media"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper proposes a graph analysis of the Ethereum blockchain. The paper could be interesting but the main issue is the size of the dataset, and its age - the data are too old. It is not clear why the authors used only 1000 transactions from 2019. This can not be useful nowadays, considering the huge amount of analysis provided on the Ethereum blockchain, such as: Temporal Analysis of the Entire Ethereum Blockchain Network, only to mention an example.1\nFor this reason, the paper can not be approved. The authors can can try to execute all the analyses on an up to date dataset, which contains millions of transactions. Only after these analyses can we try to analyse if the findings are interesting or not.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "274737",
"date": "21 May 2024",
"name": "Satpal Singh Kushwaha",
"expertise": [
"Reviewer Expertise Blockchain Technology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper titled \"Exploratory Graph Analysis of the Network Data of the Ethereum Blockchain [version 1; peer review: 1 not approved]\" presents some notable findings; however, there are significant issues with the dataset and references that undermine the credibility of the research.\nOutdated Dataset: The dataset used for evaluation is five years old. This significantly impacts the relevance and uniqueness of the research, given the rapidly evolving nature of blockchain technology and the Ethereum network in particular. Outdated References: The references cited in the paper are outdated, with no recent works included. This suggests a lack of engagement with the latest advancements and discussions in the field, which is critical for contextualizing the current study within the broader research landscape. Limited Literature Review: The related work section is sparse and does not adequately cover the breadth of existing literature. A comprehensive review of related studies is essential to situate the research within the ongoing scholarly conversation and to highlight its contributions and distinctions. Lack of Future Scope and Challenges: The paper fails to discuss future research directions and the challenges faced. This is a significant omission as it limits the paper’s usefulness for guiding subsequent research and for understanding the broader implications and limitations of the study.\nGiven these critical issues, the paper, in its current form, cannot be accepted. It is recommended that the authors update their dataset, incorporate recent references, expand the related work section, and include a discussion on future research directions and challenges.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-908
|
https://f1000research.com/articles/10-907/v1
|
09 Sep 21
|
{
"type": "Research Article",
"title": "Improving the support for XML dynamic updates using a hybridization labeling scheme (ORD-GAP)",
"authors": [
"Su-Cheng Haw",
"Aisyah Amin",
"Chee-Onn Wong",
"Samini Subramaniam",
"Aisyah Amin",
"Chee-Onn Wong",
"Samini Subramaniam"
],
"abstract": "Background: As the standard for the exchange of data over the World Wide Web, it is important to ensure that the eXtensible Markup Language (XML) database is capable of supporting not only efficient query processing but also capable of enduring frequent data update operations over the dynamic changes of Web content. Most of the existing XML annotation is based on a labeling scheme to identify each hierarchical position of the XML nodes. This computation is costly as any updates will cause the whole XML tree to be re-labelled. This impact can be observed on large datasets. Therefore, a robust labeling scheme that avoids re-labeling is crucial. Method: Here, we present ORD-GAP (named after Order Gap), a robust and persistent XML labeling scheme that supports dynamic updates. ORD-GAP assigns unique identifiers with gaps in-between XML nodes, which could easily identify the level, Parent-Child (P-C), Ancestor-Descendant (A-D) and sibling relationship. ORD-GAP adopts the OrdPath labeling scheme for any future insertion. Results: We demonstrate that ORD-GAP is robust enough for dynamic updates, and have implemented it in three use cases: (i) left-most, (ii) in-between and (iii) right-most insertion. Experimental evaluations on DBLP dataset demonstrated that ORD-GAP outperformed existing approaches such as ORDPath and ME Labeling concerning database storage size, data loading time and query retrieval. On average, ORD-GAP has the best storing and query retrieval time. Conclusion: The main contributions of this paper are: (i) A robust labeling scheme named ORD-GAP that assigns certain gap between each node to support future insertion, and (ii) An efficient mapping scheme, which built upon ORD-GAP labeling scheme to transform XML into RDB effectively.",
"keywords": [
"XML-RDB mapping",
"mapping scheme",
"XML databases",
"dynamic updates",
"XML labeling scheme."
],
"content": "Introduction\n\nExtensible Markup Language (XML) was introduced in the 1990s by the World Wide Web Consortium (W3C) to be the standard for information exchange as it is self-descriptive. Similar to Hypertext Markup Language (HTML), XML is a tag-based syntax, yet, XML can represent data within its context and is readable by machines and humans as it utilizes a natural language.1,2 Since the emergence of XML, many approaches to map XML into Relational DataBase (RDB) have existed.3,4\n\nDynamic Prefix-based Labeling Scheme (DPLS)5 extended the Dewey scheme6,7 and is based on a two stage approach: (i) constructing the initial DPLS labeling and (ii) handling any updates. Alsubai and North8 proposed a Child Prime Label (CPL) based on the prime number on the XML tree. The trees are traversed and annotated with labels (start, end, level, CPL) based on depth-first traversals. Research by Khanjari and Gaeini9 proposed the FibLSS encoding scheme, which uses binary bit values (0 and 1) to assign node labels. The authors conducted experimental evaluations of their approach against Improved Binary String Labeling (IBSL),10 which indicated that FibLSS is capable of supporting insertion without the need for relabeling.\n\nMore recently, Taktek and Thakker11 introduced the Pentagonal Scheme, a dynamic XML labeling scheme. Their algorithms support dynamic updates without redundant labels or relabeling needed. Their evaluations showed that the Pentagonal Scheme can handle several insertions yet showed a better initial labeling time as compared to some existing schemes, especially on large XML datasets. Azzedin et al.12 proposed the RLP-Scheme, which enriched Dewey labeling6 with more information. With the RLP-Scheme, an ancestor node can be computed easily, yet the storage space and central processing unit time can be minimised for XML with many identical sub-trees.\n\nIn the literature, most of the existing approaches support only static query processing by assuming that the structural information will not have any changes over time.13 This situation is impractical as the data exchanged over the Web is subject to very frequent updates. Due to this reason, we propose a mapping scheme called ORD-GAP that can support updates dynamically. Updates and delete operations are simple as they will not change the existing labeling, thus, the focus of this paper is on the insert operation as insertion will generate new or modify existing labeling.\n\n\nMethods\n\nFigure 1 depicts the architecture diagram of our proposed approach. Our proposed approach consists of the three main components, namely, XML parser, XML Encoder, and XML Mapper. The XML document is the input, while the output will be stored into RDB. The XML parser is responsible for validating XML to ensure it is well-formed before any processing takes place. The XML Encoder annotates the XML tree via a labeling scheme so that the structural relationships among the XML nodes can be identified easily even upon transformation into other underlying storage. Subsequently, the XML Mapper maps or transforms the annotated XML tree into RDB storage. Subsequently, for query retrieval, it will be issued via Structure Query Language (SQL).\n\nTree annotation of the proposed method includes both labeling and mapping schemes that work together to transform the XML tree into RDB storage. This approach adopted the node indexing of range labeling and prefix-based labeling as the initial annotation. Subsequently, we adopted the ORDPath14 labeling scheme for any dynamic update operations. Henceforth, the proposed approach is named as ORD-GAP.\n\nThis labeling is in the format of (s-e)l. The s denotes the start range while the e denotes the end range. The l expresses the level of each node position. These values for s and e are generated based on the gap g. The value g is calculated based on the formula: g= Σ (maxfan-out+maxdepth).\n\nFigure 2 illustrates the snippet view of the SIGMOD Record dataset15 labelled with the ORD-GAP scheme. This dataset is commonly used for benchmarking purpose. It was chosen as it contains various fan-outs (number of children each node has) and many levels to better demonstrate how our proposed approach works. Firstly, we need to find out the value for g, whereby we need to know the maxfan-out and maxdepth From the dataset, we observed that the maximum fan-out and maximum level is 4 and 6 respectively. As such, the gap value calculated by our algorithm (see Figure 3(a)) is 10. The root will always start with s as 1. The value of the following node is allocated from the gap value and the previous node’s value. In this case, since the gap is 10 and the value on the previous node’s is 1 (the root node), so, the node “issue” is assigned with 11 and tailed by node “author” with 21 for the s. The e value on node tree will be assigned once the s has reached the leaf node. In this case, if the s label is 31 and is a leaf node, then the e label will be assigned with 41 (by adding the s value with the gap value, such as 31+11), followed by the node “issue” with 51 as the e.\n\nFigure 3 shows the pseudocode for ORD-GAP. Figure 3(a) shows the calculation of g which is formulated based on Σ (maxfan-out + maxdepth) of the tree while Figure 3(b) shows the algorithm to assign a label. In Function GetGap, parent node and next level of current node is an input used to obtain g. The maxfan-out is the maximum number of child while maxdepth is the deepest level of the tree.\n\nMapping schemes of ORG-GAP contain two tables to map the XML data in RDB. The two tables are internal table and text table. The internal table is called iTable, which is used for storing the node that does not contain a text value. A text table is called tTable, and is used to store the leaf nodes. The attributes of both tables consists of Start, End, Level, PStart, Value; Start node keeps the s value of node, End node keeps the e value of node, and Level node keeps the depth of a node from the root. Tables 1 and 2 are the partial view of iTable and tTable based on outcome after the labeling scheme (see Figure 2).\n\nORD-GAP supports all structural relationships which are level, P-C, A-D and sibling. A-D relationship is determined based on the following conditions:\n\n\n\n• if (A(s) < D(s) < A(e)) and (D (level) – A (level) > 1).\n\nExample: Let node1 be volume (21-51)2 and node2 be SigmodRecord (1-811)0, (SigmodRecord (1) < volume (21) < SigmodRecord (811) and volume (2) – SigmodRecord (0) > 1). As such, node1 and node2 has A-D relationship.\n\nFor P-C relationship, it is determined based on the following conditions:\n\n\n\n• if (P(s) < C(s) < P(e)) and (C (level) – P (level) = 1)\n\n• Pstart for C == Start for P (Mapping Scheme)\n\nThe level difference should be equal to one since the parent would be only one level higher than the child. Another condition is the PStart value should be equal to P value.\n\nExample: Let node1 be article (111-341)3 and node2 be authors (241-331)4, (article (111) < authors (241) < article (341) and authors (4) – article (3)=1). As such, node1 and node2 have P-C relationship.\n\nLastly for Siblings, if the nodes have the same PStart from the table, they are siblings.\n\nExample: Let node1 be endPage (201-231)4 and node2 be authors (241-331)4. From iTable, both have PStart ‘6’. As such, node1 is a sibling of node2.\n\n\nResults\n\nThe dynamic update of ORD-GAP was adapted from the ORDPath.14 ORDPath encodes the P-C relationship by extending the parent's ORDPath label with a component for the child. However, in ORDPath, the even number is reserved for further node insertions. Generally, this approach is good as all four relationships could be determined easily. However, we observed that the label size grows uncontrollable with the growth of the tree. Henceforth, it may not be scalable for a huge dataset. Yet, we observed that dynamic insertion is not as huge as compared to initial tree labeling. This motivated us to use ORDPath labeling to support the insertion updates, while keeping ORD-GAP as the initial tree labeling.\n\nThe insertion consists of left-most, right-most and in-between insertion. Each insertion includes an additional node known as medium node which represents the insertion of dynamic update. Thus, this method creates an unlimited insertion on XML tree which avoids node relabeling.\n\nFigure 4 shows dynamic updates of left-most, in-between, and right-most insertion. The nodes represent the left-most insertion (21.1), in-between insertion (641.1), and right-most insertion (831.1). The insertion contains internal node and leaf node that will be mapped in the iTable (internal table) and tTtable (leaf node) as depicted in Tables 3 and 4, respectively.\n\nWe have implemented ORD-GAP using Java Development Kit (JDK) 8.0.510.16 on Netbean IDE 8.0.2 compile. Experimental evaluations were conducted to measure the performance of ORD-GAP as compared to ORDPath14 and ME Labeling16 approaches. These two existing approaches were taken for comparison because the technique does not require node re-labeling.\n\nIn the first part of the evaluation, the XML document is stored and transformed into RDB storage. The data insertion time and database storage size are recorded for all three approaches. After the storage is completed, we performed query retrieval to measure the performance of ORD-GAP, ORDPath and ME Labeling.\n\nLastly, our proposed approach ORD-GAP is put into evaluation to test for the dynamic update operations. All the experiments are performed on i7-3770 @3.4 processor with 16GB of RAM running on Windows 7. In the subsequence evaluations, we used the DBLP dataset17 to demonstrate the possibility of supporting larger dataset.\n\nIn this evaluation, insertion time was recorded four times. We discarded the first reading to omit the buffering effect for consistency of execution time. The results recorded are the average time of the three consecutive times. Table 5 shows the insertion time of ORD-GAP, ORDPath14 and ME labeling.16 ORD-GAP is the fastest followed by ME Labeling and ORDPath.\n\nDatabase storage consumption was evaluated to determine the storage space using ORD-GAP, ORDPath and ME Labeling approaches. From our experimental observation (see Table 6), we observed that ME Labeling requires higher storage space volume as compared to ORD-GAP and ORDPath due to the larger labeling size required as the depth of the XML tree increases.\n\nAs depicted, ORD-GAP reserved a gap between nodes, which delaying the initial node labelling, as ORD-GAP requires some calculation on retrieving the initial nodes. While ORDPath uses dot separated component byte-by-byte, that assigning node label is taken from the parent’s nodes toward the depth of XML tree. Whereas ME Labeling uses multiplication that causes the increases of size labels. The multiplication requires more time on the computation as the size label increase. Thus, both ORDPath and ME Labeling take less time for node labeling.\n\nTable 7 displays the query node in tree representation and XPath notation for each query.\n\nFigure 5 shows the query execution performance on various approaches. ORD-GAP is leading, followed by ME labeling and ORDPath. ORDPath require more time as compared to ORD-GAP and ME Labeling due to the number of elements in a node in DBLP. Although DBLP tree contains only three levels, it has multiple siblings in a node. Thus, the data model grows horizontally. ORDPath is prefix-based labeling that traverses using breadth-first search traversal. Likewise, ORDPath did not perform well. As the sibling’s node increases, the size label is increased. Hence, it requires more time to retrieve data in the database.\n\n\nConclusion\n\nIn this paper, we propose a labeling scheme named ORD-GAP that enables dynamic insertion by adopting ORDPath techniques. ORDPath generates unrestricted insertion of large XML trees. We carried out evaluations to compare ORD-GAP with ORDPath and ME Labeling. The performance of ORD-GAP was evaluated based on the database size, insertion, query retrieval and dynamic updates. We showed that ORD-GAP has a better performance than ORDPath and ME Labeling. However, we were not able to test ORD-GAP on a dataset size beyond 1.2GB due to hardware limitations such as hardware processor and available RAM.\n\nIn our future work, we will look into XML compression and optimization to ensure the further reduce the label size.\n\n\nData availability\n\nSIGMOD Record dataset available from: http://aiweb.cs.washington.edu/research/projects/xmltk/xmldata/www/repository.html#sigmod-record.15\n\nDBLP dataset available from:\n\nhttp://aiweb.cs.washington.edu/research/projects/xmltk/xmldata/www/repository.html#dblp.17",
"appendix": "References\n\nSingh P, Sachdeva S: A Landscape of XML Data from Analytics Perspective. Procedia Computer Science. 2020; 173: 392–402. Publisher Full Text\n\nBrahmia Z, Hamrouni H, Bouaziz R: XML data manipulation in conventional and temporal XML databases: A survey. Computer Science Rev. 2020; 36: 100231. Publisher Full Text\n\nSong E, Haw SC: XML-REG: Transforming XML Into Relational Using Hybrid-Based Mapping Approach. IEEE Access. 2020; 8: 177623–177639. Publisher Full Text\n\nOliveira A, Kohwalter T, Kalinowski M, et al.: XChange: A semantic diff approach for XML documents. Information Syst. 2020; 94: 101610. Publisher Full Text\n\nLiu J, Zhang XX: Dynamic labeling scheme for XML updates. Knowledge-Based Systems. 2016; 106: 135–149. Publisher Full Text\n\nTatarinov I, Viglas SD, Beyer K, et al.: Storing and querying ordered XML using a relational database system. ACM SIGMOD International conference on Management of data. 2020: 204–215. Publisher Full Text\n\nAl-khazraji S, North S: A relevance comparison between interval and prefix labeling schemes. IEEE International Conference on Engineering and Technology. 2017: 1–6. Publisher Full Text\n\nAlsubai S, North S: A Prime Number Approach to Matching an XML Twig Pattern including Parent-Child Edges. Int Conf Web Information Systems Technol. 2017: 204–211. Publisher Full Text\n\nKhanjari E, Gaeini L: A new effective method for labeling dynamic XML data. J Big Data. 2018; 5: 1–17. Publisher Full Text\n\nChemiavsky JC, Smith CH: A Binary String Approach for Updates in Dynamic Ordered XML Data. IEEE Transactions Knowledge Data Eng. 2010; 22: 602–607. Publisher Full Text\n\nTaktek E, Thakker D: Pentagonal scheme for dynamic XML prefix labeling. Knowledge-Based Syst. 2020; 209: 106446. Publisher Full Text\n\nAzzedin F, Mohammed S, Ghaleb M, et al.: Systematic Partitioning and Labeling XML Subtrees for Efficient Processing of XML Queries in IoT Environments. IEEE Access. 2020; 8: 61817–61833. Publisher Full Text\n\nFlorescu D, Kossmann D, Manolescu I: Integrating Keyword Search into XML Query Processing. Computer Networks. 2000, 33: 119–135.\n\nO’Neil P, O’Neil E, Pal S, et al.: ORDPATHS: Insert-Friendly XML Node Labels. ACM SIGMOD. 2004: 903–908. Publisher Full Text\n\nUniversity of Washington, XML Repository, Sigmod dataset. http://aiweb.cs.washington.edu/research/projects/xmltk/xmldata/www/repository.html#sigmod-record\n\nSamini S, Haw SC: ME Labeling: A Robust Hybrid Scheme for Dynamic Update in XML Databases. IEEE International Symposium Telecommunication Technologies. 2014: 126–131. Publisher Full Text\n\nUniversity of Washington, XML Repository, DBLP dataset. http://aiweb.cs.washington.edu/research/projects/xmltk/xmldata/www/repository.html#dblp"
}
|
[
{
"id": "93978",
"date": "21 Sep 2021",
"name": "Jiaheng Lu",
"expertise": [
"Reviewer Expertise Databases"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 studied the problem of XML update by proposing a new dynamic labeling scheme called ORD-GAP. The methods look effective and the authors perform experiments to verify the update operation and query processing for two datasets: SIGMOD record and DBLP. Experiments show that ORD-GAP has a better performance than ORDPath and ME Labeling. As they mentioned in this article, it would be better to run the experiments on larger data sets, e.g. with Amazon cloud service.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "93981",
"date": "16 Nov 2021",
"name": "Amjad Qtaish",
"expertise": [
"Reviewer Expertise XML Mapping",
"Database",
"Big Data"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper proposed a new labeling scheme for solving dynamic XML updates. Three cases of updating (insertions) are used, which are: leftmost, rightmost, and between siblings. I prefer to add another case which is the insertion of the leaf node. In addition, the proposed scheme was evaluated with others in terms of storage size, storage time, and query responses, it outperformed other labeling schemes.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-907
|
https://f1000research.com/articles/10-491/v1
|
22 Jun 21
|
{
"type": "Study Protocol",
"title": "Rates and predictors of data and code sharing in the medical and health sciences: Protocol for a systematic review and individual participant data meta-analysis.",
"authors": [
"Daniel G. Hamilton",
"Hannah Fraser",
"Fiona Fidler",
"Steve McDonald",
"Anisa Rowhani-Farid",
"Kyungwan Hong",
"Matthew J. Page",
"Hannah Fraser",
"Fiona Fidler",
"Steve McDonald",
"Anisa Rowhani-Farid",
"Kyungwan Hong",
"Matthew J. Page"
],
"abstract": "Numerous studies have demonstrated low but increasing rates of data and code sharing within medical and health research disciplines. However it remains unclear how commonly data and code are shared across all fields of medical and health research, as well as whether sharing rates are positively associated with implementation of progressive policies by publishers and funders, or growing expectations from the medical and health research community at large. Therefore this systematic review aims to synthesise the findings of medical and health science studies that have empirically investigated the prevalence of data or code sharing, or both. Objectives include the investigation of: (i) the prevalence of public sharing of research data and code alongside published articles (including preprints), (ii) the prevalence of private sharing of research data and code in response to reasonable requests, and (iii) factors associated with the sharing of either research output (e.g., the year published, the publisher’s policy on sharing, the presence of a data or code availability statement). It is hoped that the results will provide some insight into how often research data and code are shared publicly and privately, how this has changed over time, and how effective some measures such as the institution of data sharing policies and data availability statements have been in motivating researchers to share their underlying data and code.",
"keywords": [
"Systematic review",
"Meta-analysis",
"Data sharing",
"Code sharing",
"Medicine",
"Health sciences"
],
"content": "Background\n\nOver the last two decades there has been growing calls on the scientific community to improve the transparency of many elements of the scholarly research lifecycle. One key aspect that is of interest to this movement - often termed the “open science” movement - includes improving access to both the raw data underlying published research findings, as well as the syntax from relevant statistical software used to generate them (“research code”).1,2\n\nWhile open science principles are being increasingly adopted and promoted by major medical and health research stakeholders, the debate about the advantages, disadvantages, ethics, and legalities of sharing research data alongside published research is far from settled. For example, from one perspective greater availability of research data and code is considered a desirable goal as it allows for independent verification of findings, greater detection of errors, and is associated with increased scholarly impact metrics.2–4 Sharing data also facilitates more efficient and comprehensive aggregation of existing research findings, testing of secondary hypotheses not considered by the original authors, as well as evaluation of the robustness of chosen analytic strategies.3,5,6 However, in contrast, other research points to many barriers to sharing data, such as: the navigation of participant privacy concerns, proprietary data and licensing terms, a lack of incentives to share, fears among researchers concerning loss of recognition and control over the research outputs (i.e., right to publish) and the misuse or misinterpretation of shared data, as well as the time and resource burdens associated with archiving data in a way that enables reuse.7–11\n\nUltimately, despite contrasting evidence and opinions on the topic, funders of medical and health research continue to institute increasingly progressive policies governing sharing of research data and code. For example, the National Institutes of Health (NIH) and the National Science Foundation (NSF) both require grant applicants to submit comprehensive data management plans,9 with the National Institutes of Health also expecting NIH-funded researchers to share data generated from large-scale human or non-human genomic research.12 Similarly, publishers of medical research are also adopting more progressive data and code sharing policies. For example, a recent small survey of medical journal editors in 2019 by the first author observed 15% and 10% have instituted policies requiring public deposition of data and code sharing, respectively.13 The same study also noted that 28% of medical journals required authors to include a formalised data availability statement,13 which is also now stipulated by the International Committee of Medical Journal Editors’ (ICMJE) clinical trial data sharing policy for articles reporting the findings of clinical trials.14\n\nTo date, numerous studies have investigated how prevalent data and code sharing is. With regard to medicine and health, this research has reported traditionally low, but increasing rates of sharing and use of data availability statements across many fields, including but not limited to: biomedicine,15–18 cardiology,19 oncology,20 orthopaedics,21 otolaryngology,22 radiology23 and COVID-19-related research.24 Previous research has also highlighted low sharing of clinical trial data both publicly,25 as well as in response to reasonable private requests (e.g. for a meta-analysis, secondary analysis, sample size calculation).26–28 However, how common sharing of data and code is across all medical and health research, how this has changed over time, as well as how strongly it is influenced by journal and funder policymaking and community expectations - particularly in light of the COVID-19 pandemic29 - remains unclear.\n\nThe aim of this review is therefore to summarise the characteristics and synthesise the findings of this research to provide some insight into how well some of these policies are working at increasing sharing of data and code. It is hoped that the results will be able to provide some insights into how often research data and code are shared publicly and privately, how this has changed over time, and how effective some measures, such as the institution of mandatory data sharing policies and data availability statements have been in motivating researchers to share.\n\n\nObjectives\n\nTo summarise the characteristics and synthesise the findings of research that has empirically investigated (i) the prevalence of public sharing of research data and code alongside published articles (including preprints), (ii) the prevalence of private sharing of research data and code in response to reasonable requests, and (iii) factors associated with the sharing of either research output (e.g., the year published, the publisher’s policy on sharing, the presence of a data or code availability statement).\n\n\nMethods\n\nThis version of the protocol (v1.0) was developed in accordance with the PRISMA-P,30 PRISMA 202031 and PRISMA-IPD5 statements and was pre-registered on May 28th, 2021 on the Open Science Framework (https://osf.io/7sx8u). Since this review will only collect and analyse data derived from published articles, ethical review and approval was not sought.\n\nTypes of studies\n\nThis review will include studies that have empirically investigated the prevalence of data or code sharing, or both (termed “meta-research studies”), among a sample of scientific articles presenting original research from the medical and health sciences (termed “primary studies”). Studies can be published or unpublished articles (e.g., preprints) of any format (e.g., full-text article, conference abstract, research letter).\n\nWe will include meta-research studies regardless of (i) whether they have sampled primary studies in a random or non-random fashion, (ii) how much of a primary study’s data has been shared (e.g., partial sharing versus full sharing), (iii) the types of data considered for sharing (e.g., microarray data, genomic data, macromolecular data, imaging data, clinical data) or (iv) whether the availability of data and code has been verified by the authors of the meta-research study. However, we will exclude any meta-research studies that investigated data or code availability (i) as part of a single individual participant data (IPD) meta-analysis, (ii) for a single primary study (i.e., case report) or (iii) via other forms of research dissemination (e.g., clinical trial registry entries, data repository pages).\n\nTypes of data\n\nThree types of data will be of interest to this review – aggregate data (i) reported by included meta-research studies, (ii) derived from available IPD or (iii) provided on request from meta-research study authors.\n\nFor all eligible meta-research studies, reported summary statistics relating to (i) demographic variables of the primary studies, (ii) estimates of the prevalence of data or code sharing (publicly or privately) for the relevant sample of primary articles, and (iii) estimates of the association between data or code sharing (publicly or privately) and demographic variables of interest will be collected. Refer to the Data extraction and management section for further details about the specific variables of interest to the study.\n\nIf meta-research studies use differing definitions to those outlined in this protocol (e.g., consider “available on request” declarations as “shared”), we will only extract findings compliant with our protocol, or recode variables in line with definitions outlined in this protocol when possible. Similarly, if meta-research studies report relevant outcome measures in aggregate (e.g., report results for a mixture of medical and non-medical disciplines, or across an extended period of publication dates), we will only extract findings conforming to variables of interest outlined in the protocol (e.g., prevalence rates among medical and health research, prevalence rates by eligible year(s) of publication).\n\nFor studies where the above required information has been collected, but is not reported in the published article, publicly available IPD will be used to derive summary statistics of interest, such as: prevalence rates for our primary outcome measures, or risk ratios for our secondary outcome measures (see Types of outcome measures) and proposed subgroup analyses (see Subgroup analysis and investigation of heterogeneity). If IPD are not available publicly, we will request them from corresponding authors, or if authors are unwilling or unable to share IPD, they will be asked to provide the required summary statistics.\n\nIf none of the three types of data can be obtained, results will be included in the qualitative analysis (e.g., tabulated and narratively discussed), and in any relevant forest plots, but not included in the statistical synthesis. However, given the nature of the studies under review (i.e., studies investigating data and code availability among publicly available articles), and following pilot literature searching, it is expected that most of the authors of meta-research studies will have either already publicly shared IPD, or would be receptive and able to do so.\n\nTypes of methods\n\nThere are three types of data and code sharing that will be examined as part of this review:\n\n1. Public sharing of research data and code according to primary author declarations alone (reported availability).\n\n2. Public sharing of research data and code as confirmed by independent interrogation of author declarations, and verification of availability (actual availability).\n\n3. Private sharing of research data and code with an independent petitioner in response to a reasonable request (private availability).\n\n‘Public sharing’ will be broadly construed as the deposition of research data or code into a theoretically publicly accessible location (e.g., a freely accessible data repository, or an article’s supplementary material). For primary studies reporting data as “available on request”, this will not be considered as publicly available. Furthermore, if not explicitly verified by the meta-research study’s authors as available, it will be assumed that reported public sharing estimates represent ‘reported availability’. It should also be noted that ‘sharing’ in the context of this review will be defined as the sharing of data or code required to theoretically verify or reconstruct at least one of the primary study’s published findings.\n\nTypes of outcome measures\n\nWe will include three primary outcome measures for research data and code respectively:\n\nResearch data\n\n1. Declared prevalence of publicly available research data (reported availability);\n\n2. Confirmed prevalence of publicly available research data (actual availability);\n\n3. Prevalence of data sharing in response to a private request (private availability).\n\nResearch code\n\n1. Declared prevalence of publicly available research code (reported availability);\n\n2. Confirmed prevalence of publicly available research code (actual availability);\n\n3. Prevalence of code sharing in response to a private request (private availability).\n\nWe will also include five secondary outcome measures:\n\n1. The prevalence of data availability statements across study reports;\n\n2. The association between public sharing of research data (reported or actual availability) and the presence of a data availability statement, for example does requiring a data availability statement increase the likelihood of sharing data;\n\n3. The association between public sharing of research data (reported or actual availability) and the journal’s policy on data sharing (any ‘mandatory posting’ policy versus other policy);\n\n4. The association between private sharing of research data and the presence of a data availability statement;\n\n5. The association between private sharing of research data and the journal’s policy on data sharing (‘make available on request’ policy versus other policy).\n\nElectronic searches\n\nWe will search the following bibliographic databases and preprint servers from inception for relevant meta-research studies:\n\n• Ovid MEDLINE\n\n• Ovid Embase\n\n• medRxiv (RRID:SCR_018222)\n\n• bioRxiv\n\n• MetaArXiv\n\nThe search was developed by an information specialist (SM) using a sample of 14 papers deemed relevant to the topic. The search strategy was designed in Ovid MEDLINE and initially tested on a subset of the 14 papers and then iteratively refined to ensure that all papers were retrieved by the search. An analysis of the Medical Subject Headings (MeSH) applied to these 14 papers revealed several potentially relevant terms (e.g., Reproducibility of Results, Information Dissemination) but none were considered appropriate to include in the strategy because they lacked precision. The same search was applied to Ovid Embase, allowing for modifications to the search syntax. The Ovid MEDLINE search syntax was then adapted by the first author into Lucene search syntax to search MetaArXiv, and R programming language to search the medRxiv and bioRxiv preprint servers via the medrxivr package.32 No restrictions will be placed on any of the searches with regard to language of publication. The search strategies for each database are available on the Open Science Framework (https://osf.io/h75v4/).\n\nThe team will screen reference lists of relevant studies identified by the search, as well as the bibliographies of all included studies. We will also conduct citation searches of included articles using Clarivate Analytics’ Web of Science, as well as browse other preprint servers (PeerJ, Research Square) and online resources (Open Science Framework, aspredicted.org and connectedpapers.com) to help identify further published, unpublished and pre-registered studies.\n\nSelection of studies\n\nResults from all searches will be imported into Covidence (Covidence systematic review software, Veritas Health Innovation, Melbourne, Australia) and deduplicated. For the results of the preprint server searches, if published versions of preprints are available, they will be sourced and screened for eligibility, if not we will select and screen the preprint. All titles and abstracts identified by the search strategies above will be independently screened against the eligibility criteria by two authors in parallel. Following title and abstract screening, two authors will independently assess full-text articles (where available) for inclusion. We will attempt to translate foreign-language articles flagged as potentially eligible using Google Translate or native speakers known to the team. If unable to translate the document successfully, we will exclude the study. All disagreements on the eligibility of studies at each phase will be resolved via discussion, or a third author if required. We will prepare a flow diagram in accordance with both the PRISMA 2020 statement and PRISMA-IPD extension outlining the flow of identified articles throughout each stage of the review.5,31 The reasons for exclusion of full-text articles will also be documented.\n\nSummary statistics derived from meta-research studies\n\nOnce the list of included articles is determined, two authors will independently extract summary statistics from each included meta-research study using a predefined data extraction form developed for this review. Any differences in coding will be resolved via discussion, or a third author if consensus cannot be reached. The data extraction form will be pilot tested by the data extractors on at least five randomly selected included articles, and if required, modified prior to use.\n\nThe following key variables will be extracted from included articles:\n\n• Characteristics of the meta-research study, including but not limited to: study title, DOI, journal, publication date, health/medical discipline(s) of interest, the number of primary studies examined (sample size), sampling strategy, protocol availability, data availability and so on;\n\n• Data on estimates of prevalence as outlined in Types of outcome measures;\n\n• Data on factors associated with sharing as outlined in Types of outcome measures.\n\nA comprehensive list of the variables to be extracted is available on the Open Science Framework (https://osf.io/h75v4/).\n\nSummary statistics derived from individual participant data\n\nDemographic variables and outcome measures of relevance to the study that are not reported by meta-research studies but appear to have been collected by study authors will be investigated further. If the underlying IPD and data dictionary from the meta-research study are publicly available, one author (DGH) will calculate the desired information from the raw data and enter it into a pre-prepared CSV-formatted spreadsheet. If IPD are not available, the corresponding author of the meta-research study will be contacted to request the required information or the raw data. A comprehensive list of the variables that may be extracted from available IPD is available on the Open Science Framework (https://osf.io/h75v4/).\n\nThe following criteria have been created with guidance from previous Cochrane Methodology Reviews (Table 1).33,34 Two authors will independently classify each included study, with any differences in coding resolved via discussion, or a third author if consensus cannot be reached. We will contact authors of included studies for additional information when assessments are initially classified as unclear.\n\nGiven the aim to differentiate between studies with higher and lower risk of bias, a study will be deemed as having a low risk of bias if all the above criteria are assessed as low risk of bias, and high risk of bias if any one criterion is assessed as high or unclear risk of bias.\n\nFor studies that report estimates of the prevalence of data or code sharing, we will report percentages (no. of articles that shared/no. of articles assessed) and 95% confidence intervals (CI) calculated using the Wilson score interval method.35 The measures of the prevalence and association between a factor and data sharing will be dependent on the summary statistics used and reported by the authors of the meta-research studies, and the availability of IPD. For studies that have investigated the association between relevant factors and the sharing of research data (refer to Types of outcome measures for more information), we will report risk ratios with 95% confidence intervals. We will standardise our reporting so that risk ratios greater than one will indicate a higher likelihood of data availability. If authors of meta-research studies report odds ratios instead of risk ratios we will convert them to risk ratios using the formula proposed by Grant.36 Where studies do not report this information, prevalence rates and risk ratios will be calculated from the raw data if it is available, or requested from the corresponding author.\n\nIt is possible that there may be some overlap in the primary articles examined across included meta-research studies. Once the list of included studies is finalised, we will check for potential overlap by comparing reported primary article characteristics across meta-research studies (e.g., discipline(s) of interest, publication dates, publication outlets, study designs). The team will assess the degree of overlap and flag studies for which the likelihood of overlap is high, and then will check the IPD of flagged studies for duplicate primary articles by interrogating unique identifiers across datasets from included studies (e.g., DOI, PMID, study title). We will report whether this issue was able to be addressed, and if not, its likelihood of occurring and the likely impact on the findings of the review.\n\nFor eligible studies where raw data are unavailable and information on study characteristics (e.g., methods for identifying and selecting primary articles) or outcomes (e.g., prevalence of sharing by a subgroup of interest) is missing, corresponding authors will be contacted. If the required information cannot be retrieved, available information will be discussed narratively. We will not impute missing data using statistical techniques. We will instead discuss missing data narratively.\n\nWe will assess the similarity/dissimilarity of methodological aspects of included studies, particularly with respect to definitions of “data”, “code” and “sharing”. We will evaluate statistical heterogeneity by inspecting the distribution of effects within forest plots and the magnitude of corresponding I2 statistics and their 95% confidence intervals.37 We will also further evaluate statistical heterogeneity by calculating prediction intervals for our primary outcomes where more than four studies are included.38 Prediction intervals estimate the likely range of effect sizes (prevalence rates and risk ratios) that could be expected across similar studies.39,40 Prediction intervals will be calculated in R using the meta package41 which implements the formula proposed by Higgins and colleagues42 (equation 12).\n\nWe believe that the likelihood of this review being affected by publication bias is low given studies of interest to the review appear to be mostly exploratory in nature, with a focus on reporting prevalence rates rather than testing specific hypotheses. However, we will assess the risk of publication bias by searching for pre-registered protocols of eligible meta-research studies. We will also assess the risk of selective-reporting bias by comparing what authors of meta-research studies reported, with what they stated in the protocol for the study (see Assessment of the risk of bias in included studies).\n\nThis review will adopt a “two stage” approach to IPD meta-analysis, whereby we will examine meta-research studies in the first stage to extract summary statistics, or retrieve them from available IPD or from corresponding authors. Where data are available and appropriate (e.g., low heterogeneity), in the second stage, results from meta-research studies will then be pooled as per conventional meta-analysis.43 For each of the primary and secondary outcome measures, we will pool prevalence and risk ratio estimates using a random-effects model and will calculate 95% CIs for the summary effect using the method developed by Hartung-Knapp-Sidik-Jonkman.44 Prevalence rates will be transformed using the Freeman-Tukey double arcsine transformation and combined using standard inverse variance methods.45 When it is not possible to meta-analyse due to clinical and/or statistical heterogeneity we will report prevalence, risk ratios, 95% CIs and p-values in tables.\n\nWhere data are available, we will perform subgroup analyses to investigate whether the prevalence of public sharing of data is associated with the following factors:\n\n• Whether primary studies were defined by the study authors as a clinical trial (any phase) or not;\n\n• Whether primary studies studied COVID-19 or not;\n\n• Whether primary studies directly studied, or used any data derived from, human participants or not;\n\n• Whether primary studies were subject to any mandatory sharing policies by the funders of the study or not;\n\n• Whether primary studies posted a preprint or not.\n\nFurthermore, in the event that the review includes data from more than 10 studies,46 we will conduct univariate random-effects meta-regressions to investigate potential sources of variability in the prevalence of 1) data sharing (reported or actual availability) and 2) data availability statements by year of publication of primary studies, with bubble plots used to visualise regressions. If there are fewer than ten studies available to perform meta-regression, we will perform a subgroup analysis looking at differences in prevalence estimates across four time periods (Before 2010, 2010-2015, 2015-2020, 2020 onwards). These periods were chosen in order to isolate possible impacts of the COVID-19 pandemic (i.e., 2020 onwards) on prevalence rates, as well as investigate findings reporting an increase in uptake of data availability statements between 2014-2016.16\n\nThe team will perform three to four sensitivity analyses. First, we will conduct a sensitivity analysis to assess the robustness of pooled meta-analytic effect estimates based on the observed risk of bias of included studies. Specifically, we will compare pooled prevalence estimates of all studies eligible for meta-analysis against those rated as at a low risk of bias (refer to Assessment of the risk of bias in included studies for the risk of bias assessment). Second, we will conduct a sensitivity analysis to examine whether estimates from studies not providing IPD differ from those where IPD were available. Third, we will investigate differences in pooled prevalence rates when using logit-transformed proportions and generalized linear mixed models instead of Freeman-Tukey double arcsine transformations and standard inverse variance aggregation methods.47 Lastly, the team may also perform sensitivity analyses on any set of two or more studies that include a large number of the same primary articles by removing the smallest affected studies from any relevant meta-analyses.\n\n\nDiscussion\n\nTo our knowledge, this review will be the first study to estimate the prevalence of data and code sharing across the medical and health sciences. Our study will also use available IPD to investigate several aspects of data and code sharing that have not yet been well-explored, such as how sharing rates have changed over time, as well as what influence other relevant factors such as data and code availability statements and publishers’ and funders’ sharing policies have had on motivating medical and health researchers to share their data and code.\n\nOur review has several strengths. First, the study will follow recommended practices in systematic review methodology by pre-registering the methods used to identify, select, and analyse eligible meta-research studies, and will declare any deviations from the protocol in the final publication. Furthermore, the review will systematically search multiple electronic databases for eligible articles, including preprint servers for unpublished work, as well as enlist at least two researchers to perform all article screening and data extraction tasks independently in parallel to minimise the chance of coding errors. The review will also share all data, materials and code generated by the study to allow others to verify or build upon our work.\n\nHowever, there are also some limitations of this study. Given the novelty of the study, as well as appreciating that the establishment of metascience as a unique scholarly field is a relatively recent occurrence, there were few previous reviews, or universally agreed upon keywords and controlled vocabulary (e.g., MeSH and Emtree terms) with which to assist the search strategy development. Consequently, the lack of controlled vocabulary, as well as our limiting of searches to predominantly English-language databases may result in a greater risk of missing literature relevant to the research questions, when compared to other established review areas like reviews of randomised controlled trials where comprehensive guidance and established methodological search filters are available.48 Furthermore, given the likelihood that IPD will not be available for all eligible meta-research studies, it is also possible that systematic biases may be present in the results of analyses reliant on IPD that will not be able to be detected.\n\n\nConclusion\n\nThere is growing momentum among funders, publishers and the greater scientific community to increase the availability of the outputs of medical and health research. This review will provide some insight into how commonly data and code from medical and health research is shared. It will also examine how sharing rates have changed over time, and how influential some policies have been in motivating researchers to share their underlying data and code. It is expected that the findings of this research may be particularly useful to key research policymakers in developing, instituting and assessing policies on data and code sharing.\n\n\nData and software availability\n\nNo data are associated with this article. Data, materials and code from the completed review will be made freely available under a CC0 1.0 Universal license on the Open Science Framework (https://osf.io/h75v4/).\n\nOpen Science Framework: A review of data AND code sharing rates in medical and health research.\n\nhttps://doi.org/10.17605/OSF.IO/H75V4.49\n\nThis project contains the following extended data:\n\n• Appendix-1.1_Search-Strategies-MedEmbMeta_v1.0.pdf (The proposed search strategy for MEDLINE, Embase and MetaArXiv)\n\n• Appendix-1.2_Search-Strategies-MedBioRxiv_v1.0.R (The proposed search strategy for medRxiv and bioRxiv)\n\n• Appendix-2_Data-Extraction-Fields_v1.0.pdf (The variables that will be extracted from eligible meta-research studies)\n\n\nCompeting interests\n\nDGH is a PhD candidate supported by an Australian Commonwealth Government Research Training Program Scholarship. The Laura and John Arnold Foundation funds the RIAT Support Centre (no grant number), which supports the salaries of ARF and KH. KH's project was supported by the Food and Drug Administration (FDA) of the U.S. Department of Health and Human Services (HHS) as part of a financial assistance award U01FD005946 totalling US$5,000 with 100 per cent funded by FDA/HHS. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement, by FDA/HHS, or the U.S. Government. The authors declare that no grants were involved in supporting this work.",
"appendix": "References\n\nBurgelman J-C, Pascu C, Szkuta K, et al.: Open Science, Open Data, and Open Scholarship: European Policies to Make Science Fit for the Twenty-First Century. Front Big Data. 2019; 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoldacre B, Morton CE, DeVito NJ: Why researchers should share their analytic code. BMJ. November 2019; 21: l6365. PubMed Abstract | Publisher Full Text\n\nPiwowar HA: Who Shares? Who Doesn’t? Factors Associated with Openly Archiving Raw Research Data. Neylon C, ed. PLoS ONE. 2011; 6(7): e18657. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcKiernan EC, Bourne PE, Brown CT, et al.: How open science helps researchers succeed. eLife. 2016; 5: e16800. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStewart LA, Clarke M, Rovers M, et al.: Preferred Reporting Items for Systematic Review and Meta-Analyses of individual participant data: the PRISMA-IPD Statement. JAMA. 2015; 313(16): 1657–1665. 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Publisher Full Text\n\nHansen C, Bero L, Hróbjartsson A, et al.: Conflicts of interest and recommendations in clinical guidelines, opinion pieces, and narrative reviews. Cochrane Database Syst Rev. 2019; 10. Publisher Full Text\n\nPage MJ, McKenzie JE, Dwan K, et al.: Bias due to selective inclusion and reporting of outcomes and analyses in systematic reviews of randomised trials of healthcare interventions. Cochrane Database Syst Rev. 2012; 5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilson EB: Probable Inference, the Law of Succession, and Statistical Inference. J Am Stat Assoc. 1927; 22(158): 209–212. Publisher Full Text\n\nGrant RL: Converting an odds ratio to a range of plausible relative risks for better communication of research findings. BMJ. 2014; 348: f7450. PubMed Abstract | Publisher Full Text\n\nHiggins JPT, Thompson SG: Quantifying heterogeneity in a meta-analysis. Stat Med. 2002; 21(11): 1539–1558. PubMed Abstract | Publisher Full Text\n\nNejstgaard CH, Bero L, Hróbjartsson A, et al.: Conflicts of interest in clinical guidelines, advisory committee reports, opinion pieces, and narrative reviews: associations with recommendations. Cochrane Database Syst Rev. 2020; 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRiley RD, Higgins JPT, Deeks JJ: Interpretation of random effects meta-analyses. BMJ. 2011; 342: d549. PubMed Abstract | Publisher Full Text\n\nIntHout J, Ioannidis JPA, Rovers MM, et al.: Plea for routinely presenting prediction intervals in meta-analysis. BMJ Open. 2016; 6(7): e010247. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBalduzzi S, Rücker G, Schwarzer G: How to perform a meta-analysis with R: a practical tutorial. Evid Based Ment Health. 2019; 22(4): 153–160. PubMed Abstract | Publisher Full Text\n\nHiggins JPT, Thompson SG, Spiegelhalter DJ: A re-evaluation of random-effects meta-analysis. J R Stat Soc Ser A Stat Soc. 2009; 172(1): 137–159. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTierney JF, Stewart LA, Clarke M: Chapter 26: Individual participant data. In: Higgins JPT, Thomas J, Chandler J, et al. (editors). Cochrane Handbook for Systematic Reviews of Interventions version 6.2 (updated February 2021). Cochrane; 2021. Reference Source\n\nIntHout J, Ioannidis JP, Borm GF: The Hartung-Knapp-Sidik-Jonkman method for random effects meta-analysis is straightforward and considerably outperforms the standard DerSimonian-Laird method. BMC Med Res Methodol. 2014; 14(1): 25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFreeman MF, Tukey JW: Transformations Related to the Angular and the Square Root. Ann Math Stat. 1950; 21(4): 607–611. Publisher Full Text\n\nBorenstein M, Hedges L, Higgins J, et al.: Meta-Regression. In: Introduction to Meta-Analysis . John Wiley & Sons, Ltd; 2009: 187–203. Publisher Full Text\n\nSchwarzer G, Chemaitelly H, Abu-Raddad LJ, et al.: Seriously misleading results using inverse of Freeman-Tukey double arcsine transformation in meta-analysis of single proportions. Res Synth Methods. 2019; 10(3): 476–483. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLefebvre C, Glanville J, Briscoe S: Chapter 4: Searching for and selecting studies. In: Higgins JPT, Thomas J, Chandler J, et al. (editors). Cochrane Handbook for Systematic Reviews of Interventions version 6.2 (updated February 2021). Cochrane; 2021. Reference Source\n\nHamilton DG, Fraser H, Fidler F, et al.: A review of data and code sharing rates in medical and health research. 2021, June 11. Publisher Full Text"
}
|
[
{
"id": "88792",
"date": "02 Jul 2021",
"name": "Tim Hulsen",
"expertise": [
"Reviewer Expertise Data management",
"data stewardship",
"data sharing",
"bioinformatics",
"data science."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript presents a protocol on the study of sharing data and source code in the medical domain. The methodology that is described in the paper seems scientifically sound. I do have some suggestions to improve the paper:\nWhen discussing data sharing, it is important to note the existence of privacy laws such as the GDPR (EU), and HIPAA (USA), since they have such a large effect on data sharing practices (e.g. obligatory data management plans, data controller/processor definition, detailed informed consents, etc.)\n\nData sharing is a first step, but the data should also be made available in a way that it can be reused. I was surprised that the FAIR (Findability, Accessibility, Interoperability, Reusability) principles are not mentioned in the paper. Shared datasets (or code) that adhere to these guidelines are much more likely to be reused. See Wilkinson et al. (20161).\n\nSelection of studies: \"We will attempt to translate foreign-language articles flagged as potentially eligible using Google Translate or native speakers known to the team. If unable to translate the document successfully, we will exclude the study.\" Doesn't this include a bias in your study? Only if the article is written in a language known to people in your environment, or in a language that can be translated well by Google Translate, it is included.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "7101",
"date": "09 Sep 2021",
"name": "Daniel Hamilton",
"role": "Author Response",
"response": "Thank you very much for the useful feedback Tim. Please see our responses to your comments in a point-by-point manner below. When discussing data sharing, it is important to note the existence of privacy laws such as the GDPR (EU), and HIPAA (USA), since they have such a large effect on data sharing practices (e.g. obligatory data management plans, data controller/processor definition, detailed informed consents, etc.) Response: This is a very pertinent point. In response, we have added some text to the discussion concerning the impact of the recent regulatory changes on data sharing behaviours - particularly sharing health data derived from human research participants across international and intercontinental borders (refer to Discussion: Paragraph 1, Sentence 3). Data sharing is a first step, but the data should also be made available in a way that it can be reused. I was surprised that the FAIR (Findability, Accessibility, Interoperability, Reusability) principles are not mentioned in the paper. Shared datasets (or code) that adhere to these guidelines are much more likely to be reused. See Wilkinson et al. (2016). Response: We agree that when sharing data or code it should comply with the FAIR principles. The principles were certainly considered when developing the protocol, however there are a couple of reasons why we decided not to require studies to have strictly assessed the ‘FAIRness’ of shared data or code to be eligible for inclusion in the review. Firstly, given that the FAIR principles were drafted in 2015, any relevant literature published prior to this date would have to be excluded. Secondly, pilot searching demonstrated that there are likely very few (possibly no) meta-research studies conducted after 2015 that looked at data or code availability judged according to the FAIR principles (i.e. data or code were only considered ‘available’ if it met all FAIR criteria). This perhaps is not surprising as familiarity with FAIR principles remains low (10.6084/m9.figshare.13274744). Despite this, we have attempted to begin to bridge this gap via our ‘actual availability’ measure, which requires meta-researchers to have conducted some investigation into whether the data or code is indeed available (i.e. akin to assessing the ‘F’ in FAIR). However, given we suspect this will be a limitation of the majority of included studies, it will therefore also be a limitation of the review. Ultimately, we agree that not mentioning the principles in the discussion is an oversight and so have added some text (refer to Discussion: Paragraph 3, Sentences 2-4). We will also record the methods each meta-research study used to define ‘actual data availability’ and if any meta-research studies stipulated that they required shared data or code to comply with the FAIR principles in order to be considered ‘available’, we will also present a synthesis of such studies in the form of a sensitivity analysis (refer to Methods/Sensitivity analysis: Paragraph 1, Sentence 4). Selection of studies: \"We will attempt to translate foreign-language articles flagged as potentially eligible using Google Translate or native speakers known to the team. If unable to translate the document successfully, we will exclude the study.\" Doesn't this include a bias in your study? Only if the article is written in a language known to people in your environment, or in a language that can be translated well by Google Translate, it is included. Response: You are correct. Excluding foreign-language studies that cannot be successfully translated could unfortunately indeed introduce a bias. Recognising language bias to a greater or lesser extent is present in most systematic reviews (10.11124/JBIES-20-00361) we have taken steps to minimise this by attempting to translate articles in languages other than English, and note that Google Translate offers translation for over 100 languages. Further, any concerns we have around the exclusion of potentially relevant articles based on language will be addressed as a limitation of the review."
}
]
},
{
"id": "90452",
"date": "05 Aug 2021",
"name": "Jenine Harris",
"expertise": [
"Reviewer Expertise Increasing sex diversity in the STEM workforce",
"reproducible public health research"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis proposal describes a meta-analysis of studies of data and code sharing in medical and health sciences.\nThere is a vast difference in the utility of available data uploaded via scanned pdf and available data in a csv file (or other software-neutral format), I would argue that csv data “available upon request” is more accessible than publicly available scanned pdfs containing data that will likely have to be re-entered by hand in order to be used. The authors might consider/measure data accessibility in addition to availability.\n\nIs there a reason for not confirming private availability in the same/similar way to public availability?\n\nGiven the variety of search terms that could be used and non-standardized ways that journals operate and format manuscripts, would a secondary search strategy employing humans potentially capture additional candidate studies?\n\nHow will the authors handle data accessibility if the accessible data are synthetic? (E.g. when data cannot be made public due to private health info, some authors may choose to mimic important data features by providing synthetic data that will result in similar research results as the primary data)\n\nWill any attention be given to whether code that is available is in a format that can be read by open source software (e.g. Python, R) vs. making code available that can only be read with purchased software (e.g. SAS, SPSS)? Is code that someone needs to buy software to use really “open”?\n\nThe secondary outcomes are all for the data sharing and not for the code sharing; would similar secondary outcome measures for code sharing be useful as well? Journals are unlikely to have code sharing policy (in my experience) but perhaps sharing of code increases with an open data policy. It seems logical that researchers who share data might be more inclined to share code as well.\n\nWe found that researchers are more likely to share data and code when funders and employers require these things in public health (Harris et al. (20181)). The authors are collecting funder policy on data (typo in data collection form lists “date” instead of “data”) but not employer. Adding employer may provide some additional insight into why certain papers have available data/code.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "7102",
"date": "09 Sep 2021",
"name": "Daniel Hamilton",
"role": "Author Response",
"response": "Thank you very much for the useful feedback Jenine. Please see our responses to your comments in a point-by-point manner below. There is a vast difference in the utility of available data uploaded via scanned pdf and available data in a csv file (or other software-neutral format), I would argue that csv data “available upon request” is more accessible than publicly available scanned pdfs containing data that will likely have to be re-entered by hand in order to be used. The authors might consider/measure data accessibility in addition to availability. Response: We agree that data shared in machine-readable formats are much more valuable than data shared in non-machine-readable formats - this notion being a key element of the ‘Interoperability’ criterion of the FAIR principles. This comment, as well as the second comment from Reviewer #1, has motivated us to add some text to outline this study limitation (Discussion: Paragraph 3, Sentences 2-4), record more detailed information on how meta-research studies define ‘actual availability’, as well as include an extra sensitivity analysis to estimate the prevalence of FAIR sharing of data and code, and how these estimates compare with the ‘actual availability’ estimates (Methods/Sensitivity analysis: Paragraph 1, Sentence 4). Is there a reason for not confirming private availability in the same/similar way to public availability? Response: This is a great point. This was an oversight. In response, we have brought the private availability outcome measures in line with the public availability outcome measures (refer to Methods/Types of methods and Methods/Types of outcome measures). Given the variety of search terms that could be used and non-standardized ways that journals operate and format manuscripts, would a secondary search strategy employing humans potentially capture additional candidate studies? Response: Given the terms used to describe open practices such as data and code sharing vary substantially among manuscripts, we plan to screen reference lists of relevant studies identified by the search, as well as the bibliographies of all included studies. We will also contact the authors of relevant studies and others with expertise in this area, conduct forward citation searches of included articles, as well as browse other preprint servers and online resources (Open Science Framework, aspredicted.org, connectedpapers.com) to help identify further studies. How will the authors handle data accessibility if the accessible data are synthetic? (E.g. when data cannot be made public due to private health info, some authors may choose to mimic important data features by providing synthetic data that will result in similar research results as the primary data). Response: This is a very interesting point. Firstly, for the purposes of the review we will not exclude meta-research studies if they do or don't include data from in silico experiments within their scope. Secondly, we will also not exclude meta-research studies if they: 1) considered the sharing of synthetic data as acceptable or not, or 2) generated a synthetic dataset for the purposes of sharing the data from their own study. While we do not expect any of the eligible meta-research studies to have come across synthetic data when assessing data availability, nor used this approach when sharing their own data given it appears to be still in its infancy (10.7554/eLife.53275), some text has been added to the methods to clarify the above points (Methods/Types of Studies: Paragraph 2, Sentence 1). Will any attention be given to whether code that is available is in a format that can be read by open source software (e.g. Python, R) vs. making code available that can only be read with purchased software (e.g. SAS, SPSS)? Is code that someone needs to buy software to use really “open”? Response: We do not plan to differentiate between sharing code for proprietary or open-source software for the reasons discussed in Comment #1. As long as it can, in principle, be scrutinised it will be considered open for the purposes of the review. This will be a limitation that will be discussed in the final paper, along with other FAIR principles considerations, and the findings of the FAIRness sensitivity analysis. The secondary outcomes are all for the data sharing and not for the code sharing; would similar secondary outcome measures for code sharing be useful as well? Journals are unlikely to have code sharing policy (in my experience) but perhaps sharing of code increases with an open data policy. It seems logical that researchers who share data might be more inclined to share code as well. Response: Another great point. We agree that researchers who share data may be more inclined to share their code too and so have added this as an extra secondary outcome measure. We have also used this opportunity to add in two further secondary outcome measures to capture the overall prevalence of code availability statements, as well as their potential impact in incentivising researchers to share their code publicly (refer to Methods/Types of outcome measures). We found that researchers are more likely to share data and code when funders and employers require these things in public health (Harris et al. (2018)). The authors are collecting funder policy on data (typo in data collection form lists “date” instead of “data”) but not employer. Adding employer may provide some additional insight into why certain papers have available data/code. Response: Thank you for another great point. We have added this as another variable to collect and corrected the flagged typographical error (refer to version 2 of Appendix 2 on our OSF page)."
}
]
}
] | 1
|
https://f1000research.com/articles/10-491
|
https://f1000research.com/articles/10-905/v1
|
09 Sep 21
|
{
"type": "Research Article",
"title": "Effects of human capital and fund characteristics on mutual fund performance in Malaysia",
"authors": [
"Venny Sin-Woon Chong",
"Lai Ming Ming",
"Lee Lee Chong",
"Lai Ming Ming",
"Lee Lee Chong"
],
"abstract": "Background: The evolution of the mutual funds industry has changed investors’ perspective. Instead of just focusing on which fund performances are best, investors pay great attention to who is managing and delivering superior returns in their investment portfolios. Nonetheless, it is very scant of comprehensive studies concern with human capital managerial characteristics that link with fund performances. Hence, this study proposes the integration of fund performances, managerial characteristics, systematic risk, expense, and turnover ratio, with single and simultaneous equations based on asset pricing models. Methods: Using a sample of Malaysian fund managers, data from fund management companies, Thomson One database, and fund master prospectus over the periods of January 2012 to December 2014, the fund performance was measured using Jensen alpha (CAPM single factor), and Fama and French three-factor model on single and simultaneous equations. The examination was further carried out by employing the ordinary least squares and three-stage least squares methods. Results: The results suggest that for fund managers, holding a business degree was the key factor to determine the fund performance, while having Master’s degree was not the primary concern. Fund performance and risk behavior varied across fund managers of different gender. Conclusions: The expense ratio, turnover ratio, and fund objective were significantly correlated with fund performance. This study provides ultimate implications for fund management companies, when it comes to the efficient allocation of human capital. Fund management companies should focus more on the team-managed funds phenomenon, instead of on single-managed funds. Overall, this study provides significant guidance for the Malaysian Securities Commissions and fund management companies, to develop a more competent funds market in Malaysia. Specifically, by strengthening the fund industry policies, the typical agency problems, such as too-high managerial expenses, and excessive risk-taking can be alleviated.",
"keywords": [
"Human capital",
"fund manager",
"fund characteristics",
"fund performance",
"expense ratio",
"turnover ratio",
"systematic risk"
],
"content": "Introduction\n\nMutual fund is an investment vehicle for investors to yield savings and diversification. The growth of fund investments has been astounding, not only in developed countries but also in emerging markets. The unit trust industry in Malaysia has experienced phenomenal positive growth in NAV of RM536.86 billion in April 2021, and the percentage of NAV to Bursa Malaysia market capitalization showed increasing trends, from 27.36 percent in 2011 to 29.20 percent in April 2021 (Securities Commission Malaysia, 2021). Nevertheless, this growth figure was rather low compared to other advanced and mature markets. The total net assets of mutual funds managed by US investment companies in April 2021 reached more than $25.5 trillion (USD) (Investment Company Institute, 2021), while European countries achieved $14,447.20 billion (EUR) in March, 2021 (European Central Bank, 2011). This indicates that the unit trust industry is still in the infancy stage in Malaysia.\n\nNevertheless, uncertainty and reduced stability in the global financial marketplace during the COVID-19 pandemic, have given rise to tremendous challenges in the fund industry. Investors have become impatient, especially with the underperformance of funds, putting them at odds with funds managers (William, 2017). Hence, investors are now not only focused on which funds perform better than others, but on who could persistently safeguard their investment portfolios during these turbulent periods. Hence, fund managers are expected to react faster and work under pressure in this competitive market to maintain and improve their positions (PWC, 2020). The investors pay great attention to who is delivering “alpha” in their investment portfolios. However, to date, no comprehensive study has examined the relationship of fund managers’ human capital characteristics with fund performance in Malaysia. Hence, this study proposes to integrate fund performances, managerial characteristics, systematic risk, expense ratio, and turnover ratio with single and simultaneous equations based on asset pricing models. This study attempts to fill this research gap. Therefore, the results are significant for the funds industry in emerging markets.\n\nAlthough there have been many empirical studies that found funds in Malaysia performed rather worse compared with mature markets (Low & Ghazali, 2007), more recent empirical studies showed the Malaysian fund performance has outperformed the market (Lai & Lau, 2010; Nur Adiana & Aminah, 2019; Ruzita, Ling & Rasidah, 2019). Previous studies (Atkinson et al., 2003; Bliss & Potter, 2002; Chevalier & Ellison, 1999; Golec, 1996) have focused on fund managers’ managerial characteristics by looking at fund performance. Lately, the Central Bank of Malaysia has been the driving force to develop human capital in the Malaysian banking industry (Bank Negara Malaysia, 2021). The changing landscape and transformation in the financial sector could be achieved by building the right quality of human capital (The Malaysian Reserve, 2021). The concept of human capital was developed in 1954 by William Arthur Lewis. Becker (1962) has expanded this theory, stating that “people cannot be separated from their knowledge, skills, health, or values in the way they can be separated from their financial and physical assets. Education, training, and health are the most important investments in human capital”.\n\nChevalier and Ellison (1999) highlighted that most investors believed that the mutual fund market had not yet achieved efficiency. Hence, fund managers who are actively involved with security selection and focused on movement in the market will not only add value to their investment portfolio, but will also produce superior performance (Low & Ghazali, 2007). Golec (1996) and Chevalier and Ellison (1999) examined that those fund managers who held a Master’s of Business Administration (MBA) degree showed positive to fund performance. This may be explained by the fact that the possession of an MBA degree equipped the fund managers with the skills related to investment risk management. Surprisingly, the absence of a Chartered Financial Analyst (CFA) title was not significantly relevant to the fund performance.\n\nGolec (1996) highlighted that fund managers’ experience was negatively related to fund alpha. Younger fund managers had higher stamina and higher job prospects in their careers. Chen, Gao, Zhang, and Zhu (2018) examined that fund managers with prior industry analyst backgrounds showed significant stock selection ability. There is limited research that has investigated the role of fund managers’ gender on fund performance (Babalos, Caporale, & Philippas, 2015). Sargis and Wing (2018) investigated the fund performance of female fund managers. The finding indicated that male portfolio managers did not possess superior investment skills than their female counterparts. The results showed no significant difference in terms of fund performance between male and female fund managers.\n\n\nMethods\n\nThis study sampled a total of 240 domestic equity funds in Malaysia to measure the risk-adjusted performance of each fund, from January 2012 to December 2014. To avoid survivor bias, the sample excluded funds that have ceased to exist in the Malaysian fund market, and data only hold survivors’ funds. The fund performance measurements were Jensen alpha on a single-factor model (CAPM) and alpha on a Fama and French (1993) (three-factor model). The FTSE KLCI three-month Malaysian Treasury bill was chosen as a benchmark to proxy market indexes and risk-free rate of return. To address the simultaneous interactions among fund performance, systematic risk, expenses, and turnover, it is worth noting that Golec (1996) and Switzer and Huang (2007) performed single equations and simultaneous equations. Consistent with prior studies, this study performed single equations by using OLS regression and simultaneous equations estimation by 3SLS regression. STATA version 12.1 was used to conduct the statistical assessments.\n\nAll fund manager human capital data were obtained from secondary sources which are available for public access. The fund managers’ profiles, e.g., gender and education were retrieved, and hand-collected from each of the fund master prospectus and Morningstar; these data are under public access. Morningstar is a well-known Chicago-based financial services firm that provides in-depth analysis and rating system for fund performances and the fund managers investment experiences. Other human capital characteristics, e.g., investment experience and age data that are not publicly available in the Malaysian fund market, were obtained from a subscription to the Thomson One database and fund prospectus. In order to comply to the open data policy, the dataset was anonymised by attributing a number to each of the fund names; reviewers and readers may view and access the dataset without restrictions. Given that there is little and sometimes no available information on Malaysian fund managers’ age, to overcome this problem, Chevalier and Ellison (1999) and Atkinson, Baird, and Frye (2003) proposed an estimation of age by assuming that each fund manager was 21 years old upon graduation from college. Nevertheless, the average age of graduation for a Bachelor’s degree in Malaysia is approximately 24. Hence, this study estimated the fund managers’ age by adding 24 years to the number of years at work. Data on years of working experience were stated in the fund master prospectus. This research received approval number EA0372021 from the Research Ethic Committee of Multimedia University in Melaka, Malaysia.\n\nEach of the fund managers’ human capital characteristic indicators were measured using a dummy variable, defined in Table 1. Furthermore, this study examined six fund characteristics in terms of their relationship with the fund performance (Switzer & Huang, 2007; Low, 2010). The fund characteristics data were sourced mainly from the respective fund master prospectus and annual reports of all fund management companies in Malaysia. To control the characteristics of the funds, the study classified the sample funds into two dimensions on the basis of the fund objective: growth fund and income fund dummy variables. The fund data are defined in Table 2.\n\na CFA = Chartered financial analyst.\n\nb CFP = Certified financial planner.\n\nc CPA = Chartered financial analyst.\n\n\nResults and discussion\n\nTable 3 reports descriptive statistics for fund performance, fund risks, and fund characteristics of the Malaysian funds industry. The average value shows a positive Jensen alpha of 0.0024, which indicates that fund managers possessed the best stock selection ability. However, there was a significant gap in the return performance between the best and worst fund managers. The average positive Alpha 2 of 0.0005 indicates that the funds slightly outperformed the market performance over the sampled period. The Beta of 0.5936 indicates that the mutual fund is relatively less risky than the market. The additional two risk factors, SMB with an average of 0.28 and HML was 0.56. Furthermore, the average value of the expense ratio was 1.8765 while the turnover ratio of sample funds was 1.0175 percent. The average fund had RM214.44 million in assets under management.\n\na Fund performance measurements: Jensen alpha (single-factor model), Alpha on Fama & French three-factor model (Alpha 2).\n\nb Fund Risk Measurement: Beta, firm size (SMB), book-to-market value (HML).\n\nc Fund Characteristics: expense ratio (Expense), turnover ratio (Turnover), fund size (Size), age of the funds (Age).\n\nTable 4 reports the results among fund characteristics and human capital characteristics with the mutual fund performance (Jensen alpha) by using the CAPM single-factor index and alpha on Fama and French three-factor model on the single equation. The results showed that both fund performances were negatively related to fund expense, although only significant in Jensen alpha.\n\nFund age showed a positive correlation with both fund performances. This indicates that older funds generate higher returns. It is expected that older funds are more mature and established, and can keep the costs lower, which is in line with Gregory et al. (1997). On the other hand, the results revealed a significant, negative relationship between fund performances and fund managers’ possession of a business major degree and Master’s degree. Holding a Master’s degree decreased the Jensen alpha, which indicates that fund managers with a Master’s degree did not add value to their portfolio performance and their stock-picking ability. This result is consistent with Switzer and Huang (2007).\n\nThe age of managers showed a positively significant impact on both fund performances. This is consistent with Gibbons and Murphy (1992). The senior managers who are approaching retirement avoid poor performance which may hurt fund manager’s reputation and reduce their job prospects in the future. The manager team showed a positive relationship with both of the fund performances. This suggests that funds managed by a team tend to benefit the mutual fund. This is consistent with Berkowitz and Qiu (2003). On the other hand, team gender showed a negative impact on fund performances. This indicates that mixed gender in a team underperformed.\n\nTable 5 presents an integrated model of fund characteristics, human capital characteristics, and mutual fund performance, in a simultaneous equation model.\n\n3SLS regression integrated model of fund performance: fund Performance, beta, expense, and turnover from January 2012 – December 2014 in the Malaysian mutual fund industry – simultaneous equation model.\n\nBoth fund performances (Jensen alpha and Alpha 2) were statistically significantly and negatively related to the expense ratio in the simultaneous equation. The fund managers who charge higher expense fees might reduce the fund alpha. This result is consistent with Golec (1996), Switzer and Huang (2007). The turnover ratio showed a positively significant relationship with Jensen’s alpha, which is consistent with Golec (1996). Moreover, the older funds produced better alpha.\n\nThe business major degree and Master’s degree both showed statistically significant relationships with Jensen alpha. Hence, the funds managed by fund managers with business degrees tend to increase the return. Consistent with Switzer and Huang (2007), fund managers with a Master’s degree slightly decreased the Jensen alpha. However, and surprisingly, a professional certification showed no significant influence on both fund performances. Fund managers with a long investment experience had a significantly negative impact on Jensen alpha. This indicates that fund managers with more than 20 years of investment experience do not perform better.\n\nGender appeared to have a positive impact on Jensen alpha, which indicates that male managers were likely to slightly outperform. Additionally, manager age showed a positively significant effect in both of the fund performances. This indicates that senior fund managers had a longer tenure and thus better experience, which led them to generate better fund performance. In addition, the manager age was positively correlated with the fund manager’s experience tenure. On the other hand, team-managed funds showed a significant, positive relationship with Jensen alpha. This indicates that funds managed by more than one fund manager performed better than funds only managed by one.\n\nThe fund age had a positive effect on systematic risk. This result is consistent with Golec (1996). This indicates that older funds are riskier than young funds. Business major and Master’s degree possession showed a statistically significant, negative effect when accounting for the simultaneity. On the other hand, investment experience showed a negative significant relationship with systematic risk. In addition, female fund managers held a higher systematic risk in their fund portfolio, which was consistent with Barber and Odean (2002) and Switzer and Huang (2007). Although professional certification did not show a significant effect in fund performance, it showed a significant, positive effect on beta regression. This indicates that the fund managers who have a professional certification hold higher-risk portfolios.\n\nWith regards to the expense regression, the turnover coefficient was positively significant, which is consistent with Golec (1996) and Switzer and Huang (2007). This means that increased trading activity by fund managers is related to higher-expense funds. Fund size has a positive effect on the expense regression, while fund age showed a negative impact on expense ratio. On the other hand, fund managers’ possession of a Master’s degree and longer tenure of investment experience showed a negative relationship with the expense ratio. Manager age showed a positive impact on expense ratio. Senior fund managers may require higher compensation than young managers.\n\nWith regards to turnover regression, the expense ratio positively affected the turnover ratio. This result is consistent with Switzer and Huang (2007). The higher trading activity may tend to have relatively higher expense costs. The funds with larger fund sizes always showed a more active trading, while fund age had a positive impact on turnover ratio. This indicates that older funds trade more frequently. The fund managers who had business degrees showed a negative impact on portfolio turnover. While fund managers’ in possession of a Master’s degree tended to trade more often. Investment experience was significantly positively related to turnover ratio. The age of the fund managers and team managers showed a negative correlation with turnover ratio. Fund managers below 45 years of age traded more often than senior fund managers. It can be concluded that there is an interrelationship among fund characteristics, human capital characteristics, and fund performance.\n\n\nConclusions\n\nA substantial emphasis is placed on how human capital roles can affect the ultimate work performance of an individual. To date, very little attention has been devoted to seeking empirical evidence for the effects of human capital managerial characteristics especially in the funds industry. Hence, this study identified that fund managers’ education, gender, age, and team managers are significant characteristics in explaining fund performance. Hence, this study provides greater support for human capital theory (Becker, 1964). Although the findings showed that gender is a significant variable in explaining fund performance, the study was unable to provide clear evidence on whether female fund managers in Malaysia outperform their male counterparts. Hence, the relationship between gender and fund performance might need further investigation. To develop a more efficient and competent funds market and financial system, Malaysian regulators need to strengthen fund industry policies and practices, so that typical agency problems, such as excessive managerial expenses and risk-taking can be alleviated.\n\n\nData availability\n\nFigshare: Venny Chong data, https://doi.org/10.6084/m9.figshare.14870556.11\n\nThis project contains the raw human capital, fund characteristics and fund performance data for Malaysia.\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\nAtkinson SM, Baird SB, Frye MB: Do Female Mutual Fund Managers Manage Differently? J Financial Res. 2003; 26(1): 1–18. Publisher Full Text\n\nArif I, Jawaid T: Effect of fund managers’ characteristics on mutual funds performance and fee in emerging market of Paksitan. Munich Personal RePEc Archive (MPRA). 2011: 58936.\n\nBabalos V, Caporale GM, Philippas N: Gender, style diversity, and their effect on fund performance. Res Int Business Finance. 2015; 35: 57–74. Publisher Full Text\n\nBaer M, Kempf A, Ruenzi S: Team management and mutual funds. CFR Working Paper, 05-10. Cologne: University of Cologne; September 2005; 2005.\n\nBank Negara Malaysia: Human Capital Development.2021. (accessed 25th April, 2021). Reference Source\n\nBarber BM, Odean T: Boys will be boys: Gender, overconfidence, and common stock investment. Quarterly J Econ. 2001; 116: 261–292.\n\nBecker GS: A theoretical and empirical analysis with special reference to education.3rd ed.The University of Chicago Press; 1994.\n\nBeckmann D, Menkhoff L: Will women be women? Analyzing the gender difference among financial experts. Kyklos. 2008; 61(3): 364–384. Publisher Full Text\n\nCarhart MM: On persistence in mutual fund performance. J Finance. 1997; 52(1): 57–82. Publisher Full Text\n\nChevalier J, Ellison G: Are some fund managers better than others? Cross-sectional patterns in behavior and performance. J Finance. 1999; 54: 875–879. Publisher Full Text\n\nChong SW, Lai M-M, Chong LL: Venny Chong data.xlsx. figshare. Dataset. 2021. Publisher Full Text\n\nChow TK: An empirical study of mutual funds managers’ Characteristics. Unpublished master’s thesis. Canada: Simon Fraser University; 2007.\n\nDing B, Wermers R: Mutual fund “Stars”: The performance and behavior of U.S. fund managers. Working Paper. 2004. (accessed 20 October 2011). Reference Source\n\nEuropean Central Bank: 2021. (accessed 20 May 2021).Reference Source\n\nFama EF, French KR: Common risk factors in the returns on stocks and bonds. J Financial Economics. 1993; 33: 3–56. Publisher Full Text\n\nFang Y, Wang H: Fund manager characteristics and performance. Investment Analysis J. 2015; 44(1): 102–116. Publisher Full Text\n\nFederation of Investment Managers Malaysia: Industry Statistics.2014. (accessed 10 May 2015). Reference Source\n\nGottesman AA, Morey MR: Manager education and mutual fund performance. J Empirical Finance. 2006; 13: 145–182. Publisher Full Text\n\nGozbasi O, Citak L: An evaluation of the attributes considered by investment professionals in selecting mutual funds: The case of Turkey. Int Res J Finance Economics. 2010; 36: 180–195.\n\nHan Y, Noe T, Rebello M: Horses for courses: Fund managers and organizational structures.University of Oxford; 2012. (accessed 15 March 2015).Reference Source\n\nInvestment Company Institute: Investment Company Fact Book.2016. (accessed 20 May 2018).Reference Source\n\nIslamic Fund and Wealth Management Blueprint: Securities Commission Malaysia.2017. (accessed 20 May 2018).Reference Source\n\nJensen MC: The performance of mutual funds in the period 1945-1964. J Finance. 1968; 23: 389–416. Publisher Full Text\n\nKaragiannidis I: The effect of management team characteristics on risk-taking and style extremity of mutual fund portfolios. Review Financial Economics. 2012; 21: 153–158. Publisher Full Text\n\nLai MM, Lau SH: Evaluating mutual fund performance in an emerging Asian economy: The Malaysian experience. J Asian Economics. 2010; 21: 378–390. Publisher Full Text\n\nLi H, Zhang X, Zhao R: Investing in talents: manager characteristics and hedge fund performance. J Financial Quantitative. 2011; 46(1): 59–82. Publisher Full Text\n\nLow SW: Malaysian unit trust funds’ performance during up and down market conditions. Managerial Finance. 2007; 33(2): 154–166.\n\nLow SW, Ghazali NA: The price linkages between Malaysian unit trust funds and the stock market. Managerial Finance. 2007; 33(2): 89–101. Publisher Full Text\n\nMalaysian Industrial Development Finance Berhad: 2011. (accessed 15 January 2014).Reference Source\n\nMcFadden D: Chapter 6 Simultaneous Equations.1999. (accessed 16 May 2016).Reference Source\n\nMorningstar Research Report: Fund managers by gender.2015. (accessed 5 March 2017).Reference Source\n\nMorningstar.co.uk: Do you own multiple funds run by the same manager?.2015. (accessed 15 April 2017).Reference Source\n\nNiessen A, Ruenzi S: Sex matter: Gender and mutual funds. Centre for Financial Research. Working Paper. 2006. Reference Source\n\nNiessen A, Ruenzi S: Sex matters: Gender and prejudice in the mutual fund industry. SSRN. Working Paper. 2013. (accessed 15 May 2015).Reference Source\n\nNiessen A, Ruenzi S: Sex Matters: Gender bias in the mutual fund industry. SSRN. Working Paper. 2017. (accessed 10 June 2017).Reference Source\n\nNur Adiana AH, Aminah S: A comparative analysis of fixed income unit trust funds versus equity unit trust funds in Malaysia. Asian Acad Management J Accounting Finance. 2019; 15(2): 95–117. Publisher Full Text\n\nPeterson JD, Pietranico PA, Riepe MW, et al.: Explaining after-tax mutual fund performance. Financial Analysts J. 2002; 58(1): 75–86.\n\nPhilpot J, Peterson CA: Manager characteristics and real estate mutual fund returns, risk and fees. Managerial Finance. 2006; 32(12): 988–996. Publisher Full Text\n\nPlantier LC: Globalisation and the Global Growth of Long-Term Mutual Funds. ICI Global Research Perspective. 2014; 1(1). Reference Source\n\nPWC: Covid-19 and The Mutual Fund Industry.2021. (accessed 19 May 2021).Reference Source\n\nReilly FK, Brown KS: Investment analysis and portfolio management. 7th ed. New York: Thompson South-Western, Ohio; 2003.\n\nRuzita AR, Ling PS, Rasidah MR: Performance of local versus international focus Malaysian- based mutual funds. Asian Acad Management J Accounting Finance. 2019; 15(2): 53–75.\n\nSecurities Commission: Statistics for fund management industry.2011. (accessed 5 May 2016).Reference Source\n\nSecurities Commission: 2021. (accessed 5 May 2021).Reference Source\n\nSharpe WF: Mutual fund performance. J Business. 1966; 39(1): 119–138.\n\nShukla R, Singh S: Are CFA charterholders better equity fund maangers? Financial Analysts J. 1994; 50(6): 68–74. Publisher Full Text\n\nSmith A: The Wealth of Nations.1776. (accessed 5 March 2015).Reference Source\n\nSwitzer LN, Huang YF: How does human capital affect the performance of small and mid-cap mutual funds? J Intellectual Capital. 2007; 8(4): 666–681. Publisher Full Text\n\nSwitzer LN, Mariane K: Do company visits add value for professional investors?. J Appl Finance. 2013; 23(1): 71."
}
|
[
{
"id": "93843",
"date": "07 Oct 2021",
"name": "Yi Fang",
"expertise": [
"Reviewer Expertise Asset pricing",
"Financial market"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 investigates the effects of human capital and fund characteristics on mutual fund performance in Malaysia. It discusses risk-adjusted return, risk factors, and team-managed funds. Therefore, it is an interesting piece of work.\nGeneral conclusion\nFrom my point of view, the study should be revised so that it can be modified better and make further contributions. More detailed comments and suggestions are listed as follows. I am totally willing to review a revised version of this paper if the authors correct and revise the paper based on my review.\nThe paper adopts Jensen alpha and alpha on a Fama and French (1993)1 to disentangle fund performance from risk and discuss the effect of risk factors. However, the principal-agent problem of mutual funds most relates to total risk (See, for example, Jorion, 2003, FAJ)2. So the paper can provide some examinations similar to Fang and Wang (2015, IAJ)3. It might find evidence about risk-taking under the framework of performance associated with total risk.\n\nTeam-managed fund decision is a very interesting topic. However, the paper should do more work. I think the test of fund manager effects of human capital and fund characteristics should be in a different framework. Team characteristics are more important.\n\nIn addition, we also can find one manager regulates several funds. The paper should also discuss the phenomenon.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "99131",
"date": "23 Nov 2021",
"name": "Fadillah Mansor",
"expertise": [
"Reviewer Expertise Islamic finance",
"mutual fund",
"fund performance"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe introduction is okay.\n\nThe literature review is adequate, however, most of the previous studies were not recent. Also, I notice that the findings of some previous studies mentioned as support for this study's results were not explained in the literature review section, e.g. Switzer & Huang (2007), Low (2010).\n\nMethodology - the data is quite outdated, perhaps need to justify why the period was chosen. The equation of the tested models was also not presented in this study.\n\nStatistical analysis - In Table 1, mentioned dummy measures, 1; 0, but why results in Table 5 cannot capture and display this measurement, e.g. result of gender between male and female (as mentioned in the conclusion). Others, e.g. results of the dummy variable, fund managers' experience, or less experience. I believe that the statistical part needs rigorous analysis such as normality test and robustness test for clarity.\n\nReferring to the results and discussion section, it needs further explanation about the findings, e.g. on risk, why results have shown that using SMB, the value is smaller/difference, rather than using the two other risk factors. For expense ratio and turnover ratio results, it needs to justify whether the results are supported or not supported by the previous studies.\n\nI also suggest putting a note under the regression tables of the data analysis.\n\nPresentation- some sentences were incomplete. eg. ..this is consistent with xx(xxxx). It needs further clarification (see paragraph before Table 5 for example).\n\nConclusion - not clearly concluded effects of human capital, as well as the significance fund characteristics that influence fund performance was not highlighted in the conclusion section. The key findings were not clearly highlighted. Also, I cannot find Becker's (1964) theory discussed in the earlier section. Please justify.\n\nReferences - recent previous studies are very limited. please add on relevant recent studies especially in the years 2019-2021.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-905
|
https://f1000research.com/articles/10-904/v1
|
09 Sep 21
|
{
"type": "Policy Brief",
"title": "Strengthened family planning is critical to help accelerate the reduction of maternal mortality in Indonesia",
"authors": [
"Budi Utomo",
"Nohan Arum Romadlona",
"Budi Utomo"
],
"abstract": "The still stubbornly high maternal mortality ratio challenges Indonesia to improve health program strategies to achieve the Sustainable Development Goal 3.1 target of a maternal mortality ratio below 70 per 100,000 live births by 2030. Indonesia has already adopted maternal-neonatal health experts’ recommendation of four core program strategies to reduce maternal mortality: (1) family planning with related reproductive health services; (2) skilled care during pregnancy and childbirth; (3) timely emergency obstetric care; and (4) immediate postnatal care (WHO, 1996). These four core strategies would reduce maternal mortality through reduced high-risk births. To be effective, however, these four core program strategies require continued strong quality assurance and central and local government support to ensure program effectiveness yielded towards widely accessible, sustained, quality family planning and maternal and neonatal emergency services. This paper provides evidence for the importance of family planning to help health program strategies to accelerate maternal mortality reduction.",
"keywords": [
"family planning",
"maternal mortality",
"Indonesia"
],
"content": "Introduction\n\nThe still stubbornly high maternal mortality ratio challenges Indonesia to improve health program strategies to achieve the Sustainable Development Goal 3.1 target of a maternal mortality ratio below 70 per 100,000 live births by 2030. The available estimates of maternal mortality ratio for the period of 2000-2017 ranged widely between 175 and 350 maternal deaths per 100,000 live births (Soemantri 2014; Statistics Indonesia 2015; Hasbullah et al., 2016; WHO, 2019).1 The UNFPA Indonesia panel of mortality estimation working group, using only the past year’s direct record of maternal mortality data from the Intercensal Population Survey (SUPAS) 2015, produced an estimate of 237 maternal deaths per 100,000 live births (UNFPA Indonesia, 2018).2 The Indonesian maternal mortality ratio is a paradox, as other countries with similar levels of socio-economic development have much lower maternal mortality ratios; for example, the following ratios for South-East Asian countries were measured in 2017: Cambodia 160, Indonesia 177, Malaysia 29, Myanmar 250, Philippines 121, Thailand 37, Vietnam 43, and Singapore 8 (WHO, 2019). In contrast, the maternal mortality ratios in several developed countries are much lower, amounting to 5 or below: Denmark 4, Netherlands 5, Norway 2, Spain 4, and Sweden 4 (WHO, 2019).\n\nIndonesia has already adopted maternal-neonatal health experts’ recommendation of four core program strategies to reduce maternal mortality: (1) Family planning with related reproductive health services; (2) skilled care during pregnancy and childbirth; (3) timely emergency obstetric care; and (4) immediate postnatal care (WHO, 1996). These four core strategies would reduce maternal mortality through reduced high-risk births. Unlike the other core strategies, family planning would also reduce maternal mortality via reduced births. Voluntary family planning would reduce unwanted pregnancies and the four ‘too’ high-risk births: too old, too young, too frequent, and too many births. To be effective, however, these four core program strategies require continued strong quality assurance and central and local government support to ensure program effectiveness yielded towards widely accessible, sustained, quality family planning, and maternal and neonatal emergency services. This paper provides evidence for the importance of family planning to help health program strategies to accelerate the reduction in maternal mortality.\n\n\nPolicy outcomes and implications\n\nFamily planning is a strategic nation-building program with an intended double effect: (a) promote healthy mothers, children, families and communities (Smith et al., 2009); and (b) ensure sustainable development by balancing population with the state of development and the living environment (Starbird et al., 2016). Family planning protects women from unwanted and high-risk pregnancies. Women with an unwanted pregnancy might try a number of means to abort their pregnancy (Hull et al., 1993). These women, in a setting where abortion is illegal, tend to seek care with a clandestine provider who performs unsafe abortions, facing high risks of maternal complications and mortality.\n\nFamily planning, through the use of contraceptives, regulates pregnancies so that they occur only when women or couples are physically, mentally and socially ready. The four ‘too’ pregnancies - too young or too old to be pregnant, too little time between pregnancies, or too many pregnancies - put women and their pregnancy at a high risk of maternal complications and death. Effective family planning, by ensuring every pregnancy is at the lowest risk of maternal complications and death, would promote healthy pregnancies and newborns. Family planning, through reduced births, controls population growth and balances it with socio-economic development and the living environment, and through reduced high-risk births reduces the risk of maternal mortality for each birth. Voluntary family planning ensures sustainable development and builds healthy generations (Aspen Institute, 2011). Moreover, one review suggests investing in family planning could accelerate achievements for all the Sustainable Development Goal themes of People, Planet, Prosperity, Peace, and Partnership (Starbird et al., 2016).\n\nThe Indonesian family planning program has been considered successful in reducing fertility and maternal mortality. Within three decades of its initiation, from the early 1970s to early 2000s, the program brought the contraceptive prevalence rate from 5% to over 50%, and brought down the total fertility rate from 5.0 to 2.3 (Hull and Mosley, 2009). The program’s success was related in part to international support and the government’s strong commitment to family planning. However, social and political changes linked to decentralizing development occurring in the early of 2000s, have disrupted the progress of many development programs, including family planning. Since then, many development programs have slowed down or even stagnated to reflect decelerated developments (Bappenas, 2007, 2011) and the total fertility and contraceptive prevalence rates, used as the family program achievement indicators, had stagnated around 2.6 and 55%, respectively (BPS, BKKBN, Kemenkes, and ICF International, 2018).\n\nTo this day, the regional disparity of contraceptive access and service quality remains striking. The national modern contraceptive prevalence rate among currently married women accounts for 57%, but the rates remain much lower for some parts of Sumatra, Nusa Tenggara, Sulawesi, Maluku and Papua (BPS, BKKBN, Kemenkes, and ICF International, 2018:152). The use of short-term contraceptive methods dominate.\n\nGeographic isolation hampers women’s access to long-term contraceptive methods, i.e. intrauterine device (IUD) and sterilization (Febriani, 2012). The unmet need for contraception (UNC) - defined as the percentage of women of reproductive age who want to postpone pregnancy or do not want more children, but are not using contraceptives – has remained stable during the past three decades, at 12% in 1991 and 11% in 2017 (BPS, BKKBN, Kemenkes, and ICF International, 2018:108). The still relatively high UNC translates to around five million women of reproductive age who are sexually active being at risk of unwanted pregnancies (BPS, 2018)3.\n\nThe low use of contraceptive or the high UNC implies low access by women or couples to family planning information and services. Several factors associated with low use of contraceptives include: fear of contraceptive side effects, husband disapproval of use of contraceptive, and cost constraints (Bongaarts et al., 2012). In Papua, the public misperception that contraceptive use would cause infertility has prompted the high UNC (Tjiong, 2012). Common traditional beliefs unfavorable to family planning, such as 'a family should have a boy' and 'many children bring a lot of luck', have persisted in some communities, restricting the search for family planning services (Febriani, 2012).\n\nThe family planning program’s effectiveness has declined during the past decade and a half, as indicated by the increasing dropout rates of contraceptive use and the shift from predominantly long-term to predominantly short-term contraceptive methods. The proportion of women who started using a contraceptive, but discontinued use within 12 months has increased from 25% during 1991-2012 to 34% in 2017 (IDHS). Side effects and/or health concerns were the most cited reasons for contraceptive use discontinuation (BPS, BKKBN, Kemenkes, ICF International, 2018:101).\n\nThe shift in contraceptive method mixed (Figure 1) reflects the declining quality of the family planning program (Hayes, 2012). The cost of contraceptives is one key factor limiting the choice of contraceptive method. The poorest quintile population used less effective short-term methods, while the richest used more effective long-term contraceptive methods (BPS, BKKBN, Kemenkes, and ICF International, 2018:117-118). For the provider, offering short-term contraceptive methods is more practical than providing long-term ones; while for the clients the use of injections is simpler as it requires only one visit every three-months and does not need invasive examination (Febriani, 2012).\n\nSF (sterilization of female); SM (sterilization of male); IUD, intrauterine device.\n\nSource: Indonesia Demographic Health Survey 1987-2017.\n\nThe country’s two main sources of family planning services, i.e. health centers and midwife private practices, have a limited capacity to offer quality services. The national survey of health centers conducted in 2011 showed 61% did not have a counseling room, 19% operated in a dilapidated building, 28% had no clean water infrastructures, and 55% did not have a safe waste disposal system (Kemenkes, 2012). One study in Bogor Regency reported most midwife private practices did not offer counseling on contraceptive options (Habsjah, 2009). Proper counseling is critical to assist clients in choosing the most suitable method of contraceptive for them, to ensure contraceptive use effectiveness and minimize side effects (Bruce, 1990). One field study demonstrated that enhancing counseling and clinical management skills of service personnel could lead to increased use of long-term contraceptives (Febriani, 2012).\n\nFamily planning reduces maternal deaths via two mechanisms: reduced births and reduced high-risk births (Ross and Blanc, 2012). Reduced births lead to reduced maternal deaths since the probability of a fatal outcome decreases with a lower number of pregnancies. Reduced high-risk births lead to a lowered risk of maternal death per birth. Worldwide studies have provided consistent results showing that family planning programs reduce fertility and contribute highly to reducing maternal mortality (WHO, 1996; Ross JA et al., 2012; Cleland et al., 2012; Ahmed et al., 2012).\n\nUsing a counterfactual modeling approach, Ahmed et al. (2012) showed that the contribution of contraceptive use to reducing maternal deaths across 172 countries ranged from 7% and 60%, or 44% overall (Ahmed et al., 2012). An additional 29% reduction of maternal deaths could happen by satisfying the UNC. The size of family planning’s contribution to reducing maternal deaths depends on the levels of contraceptive use and UNC. Stover and Ross (2010) in a different analysis showed that the increasing contraceptive use in all developing countries studied from the historically low levels to a high-level is parallel to 31% of the overall decline of maternal mortality ratio (Stover and Ross, 2010).\n\nMaternal deaths decomposition analysis\n\nA recent study based on a decomposition analysis showed that the Indonesian family planning program has contributed highly to reducing maternal mortality (Utomo et al., 2021). The analysis showed that the Indonesian family planning program averted 150.5 million births between 1970-2017, a 40.7% reduction in births. The majority of the 94.8 million averted births occurred after the year 2000 when the contraceptive prevalence rate had already surpassed 50%. The Indonesian national family planning program averted 592.5 million maternal deaths between 1970 and 2017, a 40.4% reduction. Of the maternal deaths averted, 57% occurred after the year 2000.\n\nSurvival analysis: use of contraceptive and the reproductive aged women risk of mortality\n\nThe Cox regression survival analysis of women of reproductive age, using panel data from the Indonesia Family Life Survey rounds: 1993, 1997, 2000, 2007, and 2014, showed the use of contraceptives reduced the risk of mortality of reproductive-aged women (Besral et al., 2019). The analysis prospectively evaluated the effect of contraceptive use duration on survival status of women of reproductive age, controlling for socio-economic, demographic and health service factors (Table 1). This complete analysis will be presented in the separate paper.\n\nCox regression survival analysis of women of reproductive age by contraceptive use duration, the Indonesia Family Life Survey rounds 1993, 1997, 2000, 2007, and 2014 (n = 11,492 women of reproductive age).\n\nThe analysis demonstrates the dose-response effect of contraceptive use duration on reducing the risk of mortality in women of reproductive age. The longer the use of contraceptives, the lower the number of women of reproductive age at risk of mortality. The dose-response effect of contraceptive use duration on reducing women of reproductive age’s risk of death persists, even controlled by the woman’s education, age, residential site, household socio-economic status, and health service access factors. Women of reproductive age with contraceptive use durations of more than 13 years had a four times lower risk of death than the women of reproductive age who never used a contraceptive.\n\nSUPAS 2015 and Village Potential Census (PODES) 2014 data analysis: contraceptive use and maternal mortality\n\nA community-level ecological multivariable log-linear regression analysis using SUPAS 2015 and Village Potential Census (PODES) 2014 data showed that contraceptive use lowers the risk of maternal mortality (Aryanty et al., 2021). The analysis included a sample of 40,728 census blocks (each block with a sample size of 16 households) dispersed across the country major islands. The PODES 2014 database was merged with the SUPAS 2015 dataset to obtain the health service supply variables. Census blocks with high use of contraceptive had lower risks of maternal mortality than the census blocks with low use of contraceptive (Figure 2). The analysis also found a lower risk of maternal mortality associated with higher hospital densities in the locality; in addition, the lower the household’s socio-economic status, the higher the risk of maternal mortality. Surprisingly, a higher traditional birth attendant (TBA) density in the village led to a higher risk of maternal mortality. Hence, the presence of TBAs in the village likely slows down the maternal complication case referral process.\n\nReference = The left side below zero represents low risk, the right side above zero represents high risk.\n\nTBA = traditional birth attendant.\n\nFigure source: Aryanty et al. (2021).\n\nData sources: Indonesia Intercensal Survey 2015 (SUPAS) and Village Potential Census 2014 (PODES).\n\nSimulation: could strengthened family planning further reduce maternal mortality?\n\nIndonesia’s maternal mortality ratio has been declining, with an annual reduction rate of six points from over 500 in the early 1970s, to slightly below 300 maternal deaths per 100,000 live births in the early 2000s (MoH, 2019; Cameron, et al., 2019; Fortney et al., 1988). Since then, the maternal mortality ratio declining trend has slowed down, or even stagnated to an annual reduction rate of only two points (Figure 3). Following this slowed down declining trend, the maternal mortality ratio is predicted to be at 243 by 2030, which is 173 points above the SDG 3.1 target of a maternal mortality rate below 70. Additional programmatic efforts will be required to achieve the SDG 3.1 target.\n\nSources: Population Censuses (1971, 1980, 1990, 2000, and 2010) and Inter-Censal Population Surveys (1985, 1995, 2005, and 2015).\n\nHow could family planning further reduce maternal mortality? The future potential contribution of family planning to reduce maternal mortality is clear: (a) the UNC is still relatively high, reported at 11% in 2017 (ranging by province from 4% to 24%) (BPS, BKKBN, Kemenkes, and ICF International, 2018: 293), and (b) the notable geographical inequality of contraceptive service access, i.e. the national average modern contraceptive prevalence rate among currently married women was 57.2% in 2017, while as many as 15 provinces had a modern contraceptive prevalence rate of 50% or below, and five provinces had a rate below 45% (BPS, BKKBN, Kemenkes, and ICF International, 2018: 290). Thus, family planning has the potential to reduce the UNC and increase the contraceptive prevalence rate, particularly in these 15 provinces. Reducing the UNC means reducing high-risk pregnancies and, thus, reducing the risk of maternal mortality per birth. Similarly, increasing the contraceptive prevalence rate means reducing the number of births and, thus, reducing the risk of maternal death per mother.\n\nUtomo et al. (2021) carried out a simulation to compare declining trends of maternal mortality ratio between 2017-2030 depending on three different situations: (1) continued stabilization of a contraceptive prevalence rate (CPR) of 63% and UNC of 10%; (2) CPR increases linearly from 63% to 70% and UNC reduces from 10% to 7%; and (3) CPR increases linearly from 63% to 75% and UNC reduces from 10% to 5%. The simulation analysis showed that by increasing CPR from 63% to 70% and reducing UNC from 10% to 7% (Situation 2) as compared to Situation 1 corresponding to stabilization of CPR and UNC, family planning could further avert 35,897 additional maternal deaths (19.5%) between 2017 and 2030. Further, by increasing CPR from 63% to 75% and reducing UNC from 10% to 5% (Situation 3), as compared to Situation 1, family planning could further avert 53,247 additional maternal deaths (28.9%) between 2017 and 2030. Regarding the reduction of the maternal mortality ratio in the period 2017-2030, the maternal mortality ratio under Situation 1 (stabilized family planning) would reduce from 255 to 221; however, under Situation 2, it would decrease from 255 to 164, while under Situation 3, it would reduce from 255 to 125. This simulation analysis demonstrates that a strengthened family planning, increasing CPR from 63% to 75% and reducing UNC from 10% to 5%, could bring down the maternal mortality ratio by about 50%, to reach 125 maternal deaths per 100,000 live births. With a strengthened family planning program, the health sector’s task of accelerating the decrease of maternal mortality rates becomes less of a burden, not to bring down MMR from 255 to 70 but from 125 to 70 to achieve the SDG 3.1 target by 2030.\n\n\nActionable recommendations\n\nThe National Family Planning Board (BKKBN) is developing strategic plans for a rights-based family planning program (BKKBN, 2019). The rights-based family planning program, if implemented as planned, would contribute to improving the quality of human resources, through training and provision to health practitioners that represent and covered geographic inequities in health resources, in provinces and districts in the eastern part is relatively under-developed compared to Java-Bali. For decentralized family planning, the national strategic plans should be translated to the district/city-locally strategic plans to guide micro-managing family planning programs and services. Attention needs to be directed in priority towards rectifying remaining geographic and socioeconomic inequities in the access to accurate information and services, more effectively addressing local barriers and constraints to family planning uptake, providing informed choices across a full range of contraceptive methods, and improving the service quality. Challenges to decentralized rights-based family planning services would include: (1) coordination of stakeholders; (2) local institutional capacity strengthening; (3) the family planning information system; (4) provision of rights-based family planning services; (5) mechanisms of purchasing and financing family planning services; (6) evidence-based advocacy to local leaders; and (7) integration of family planning into other reproductive health services.\n\n\nConclusions\n\nThe analyses presented above show that a family planning program is a strategic national intervention to help reduce maternal mortality. Substantial reductions in maternal mortality between the years 1970 and 2017 can be attributed to the successes of the national family planning program. A decline in quality of family planning, has been occurring since the early 2000s, parallel to social change and reduced international and government support; however, this could potentially be reversed towards strong voluntary family planning, as the country has experience of managing successful family planning during the first three decades from its initiation. Government support and strengthening national and local governance to manage effective voluntary family planning is critical to ensure quality family planning and reach women in need.\n\n\nData availability\n\nThe data used in the policy brief were produced by the Government of Indonesia, Central Statistics Bureau (Badan Pusat Statistik - BPS), please consult the BPS website for further information on publications and access to data. The Indonesian Demographic and Health Survey (IDHS) reports and data files used in the study are accessible via the DHS/IRC website. Indonesia Family Life Survey are available online.\n\nData sources of Figure 1\n\n- Raw data and report from Indonesia Demographic Health Survey 1987, 1991, 1994, 1997, 2002, 2007, 2012, and 2017.\n\n- This data is open access and can be accessed at https://www.dhsprogram.com/.\n\nData sources of Table 1\n\n- Raw data from Indonesia Family Life Survey 1993, 1997, 2000, 2007, 2014.\n\n- This data is open access and can be accessed at https://www.rand.org.\n\nData sources of Figure 2\n\n- Indonesia Intercensal Survey 2015 (SUPAS) and Village Potential Census 2014 (PODES) from Central Statistics Bureau (Badan Pusat Statistik - BPS)\n\n- This raw data is not open for public and need to consult to BPS to access the data. Report is available and can be accessed at https://www.bps.go.id/v.\n\n- This figure is originally presented from our publish research that can be accessed at https://doi.org/10.1186/s12978-020-01022-6\n\nData sources of Figure 3\n\n- Population Censuses (1971, 1980, 1990, 2000, and 2010) and Inter-Censal Population Surveys (1985, 1995, 2005, and 2015)\n\n- Data from figure 3 was generated from the report of Population Censuses and Inte-censal Population Surveys that can be accessed at https://www.bps.go.id/.",
"appendix": "References\n\nAhmed S, Li Q, Liu L, et al.: Maternal deaths averted by contraceptive use: an analysis of 172 countries. Lancet. 2012; 380: 111–25. Published Online July 10, 2012. PubMed Abstract | Publisher Full Text\n\nAryanty RI, Romadlona N, Besral B, et al.: Contraceptive use and maternal mortality in Indonesia: a community-level ecological analysis. Reprod Health . 2021; 18: 42. Publisher Full Text\n\nAspen Institute: Population Growth, Reproductive Health and Sustainable Development Policy Brief, December. Global Leaders Council for Reproductive Health. 2011; Reference Source\n\nBappenas: Report on the Achievement of Millennium Development Goals in Indonesia.Jakarta; 2007.\n\nBappenas: Report on the Achievement of Millennium Development Goals in Indonesia.Jakarta; 2011.\n\nBesral, Kurniawan R, Utomo B, Aryanty RI, et al.: Contraceptive use among women of reproductive age reduces the risk of maternal mortality – Analysis of panel data of IFLS 1993-2014.2019. Manuscript.\n\nBongaarts J, Cleland J, Townsend JW, et al.: Family Planning Programs for the 21st Century: Rationale and design . New York: Population Council; 2012.\n\nBruce J: Fundamental Elements of the Quality of Care: A Simple Framework. Stud Fam Plann . 1990; 21(2): 61–91. PubMed Abstract\n\nCameron L, Contreras Suarez D, Cornwell K: Understanding the determinants of maternal mortality: An observational study using the Indonesian Population Census. PloS one . 2019; 14(6): e0217386. Publisher Full Text\n\nCleland J, Conde-Agudelo A, Peterson H, et al.: Contraception and health. Lancet. 2012; 380(9837): 149–156. Publisher Full Text\n\nFebriani E: The Regency Family Planning Situation Analysis: Report . Jakarta: UNFPA Indonesia; 2012.\n\nFebriani E: Report of Situation Analysis Result of the Family Planning Program in the Regency . Jakarta: UNFPA Indonesia; 2012.\n\nFortney JA, Susanti I, Gadalla S, et al.: Maternal mortality in Indonesia and Egypt. Int J Gynaecol Obstet. 1988; 26(1): 21–32. PubMed Abstract | Publisher Full Text\n\nHabsjah A: Contraception in the Decentralization Era in Indonesia. The Asia-Pacific Resource & Research Centre for Women (ARROW). Kuala Lumpur, Malaysia; 2009.\n\nHasbullah MS, Surbakti IM, dan Handiyatmo D: Kematian Maternal di Indonesia Hasil Supas 2015. Forum Masyarakat Statistik . Statistical and Policy Brief. Edisi 8; 2016.\n\nHayes AC: The UNFPA-BKKBN Partnership Regarding Family Planning under the 8th Country Programme . UNFPA, Jakarta: Strategy Paper; 2012.\n\nHull TH, Mosley H: Revitalization of Family Planning in Indonesia . Jakarta: The Government of Indonesia and United Nations Population Fund; 2009.\n\nHull TH, Sarwono SW, Widyantoro N: Induced Abortion in Indonesia. Stud Fam Plann. 1993; 24(4): 241–251. PubMed Abstract\n\nMoH (KemKes): Laporan Akhir Riset Fasilitas Kesehatan 2011, Puskesmas . Jakarta: Badan Litbangkes; 2012. Reference Source\n\nMoH (Kemkes): Profil Kesehatan Indonesia Tahun 2018 . Jakarta: Kementerian Kesehatan RI; 2019; 2019. . 978-602-656-446-4.\n\nRoss JA, Blanc AK: ‘Why Aren’t There More Maternal Deaths? ‘A Decomposition Analysis’. Matern Child Health J. 2012; 16: 456–463. Published online: 24 March 2011. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSmith R, Ashford L, Gribble J, et al.: Family Planning Saves Lives . Fourth ed . Washington, DC: Population Reference Bureau; 2009. Reference Source\n\nSoemantri S: Telaah Perkiraan AKI (MM Ratio) Untuk Indonesia. Forum Masyarakat Statistik. Statistical and Policy Brief. Edisi 4; 2014.\n\nStatistics Indonesia (BPS): Proyeksi Penduduk Indonesia 2015-2045 Hasil SUPAS 2015.Jakarta, Indonesia: BPS; 2018; 978-602-438-189-9.\n\nStatistics Indonesia (BPS), National Population and Family Planning Board (BKKBN), Ministry of Health (Kemenkes), and ICF International: Indonesia Demographic and Health Survey 2017 . Jakarta, Indonesia: BKKBN, BPS, Kemenkes, and ICF; 2018.\n\nStarbird E, Norton M, Marcus R: Investing in Family Planning: Key to Achieving the Sustainable Development Goals. Glob Health Sci Pract. 2016; 4(2): 191–210. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStover J, Ross J: How increased contraceptive use has reduced maternal mortality. Matern Child Health J . 2010; 14: 687–695. PubMed Abstract | Publisher Full Text\n\nTjiong R: Isu Strategis KB di Papua. Presented at Development of Family Planning Training Packaged, Jayapura, 3-5 July.2012.\n\nUNFPA Indonesia: Maternal Mortality Estimation in Indonesia: A Panel Review. Report. 2018. Publisher Full Text\n\nUtomo B, Sucahya PK, Romadlona NA, et al.: The impact of family planning on maternal mortality in Indonesia: what future contribution can be expected? Popul Health Metr . 2021; 19: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Mother–baby package: implementing safe motherhood in countries.Geneva: World Health Organization; 1996. (accessed 24 March, 2019).Reference Source\n\nWHO: Trends in maternal mortality 2000 to 2017: estimates by WHO, UNICEF, UNFPA, World Bank Group and the United Nations Population Division.Geneva: World Health Organization; 2019. Licence: CC BY-NC-SA 3.0 IGO.\n\n\nFootnotes\n\n1 Lower estimates provided by the Maternal Mortality Estimation Inter-Agency Group (MMEIG) WHO, UNICEF, UNFPA, World Bank Group and the United Nations Population Division; and higher estimates provided by Badan Pusat Statistik (Indonesia Statistics). See also Hasbullah et al., 2016; Soemantri, 2014.\n\n2 Using one-year recall of maternal death, instead of five-year recall as done in the official estimate, would result in less under-reporting of death.\n\n3 Computation based on the unmet need for contraception and the sexually active reproductive aged women 2017 from Indonesia data population projection 2015-2045."
}
|
[
{
"id": "94219",
"date": "04 Oct 2021",
"name": "Maria Gayatri",
"expertise": [
"Reviewer Expertise Family planning program",
"biostatistics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript submitted by Budi Utomo and Nohan Arum Romadlona aims to provide some strategies based on the evidence to strengthen family planning program in Indonesia. Overall, the article presents evidence that would be of interest the Government and community of scientists concerned with the problem of maternal and child health. Prior to indexing, the following points should be addressed.\nPlease provide more detailed action recommendations.\n\nPlease add some evidence related to the performance of field workers in the family planning programs.\nThank you. The article is already comprehensive.",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-904
|
https://f1000research.com/articles/10-903/v1
|
08 Sep 21
|
{
"type": "Research Article",
"title": "Detecting industrial motor faults with current signatures",
"authors": [
"Shashikumar Krishnan",
"Vijayakumar Vengadasalam",
"Vijayakumar Vengadasalam"
],
"abstract": "Background: A major player in industry is the induction motor. The constant motion and mechanical nature of motors causes much wear and tear, creating a need for frequent maintenance such as changing contact brushes. Unmannered and infrequent monitoring of motors, as is common in the industry, can lead to overexertion and cause major faults. If a motor fault is detected earlier through the use of automated fault monitoring, it could prevent minor faults from developing into major faults, reducing the cost and down-time of production due the motor repairs. There are few available methods to detect three-phase motor faults. One method is to analyze average vibration signals values of V, I, pf, P, Q, S, THD and frequency. Others are to analyze instantaneous signal signatures of V and I frequencies, or V and I trajectory plotting a Lissajous curve. These methods need at least three sensors for current and three for voltage for a three-phase motor detection. Methods: Our proposed method of monitoring faults in three-phase industrial motors uses Hilbert Transform (HT) instantaneous current signature curve only, reducing the number of sensors required. Our system detects fault signatures accurately at any voltage or current levels, whether it is delta or star connected motors. This is due to our system design, which incorporates normalized curves of HT in the fault analysis database. We have conducted this experiment in our campus laboratory for two different three-phase motors with four different fault experiments. Results: The results shown in this paper are a comparison of two methods, the V and I Lissajous trajectory curve and our HT instantaneous current signature curve. Conclusion: We have chosen them as our benchmark as their fault results closely resemble our system results, but our system benefits such as universality and a cost reduction in sensors of 50%.",
"keywords": [
"Hilbert Transform",
"AI",
"3-phase",
"Induction Motor"
],
"content": "Introduction\n\nThere are many common causes of motor failures that happen in industry, such as voltage imbalance, transient voltage, harmonic distortion, sigma currents, operation overloads, shaft voltage and many more. A three-phase induction motor is the most common, significant machine used in industry compared with direct current (DC) motors.1\n\nThis induction motor is exposed to a variety of conditions that will cause motor failure such as shaft imbalance, which will subsequently reduce its lifetime. Therefore, faults such as a fractured rotor bar and irregular air gap eccentricities must be detected at the earliest stage possible2 to prevent the motor from sustaining worse damage and deteriorating in performance.3 There are many conventional methods available in order to maintain a motor's condition; for example, an engineer or technician might carry out scheduled check-ups in order to inspect the condition of a motor and rectify any faults. One of the fault detection systems available in the market is the Motor Current Signature Analysis (MCSA).\n\nThe fundamentals of applying MCSA,4 the current and voltage waveform, will be analyzed to produce the power signal known as motor signatures. The obtained unique waveform will help the user in distinguishing and sorting out the healthy from the unhealthy motors.5 MCSA is able to detect various types of faults such as air gap irregularities, which are divided into static, dynamic or both.6 Throughout recent years, the advancement of Appliance Load Monitoring (ALM) has been proposed to carry out particularized energy sensing and to give information on the separation of the energy.7 ALM was classified into non-intrusive8 and intrusive9,10 load monitoring. Normal electrical and mechanical conditions which lead to machine failure need to be tracked.11 In previous years, Fast Fourier Transform (FFT) of MCSA was widely used in detecting faults. Then, a new method called Park’s vector method was proposed for further investigation of motor faults.12 Some methods involving artificial intelligence had been used for identifying faults by using fully automated pattern recognition.13,14 In literature15 active real power signatures have been used as the basics of fault identification, while other research has used raw single-cycle current, instantaneous power and admittance spectrum for this purpose.16 V-I trajectory is a measurement that refers to voltage and current waveform in implementing nomenclature of device signatures.17\n\nThis project was conducted to detect and monitor the faults for three-phase machines, which will help technicians and engineers working in industry in detecting the faults. This would also help in improving the maintenance and productivity of an industry. We designed this project by applying artificial intelligence to distinguish between a healthy and faulty electrical machine in industry, which would help create an easier to use and cost-effective design. A minimum of 10 training data samples of motor faults that have minimum variations from the actual data are used for comparison and analysis.18 Convolution Neural Network (CNN) is used for disaggregation purposes and is often used in computer recognition.19 Hilbert Transform (HT) application in this project has been helpful in detecting faults with clear visualization by using a minimum number of sensors. We designed a three-phase machine monitoring and pre-fault detection system to aid engineers for preventive maintenance. By the end of this project, we were able to monitor and detect the healthy condition of the three-phase machine, and to differentiate each of the faults occurring and propose a suitable artificial intelligence method to solve the faults.\n\n\nMethods\n\nThere are two types of load monitoring7 non-intrusive load monitoring (NILM)8 and intrusive load monitoring.9 We are using the non-intrusive type as it does not need to physically hijack the wires of the three-phase motor, granting ease of installation with plug and play. The microcontroller we have chosen is Arduino Mega 2560 R3 which is suitable to use as a high-speed logger for the 50Hz power signals.20 The Arduino was inserted with ethernet shield W5100 module and micro SD card, AC potential sensor 2mA single phase transformer ZMPT101B and the NILM split-core AC current sensor SCT 013-030 rated 30A manufactured by YHDC as shown Figure 1. This Arduino Mega hardware setup was combined with implementation of Arduino Software IDE Version 1.8.15 for coding and programming. The high sampling rate of 8500 samples/second per input were taken.\n\nThe hardware system used in Figures 1 and 2 is for benchmarking two methods: V and I Lissajous trajectory curve, and our HT instantaneous current signature curve. Our system alone would result in deleting the VT sensors.\n\nThe potential or voltage sensor (VT) and current sensor (CT) data was captured and stored inside the micro SD card in comma-separated value “.csv” files. The whole process is shown in Figure 3 block diagram. The MatLAB version 2019b or SicLAB version 6.0.2 software was used to process the data. The analysis process resulted in two different graphs: HT plot and V-I trajectory plot. Figure 4 shows a portion of the MatLAB/SicLAB code used to plot the two different graphs. The first part of the code is used to plot VI instantaneous curve using the raw VT and CT sensor data of the red phase. The second part of the code used the raw VT and CT sensor data of the red phase normalized to 0 to 1 of amplitude and plotted them as VI Lissajous trajectory. The final part of the code used only the raw CT sensor data of the red phase that is normalized and creates two sets of data, real and imaginary. Both of them are plotted into a Lissajous plot that we refer to as HT of I only plot.\n\nFor manual user interface detection of motor faults by employees (technicians) viewing our HT plot installed in a computer, this would only involve phases one and two as described above. This process involves the comparison of pre-determined plots of faults of the motor charts, and technicians could compare them with current real-time HT plots.\n\nAn automated artificial intelligence (AI) fault detection involves our method’s phase three, where we have used pre-determined charts or plots of faulty and normal running (healthy) motors to classify types of fault automatically without the involvement of humans.4,5 The Jupyter Notebook (IPython 7.11.1) was used here to train and test the data for further processes. The system also needs the machine learning libraries from scikit-learn version 0.22 with all the algorithms available there. Next, the directories of testing and training data needed to be set up. This involves 10 samples of HT of current plot for each data sample of the motor faults. The 10 samples taken should have minimum deviation or variations between them, and this is repeated for all the five types of faults detected in this paper. It also requires 10 sample of HT of current plot data samples of normal running (healthy) motor for comparison and analysis. Next, disaggregation algorithms were applied to the datasets and boundaries were drawn to classify that the motor was either in a normal running (healthy) or faulty condition. The system would then determine to which dataset the boundaries belong to according to the similarities, by comparing the figures inside training dataset. Increasing the amount of data trained would significantly increase the system accuracy. There are three algorithms21 used to disaggregate the data sample: vector machine,22 naïve Bayes23 and k-nearest neighbours.24 This would print the predictions based on their respective algorithms. Lastly, the result of machine learning was produced based on the training of the 10 samples. In order to increase its accuracy, as much data needed to be collected as possible.\n\n\nResults\n\nFigure 5a shows the three-phase instantaneous current and voltage raw data samples taken for a normal running at healthy conditions of a three-phase motor. Approximately 56000 samples of VT and CT were taken in 6.5 seconds. The V-I trajectory and HT graph were put into one plane according to its phase. Based on the observations, there was a small gap in between each of the phases, where it determined the differences in voltage and current in the system were quite small when the graphs were overlaid on each other. The shapes from each phase merely look alike and appear as round or oval shapes. Hence, these observations indicated the system was in a healthy condition. Figure 5c, which used only our HT current signatures curve method, shows the same result observed in Figure 5b using Lissajous voltage and current signatures curve.25\n\nThe three-phase 1-2-3 is represented in this paper as red-yellow-blue colours. Figure 5a shows the three-phase instantaneous current and voltage raw data sample that were taken, approximately 150000 samples of VT and CT in 6.5 seconds for mode 2 faulty motor. The fault was performed by allowing the motor to run in normal condition for approximately 5.3 seconds, before the second sequence phase (yellow phase) was pulled out of the motor terminal. Figure 6a shows that some noise occurred after the yellow phase was pulled out. The yellow phase current was completely out and became zero, which affected the other two remaining phases.\n\nThe V-I trajectory and HT graphs of Figures 6b and c, respectively, clearly show some distortion and difference in their shapes when compared with the normal running (healthy) condition (mode 1) in Figure 5. The bottom left quadrant of Figures 6b and c shows the combined phase graph that represents the different behavior of each graph right after the yellow phase was pulled out. Then, it was observed that there were gaps in between each phase when they were put in one plane. The gaps proved the difference in voltage and current in the system that appeared when the graphs were overlapped to each other. This observation indicated the system was in a faulty condition since there were gaps and differences when compared with the healthy condition. Figure 6d shows the value calculated from MATLAB obtained from the raw data. The value of maximum voltage and current were increased slightly due to some noise occurring after the yellow phase was pulled out.\n\nThe phases extracted from the graphs, as are shown in Figure 7a, show the condition of each phase voltage and current taken, approximately 95000 samples in 6.5 seconds for mode 3 faulty motor. The currents for all the phases were almost zero before the motor starts where else there will be voltage across the motor measured even though motor is in halt position. Then the second sequence (yellow phase) was pulled out just before starting the motor as shown in the Figure 7a. The current was increased instantly during this time, while the voltage waveform became a bit noisy in a fraction of a second (transient). There were large differences between each of the phases in Figures 7b and c where these determined the difference of voltage and current in the system after the graph overlapped with each other. The shapes produced from the HT and V-I trajectory were very different from the oval shape displayed by the normal running condition (mode 1), due to the transient effect after the yellow phase was pulled out. Therefore, this indicated that the system is in fault condition. The numerical data calculated from MatLAB in Figure 7d showed a different value pattern with the healthy condition. The value of the maximum current rose to extremely high levels compared to the normal current condition (mode 1).\n\nFigure 8a shows the three-phase instantaneous current and voltage raw data samples that were taken, approximately 95000 samples of VT and CT in 6.5 seconds for mode 4 faulty motor. Initially the current for all phases was increased to almost double the normal current, as shown in Figure 8a. Once the fault mode 3 was present, the current suddenly increased, for the other two phases but the rotor of the motor did not turn off as one of the phases was already being pulled out. Figure 8a shows the three-phase instantaneous current and voltage raw data sample that were taken, approximately 56000 samples of VT and CT in 6.5 seconds for mode 4 faulty motor. During these few seconds, the motor became stressed due to the high current and the protection immediately cut off the power supply to avoid damage to the equipment. The current of all phases fell to zero once the protection tripped. Based on the graph observation in one plane as shown in Figures 8b and c, there were peculiar shapes in every phase except for the red phase, and in between each phase where it determined the difference in voltage and current in the system after the graphs were overlapped with each other. The shapes from each phase showed an identical pattern and were almost the same as the distorted shape, except for yellow phase which showed only straight horizontal lines due to there being no current. This observation indicated the system was in a faulty condition. Figure 8d shows the value of the maximum current rose to extremely high levels compared to the normal current (mode 1) condition, where the high current in red and blue phases caused the trip in the protection.\n\nFigure 9a plot shows approximately 46000 samples taken in 10.8 seconds with unnormalized values of three phase voltage and current respectively. It shows a normal condition with normal running (mode 1) condition of the motor. The shape of the V-I trajectory and HT of Figures 9b and c are round; these were the normal condition with no distortion on the shapes. The values of the voltage and current from each phase were only slightly different to each other, as shown in Figure 9d.\n\nFor mode 6, the voltage was varied by using the auto-transformer (Siemens model IBC 3P-15kW) where the second phase sequence (yellow phase) voltage was varied in a loaded condition. The voltage was varied from the standard voltage to a slightly lower voltage and then increased to be slightly higher. The graph in Figure 10a shows approximately 115000 samples taken in 10.8 seconds, where there are some variations of current and voltage in the yellow phase, as the voltage was in an unbalanced system. Based on this observation, it appears there was some unusual noise occurring while the voltage was explicitly varied on the yellow phase. However, the other two phases were not affected by this yellow phase. After data was analyzed by MatLAB, the graphs were put in one plane according to its phase as shown in Figures 10b and c. It was observed that there were different kinds of shapes that appeared in between each of the phases, where it determined the differences in voltage and current in the system for each phase after the graphs were overlapped with each other. The red phase showed a closed to round shape while the other two phases showed superimposed with two oblong oval shape. This indicated the faulty condition of the system. Based on Figure 10d, the current for red and blue phases had increased to almost 10 times their normal value as the yellow phase voltage lowered with auto-transformer.\n\n\nConclusions\n\nThis project involves hardware, programming and data analysis software. We have successfully conducted and completed the experiment for two three-phase induction motors with four fault simulations in a laboratory environment. There are many types of faults that can be monitored and identified but we have only chosen these four types as they could be simulated without damaging the experiment hardware sets in the campus laboratory. In this project, it was found that our HT instantaneous current signature fault detection method is a better choice in a disaggregation approach, as it was able to show obvious differences in healthy and faulty curves. The better diversity in the visualization of fault curves helps to increase the accuracy of the interpretation of AI software, and will help a maintenance crew to pinpoint or identify the fault in real time via LCD monitors as each fault will give a specified fault curve signature. From the experiment, we conclude that our system is also able to identify pre-faults. This pre-fault can be detected when a slight defection starts to occur towards a pre-determined known fault curve in our database. Detection of pre-faults would help the maintenance period by pre-stocking parts needed with scheduled downtime; otherwise, unscheduled downtime will occur with will incur losses in production profit for industries that rely on this main horsepower. Another big advantage in our system is the hardware cost for the sensor is reduced by 50%, as only three current transformers are needed, while other systems in the market need another three potential transformer sensors. For future work we would recommend testing our system design in an actual production factory environment for three-phase induction motors, synchronous motors and other types of motors.\n\n\nData availability\n\nZenodo: drshashikumar/rawdata: Raw data Excel. https://doi.org/10.5281/zenodo.5229187.25\n\nThis project contains the following underlying data:\n\n- Mode1.csv: Healthy motor Mode 1, raw data excel file three-phase for voltage and current\n\n- Mode2.csv: Motor fault Mode 2, raw data file\n\n- Mode3.csv: Motor fault Modes 3, raw data file\n\n- Mode4.csv: Motor fault Modes 4, raw data file\n\n- Mode5.csv: Motor fault Mode 5, raw data file\n\n- Mode6.csv: Motor fault Mode 6, raw data file\n\n- readme.txt: data key\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 take this opportunity to thank the university.\n\n\nReferences\n\nBednarczyk JR: Induction Motor Theory. Fairfax: PDH Online; 2012.\n\nThomson WT: Motor Current Signature Analysis to Detect Fault in Induction Motor. In: Proc Thirty-Second Turbomachinery Sysmposium. Scotland; 2003.\n\nPenrose HW: The Multi-Technology Approach to Motor Diagnostics. Old Saybrook: ALL-TEST Pro; 2019.\n\nBonaldi EL: Chapter 20 - Predictive Maintenance by Electrical Signature Analysis to Induction Motors. In: Induction Motors - Modelling and Control. InTechOpen2012; pp. 2–35.\n\nMiljkovic D: Brief review of motor current signature analysis. IEEE Industry Applications Magazine. 2015; 5(1): 14–26.\n\nVerucchi CJ: A review on fault diagnosis of induction machines. Latin American Applied Res. 2008; 38(2): 113–121.\n\nZoha A: Non-intrusive Load Monitoring approaches for disaggregated energy sensing: A survey. Sensors (Switzerland). 2012; 12(12): 16838–16866. Publisher Full Text\n\nBurbano D: Intrusive and Non-Intrusive Load Monitoring (A Survey). Latin American Journal of Computing Lajc. 2015; 2(1): 45–53.\n\nRidi A: A survey on intrusive load monitoring for appliance recognition. In: Proceedings - International Conference on Pattern Recognition. Switzerland; 2014.\n\nWeiss M: Leveraging smart meter data to recognize home appliances. 2012 IEEE International Conference on Pervasive Computing and Communications, PerCom 2012.2012; no. March, pp. 190–197.\n\nLam HY: A novel method to construct taxonomy electrical appliances based on load signatures. IEEE Transactions on Consumer Electronics. 2007; vol. 53, no. 2, pp. 653–660. 112\n\nDe Baets L: On the Bayesian optimization and robustness of event detection methods in NILM. Energy Buildings. 2017; 145: 57–66. Publisher Full Text\n\nRussakovsky O: ImageNet Large Scale Visual Recognition Challenge. Int J Computer Vision. 2014.\n\nShashikumar K, Venkataseshaiah C, Sim KS: Juggling an Arduino for Multi-Meter, Load Profiling and Novel Waveform Capture Logger Application. 12th International Colloquium on Signal Processing & its Applications of IEEE.2016; pp. 119–123. (Scopus). Publisher Full Text\n\nGandhi R: Support Vector Machine — Introduction to Machine Learning Algorithms. Towards Data Science. 08 June 2018. [Accessed 10 January 2020]. 111. Reference Source\n\nGupta P: Naive Bayes in Machine Learning. Towards Data Science. 07 November 2017. Reference Source\n\nKorgh A: Chapter 4 - An introduction to hidden Markov models for biological sequences. Computational Methods in Molecular Biology. Salzberg: Elsevier Science; 1998; 45.\n\nHarrison O: Machine Learning Basics with the K-Nearest Neighbors Algorithm. Towards Data Science. 11 September 2018. Reference Source\n\nThorsen OV: A Survey of Faults on Induction Motors in Offshore Oil Industry, Petrochemical Industry, Gas Terminals, and Oil Refineries. IEEE Transactions on Industry Applications. 1995; 31(5): 1186–1196. Publisher Full Text\n\nCruz SM: Rotor cage fault diagnosis in three-phase induction motors by extended Park's Vector approach. Electric Power Components and Systems. 2000; 28(4): 289–299. Publisher Full Text\n\nMartins JF: Unsupervised neural-network-based algorithm for an on-line diagnosis of three-phase induction motor stator fault. IEEE Transactions on Industrial Electronics. 2007; 54(1): 259–264. Publisher Full Text\n\nHassan T: An empirical investigation of V-I trajectory based load signatures for non-intrusive load monitoring. IEEE Transactions on Smart Grid. 2014; 5(2): 870–878. Publisher Full Text\n\nCole A: Nonintrusive Identification of Electrical Loads in a Three-phase Environment Based on Harmonic Content.2000; no. 7 16, pp. 24–29. Publisher Full Text\n\nLiang J: Load signature studypart II: Disaggregation framework, simulation, and applications. IEEE Transactions on Power Delivery. 2010; 25(2): 561–569. Publisher Full Text\n\nShashikumar K, Vijayakumar V: dr.shashikumar/rawdata: Raw data Excel (Version 1.0). Zenodo. 2021, July 2. Publisher Full Text"
}
|
[
{
"id": "93826",
"date": "28 Sep 2021",
"name": "Jeyraj Selvaraj",
"expertise": [
"Reviewer Expertise Power Electronics and Drives"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 involves monitoring faults in three-phase industrial motors Hilbert Transform instantaneous current signature curve. The system detects fault signature accurately at any voltage and current levels. The authors may address these comments in order to improve the manuscript:\nWhere would be the possible implementation of this method?\n\nHow robust is the system compared to conventional systems?\n\nIs there any increase or decrease in the efficiency of the motor by adopting this method?\n\nCan the method be used in other motors besides induction motors?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "151359",
"date": "03 Nov 2022",
"name": "Chandima Gomes",
"expertise": [
"Reviewer Expertise Electrical and high voltage engineering"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents a relatively novel method of detecting 3-P industrial motor faults, that requires only Hilbert Transform (HT) instantaneous current signature curve as the input parameter. The outcomes have been compared with the results obtained from other methods. The paper is technically sound. However, there are redundant sentences such as the very first sentence of the abstract. It is recommended to remove such. I would also like to recommend the author pay attention to the way of presenting the information. Although the English grammar is acceptable, the clarity of the presentation of outcomes could vastly be improved.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-903
|
https://f1000research.com/articles/10-902/v1
|
08 Sep 21
|
{
"type": "Research Article",
"title": "The potential of lunasin extract for the prevention of breast cancer progression by upregulating E-Cadherin and inhibiting ICAM-1",
"authors": [
"Kusmardi Kusmardi",
"Elvan Wiyarta",
"Numlil Khaira Rusdi",
"Andi Muh. Maulana",
"Ari Estuningtyas",
"Hadi Sunaryo",
"Numlil Khaira Rusdi",
"Andi Muh. Maulana",
"Ari Estuningtyas",
"Hadi Sunaryo"
],
"abstract": "Background: Research in natural substances for their anticancer potential has become increasingly popular. Lunasin, a soybean protein, is known to inhibit cancer progression via various pathways. The aim of this study was to investigate the effect of Lunasin Extract (LE) on the expression of Intercellular Adhesion Molecule 1 (ICAM-1) and epithelial cadherins (E-Cadherin) in breast cancer. Methods: In this true-experimental in vivo study, 24 Sprague-Dawley rats that were induced by 7,12-Dimethylbenz[a]anthracene (DMBA), were used. Based on the therapy given, the groups were divided into, normal, positive control (PC), negative control (NC), adjuvant, curative, and preventive. Lunasin was extracted from soybean seeds of the Grobogan variety in Indonesia. Tissue samples were obtained, processed, stained with anti-ICAM-1 and anti-E-Cadherin antibodies, examined under a microscope, and quantified using H-score. The data were analyzed using ANOVA, which was then followed by Duncan's test. Results: Statistically significant difference in ICAM-1 expression was observed between the following groups: adjuvant and NC, normal and NC, PC and NC, adjuvant and preventive, normal and preventive, PC and preventive, adjuvant and curative, normal and curative, PC and curative. E-Cadherin expression was significantly different between preventive and NC, adjuvant and NC, PC and NC, normal and NC, adjuvant and curative, PC and curative, normal and curative, normal and preventive. Significant negative correlation was found between ICAM-1 and E-Cadherin [-0.616 (-0.8165; -0.283)] with p = 0.001. Conclusion: Preventive dose of LE was able to reduce ICAM-1 expression while increasing E-Cadherin expression.",
"keywords": [
"Lunasin",
"ICAM-1",
"E-Cadherin",
"Breast Cancer",
"Cancer Prevention"
],
"content": "Introduction\n\nBreast cancer is the most frequent type of cancer in women across the world.1 In 2012, according to statistics from the Global Burden of Cancer Study, an estimated 1,671,149 new cases of breast cancer and 521,907 breast cancer deaths occurred in women worldwide, resulting in a prevalence of 25.1% of all cancers.1 The 2018 Globocan statistics indicated that there was an 11.6% decline in the prevalence of breast cancer compared to the 2012 Globocan data. However, the prevalence of breast cancer remains the greatest in women.2\n\nBreast cancer, in specific a metastatic subtype, is an intricate and multi-staged malignant tumor.3 A study by Müllar et al.4 has shown that alterations in the intercellular adhesion molecules can play a vital role in the metastasis of breast cancer. Intercellular Adhesion Molecule 1 (ICAM-1) as a surface glycoprotein, functions as an adhesion molecule on tumor cells that could rearrange actin, promote pro-inflammatory cascade, and mediate multiple signaling pathways to regulate cell metastasis.5 Although ICAM-1 expression varies depending on the breast cancer subtype,6 its expression is significantly increased, especially in metastatic breast cancer.7 Different from ICAM-1, epithelial cadherins (E-Cadherin) is a glycoprotein that functions as an adhesion protein between cells to maintain tissue integrity.8 Therefore, low expression of E-Cadherin is associated with the progression of epithelial-mesenchymal transition (EMT) in breast cancer.8 Due to the high prevalence of this disease, developing breast cancer treatments have become a priority. Cancer is now treated with surgery, chemotherapy, radiation, and targeted therapy,9 which have negative side effects. Chemotherapy as one of the most common cancer treatments has many significant side effects such as mucositis, neurotoxicity, chemotherapy-induced peripheral neuropathy, reduced renal function, and bone marrow depression.10 Many investigations are now developing cancer treatments using natural substances that might be capable of reducing these negative side effects.11\n\nOver the last several decades, an increasing number of plant-derived products, including soybean [Glycine max (L.) Merr.], have been explored, as it is cheap, easy to grow, and abundant in nature.12 Soy products are also known to lower the incidence and mortality of breast cancer, prostate cancer, colon cancer, and lung cancer.13-15 The molecule in soybeans that works as an anti-cancer is considered to be a bioactive peptide called lunasin. This peptide was first discovered from a sample of commercially accessible soybean germplasm, originating in the United States.16 Lunasin is a lipophilic peptide component made up of 44 amino acids that have anti-cancer, anti-oxidant, and anti-inflammatory properties, as well as the ability to control cholesterol biosynthesis in the body.17,18\n\nThe challenges with synthetic lunasin are that the commercial price is quite high due to its costly and time-consuming synthesis process. Additionally, effective techniques for obtaining a significant amount of pure lunasin from plant sources do not exist.19 Although Lunasin Extract (LE) from the Grobogan type has been shown to have anti-inflammatory and anti-cancerous effects in the colon, studies into various anti-cancer pathways of LE are required to better understand its molecular effect on breast cancer.12\n\nAs such, this study aims to investigate the anti-cancer effects of LE from the Grobogan variety in Indonesia. We hypothesized that LE administration could suppress breast cancer progression by decreasing ICAM-1 expression while increasing E-Cadherin expression. By examining the effects of LE on these two molecules, this study is expected to investigate the potential of LE for the prevention of breast cancer progression via ICAM-1 and E-Cadherin expression pathway.\n\n\nMethods\n\nSoybean seeds (Glycine max (L.) Merr) of Grobogan variety were obtained at the Research Institute for Various Nuts and Tubers, Malang, East Java. Soybean seeds undergo the process of defatting in several stages. These seeds were washed with water, and ground using a 3 mm grinder (AEG type AMEB 80 FX). The powder was then wrapped in gauze and pressed at 100-150 atm for 30 minutes at 120°F, to create plates.\n\nThe plates are turned into powder by using a mortar and pestle, as well as a blender. The powder obtained was sieved using a mesh sieve (Size 40) and placed into a plastic container and stored at 4°C until the maceration process. Extraction was carried out by the maceration process11 with the use of Phosphate Buffer Saline solvent (PBS) at pH 7.4 (Abcam, ab270748). Soybean powder was added with PBS, stirred until homogeneous, and macerated for 60 minutes with occasional stirring. The maceration product was filtered using a Whatman 54 filter paper. The filtrate was collected and stored at 4°C. Finally, the filtrate was then dried using a rotary evaporator to obtain a thick extract.\n\nStandardization was performed for the viscous extract. The parameters included water content, acid insoluble ash content, heavy metal contamination, and microbial contamination. In this study, standardization of phytochemical components was also carried out, which included tests for alkaloids, flavonoids, saponins, steroids, polyphenols, tannins, and triterpenoids.\n\nThe levels of lunasin concentration in the thick extract were determined after some of the parameters were standardized. This process was done by dissolving 100 mg of thick extract in 8 mL of distilled water. The solution was sonicated for 30 minutes, and distilled water was added to a final volume of 10 mL (10,000 ppm solution), then centrifuged at 12,000 rpm for 30 minutes. The resulting supernatant was filtered through a 0.22 mm millipore sieve, resulting in a clear and colorless solution. High-performance liquid chromatography was used to determine the solution content. Extracts that provide higher concentrations of dissolved lunasin were used as LE in this study.\n\nThis study is a true-experimental in vivo laboratory study, which included Sprague-Dawley rats induced by 7,12-Dimethylbenz [a] anthracene (DMBA). This research was conducted from December 2020 to June 2021 at the Molecular Biology and Proteomics Core Facilities, Faculty of Medicine Universitas Indonesia Laboratory. The experimental protocols were approved by the Ethics Committee of the Faculty of Medicine, the University of Indonesia with protocol number KET-647/UN2.F1/ETIK/PPM.00.02/2019.\n\nThe experimental animals used in this study were female white rats (Sprague-Dawley) obtained from the National Agency for Drug and Food Control (Indonesia), aged 4-6 weeks, with bodyweight (BW) ranging from 60-80 grams. During the experiment and the analysis, no rats were excluded due to illness or any other reasons. Breast cancer induction was done using DMBA (Merck, D3254) at a dose of 20 mg/kg BW. All samples (n = 24) were divided into six groups consisting of four rats each. The groups were divided into normal, negative control (NC), positive control (PC), curative, adjuvant, and preventive. The sample size was determined by Federer’s formula.\n\nFederer’s formula: (T-1) (N-1) > 15\n\nT = Number of groups\n\nN = Number of rats\n\nAll samples were randomly allocated in each group using a random number generator. To avoid bias, the grouping data was only accessed by one researcher (E.W.). Other researchers were blinded until the research process was completed.\n\nPrior to the experiment, all samples in each group were acclimatized for 1 week. Then, each sample received a different treatment depending on their respective groups. The Normal group did not receive any treatment. The rats in the NC group only received DMBA induction until the end of the experiment. In the PC group, DMBA-induced rats with a tumor volume of 1-2 cm3 were given Tamoxifen (Merck, 579002) (10 mg/kg BW) for 8 weeks. In the curative group, DMBA-induced rats with a tumor volume of 1-2 cm3 were given LE (500 mg/kg BW) for 8 weeks. The adjuvant group, DMBA-induced rats with a tumor volume of 1-2 cm3, were given a combination of LE (500 mg/kg BW) and Tamoxifen (10 mg/kg BW) for 8 weeks. The rats in the preventive group received LE (500 mg/kg BW) in week 1, followed by DMBA. Then they were given LE (500 mg/kg BW) until the end of the study. Tumor volume was calculated using the formula: (length) × (width2)/2.20 The total experiment lasted for 24 weeks.\n\nAfter being euthanized, paraffin blocks of breast cancer tissue from each rat were made for immunohistochemistry (IHC) staining. Unreliable paraffin blocks (e.g., broken/damaged paraffin blocks and/or paraffin blocks where the tumor mass was eaten by animals) were excluded.\n\nThe experimental protocols were approved by the Ethics Committee of the Faculty of Medicine, University of Indonesia with protocol number KET-647/UN2.F1/ETIK/PPM.00.02/2019. The treatment and maintenance of the animals are following the Guide for the Care and Use of Laboratory Animals by the Animal Care and Use Committee, namely by monitoring the temperature of 25°C, 12 hours of light-dark cycle, 55% humidity, as well as standard food and drink.20 Anesthesia and euthanasia procedures are performed according to the American Veterinary Medical Association (AVMA) Guidelines for the Euthanasia of Animals.21 Anesthesia was performed with ketamine (Merck, NMID686C) at 75-100 mg/kg BW and xylazine (Merck, X1126) at a dose of 10 mg/kg BW intraperitoneally. All efforts were made to ameliorate any suffering of animals. All results are reviewed and reported following the reporting guidelines for animal pre-clinical studies, namely the Animal Research: Reporting of in vivo Experiments (ARRIVE guideline).22,23\n\nBreast cancer tissue in each sample was placed in a formalin buffer solution (Merck, HT501128), and cut into 3-5 mm thickness with a scalpel. Tissue samples were immersed in 96% ethanol (Merck, 443611) for 30 minutes, this process was repeated five times. The tissue was immersed in the xylol (Merck, 108297) solution for 15 minutes. The tissue was planted in solid paraffin with a melting point of 60-70°C for 30 minutes and placed in a 4oC freezer for 10-15 minutes. The tissue in the paraffin block was cut using a microtome with a thickness of 3 mm and placed on a glass slide that had been coated with poly-L-lysine and heated in an oven at 60°C overnight. The tissue samples were deparaffinized with xylene three times for 3 minutes each and rehydrated with 100%, 95%, and 70% ethanol for 2, 2, and 1minute, respectively. The tissue samples were immersed in 0.01 M citrate buffer (Merck, 21545) pH 6.0 in the microwave for 5 minutes, and dripped with 3% hydrogen peroxide to remove endogenous peroxide for 5 minutes at room temperature. Each tissue sample was incubated with anti-ICAM-1 antibodies (MyBiosource, MBS2543949) and anti-E-Cadherin antibodies (Abcam, ab134047) in PBS for 2 hours at room temperature in a humidity chamber followed by overnight incubation at 4°C. The N-Universal negative control (Merck, 939B) was used as a negative control. The tissue samples were then incubated with the Novolink Polymer DS 250 test (Novolink, RE7140-CE) for 1 hour at room temperature, followed by incubation for 30 minutes with horseradish peroxidase-conjugated streptavidin (Abcam, ab7403). Proteins were visualized using 3,3′-diaminobenzidine (DAB) for 10 minutes at room temperature, which makes the expression of ICAM-1 and E-Cadherin observable based on the intensity of the brown color. Finally, hematoxylin-eosin counterstain, dehydration, and mounting of the tissue were performed.\n\nEach tissue was observed using a light microscope at a total magnification of 400× and documented using a computer with Leica Application Suite (LAS) EZ V3.0.0 software (Leica Microsystems, Switzerland) and a camera that had been integrated with Leica DM750 microscope. Photographs were taken randomly with a total of ten visual fields per one tissue and standardized using a global white balance. The brown color intensity was calculated using the plugin program in Image J, IHC profiler,24 which will quantify the intensity of the images. The results of quantification were converted into H-Score25 based on the formula:\n\n(% low positive × 1) + (% positive × 2) + (% high positive × 3).\n\nData collection was entered into the main table using Microsoft Excel 2013 (Microsoft Corporation). The tabulated data were analyzed using the Statistical Package for Social Sciences (SPSS) version 20 and visualized using GraphPad Prism 8 (RRID: SCR_002798). Data analysis was with the use of One-Way Analysis of Variance (ANOVA), followed by Duncan Post Hoc test to compare the differences. Differences of p < 0.05 are considered statistically significant. The correlation analysis between ICAM-1 expression and E-Cadherin was also analyzed using Pearson Correlation. The stronger the correlation, the closer the correlation coefficient value (r) is to 1 or −1. A positive r indicated a directly proportional correlation, while a negative r indicated an inverse correlation. The correlation model of the two biomarkers was also analyzed by simple linear regression.\n\n\nResults\n\nThe representative image of IHC staining for ICAM-1 and E-Cadherin in breast tissue is shown in Figure 1. Each image depicts a different expression based on the group and the biomarker (ICAM-1 and E-Cadherin). Some images, such as Figure 1 B, D, F, G, I, K, and L, show a greater brown color intensity than others, which suggests that the associated biomarker is expressed at a greater level.\n\nScale bar represents 50 μm. All images were taken at 400× magnification.\n\nHowever, qualitative evaluation alone is insufficient for reaching a conclusion. As a result, H-score quantification was used to quantify the quantitative expression of ICAM-1 and E-Cadherin. Table 1 shows the mean H-score in every group on ICAM-1 and E-Cadherin. Complete H-score data can be accessed in the extended data.26 Figures 2 and 3 show ICAM-1 and E-Cadherin mean H-score differences between groups, respectively.\n\nNormal, positive control (PC), curative, adjuvant, and preventive groups have significantly different ICAM-1 expressions compared to the negative control (NC). Duncan Test was used to determine the difference between groups. * represents significant difference (p < 0.05) of groups versus NC. ○ represents a significant difference (p < 0.05) of groups versus preventive.\n\nDuncan Test was used to determine the difference between groups. * represents significant difference (p < 0.05) of groups compared to NC. • represents significant difference (p < 0.05) of groups compare to curative. ○ represents a significant difference (p < 0.05) of groups compare to preventive.\n\nOne-Way ANOVA for ICAM-1 showed significant results (p < 0.001). Meanwhile, Duncan’s test results showed that there were significant differences in ICAM-1 expression between adjuvant and NC, normal and NC, PC and NC, adjuvant and preventive, normal and preventive, PC and preventive, adjuvant and curative, normal and curative, PC and curative as seen in Figure 2.\n\nOne-Way ANOVA analysis for E-Cadherin indicated significant results (p < 0.001). Meanwhile, Duncan’s test results showed there were significant differences between preventive and NC, adjuvant and NC, PC and NC, normal and NC, adjuvant and curative, PC and curative, normal and curative, normal and preventive as seen in Figure 3.\n\nThe results of the Pearson correlation analysis showed r = −0.616 (−0.8165; −0.283) with p = 0.001. The correlation between ICAM-1 and E-Cadherin expressions was negatively correlated with moderate strength. Further regression analysis produces a correlation model between E-Cadherin and ICAM-1 expressions through the equation y = −1.214x + 109.7, where y is E-Cadherin expression and x is ICAM-1 expressions, as seen in Figure 4.\n\n\nDiscussion\n\nIn this study, the relationship between LE administration in the DMBA-induced breast cancer model was assessed. ICAM-1 and E-Cadherin, molecules involved in breast cancer adhesion and progression, were evaluated in each group to determine their effect. In the breast cancer model, results revealed an inverse correlation between ICAM-1 and E-Cadherin expressions. Additionally, Tamoxifen, adjuvant LE, and preventative LE all had a significant effect on either lowering ICAM-1 expression or promoting E-Cadherin expression.\n\nDMBA as a breast carcinogen is commonly used to simulate mammary carcinogenesis for tumor research.27,28 In this study, DMBA had a substantial influence on the expression of ICAM-1 and E-Cadherin. As demonstrated in Figures 2 and 3, there is a substantial difference between NC and normal tissue samples. DMBA-induced breast models showed a significantly increased ICAM-1 expression. This is consistent with the fact that ICAM-1 expression rises with cancer progresses,29 especially during metastasis,30 although it is expressed at lower levels in normal tissues.31 Several studies have also investigated DMBA as a tumor model and discovered a significant increase in ICAM-1 expression.32-34 Although the evidence is inconclusive, the nuclear factor-kappaB (NFkB) pathway is considered to play a role in DMBA-induced ICAM-1 upregulation.35,36 DMBA is able to potentiate NFkB37,38 via Ras mutation in the Ras/Raf/mitogen-activated protein kinase/ERK kinase (MEK)/extracellular-signal-regulated kinase (ERK) pathway,39,40 thereby increasing ICAM-1 expression.35,36 DMBA, however, decreased E-Cadherin expression. This is consistent with the hypothesis that E-Cadherin is expressed in normal cells, with its absence being a hallmark of EMT and a more migratory, invasive cancer.41,42 These results are also consistent with other research that demonstrate a reduction in E-Cadherin expression following DMBA induction.42,43 DMBA's impact on E-Cadherin, like that of ICAM-1, is mediated via NFkB activation37,38 via the Ras-Raf-MEK-ERK pathway39 thus causing E-Cadherin repression due to transcription factor TWIST expression.44 DMBA can also activate aryl hydrocarbon receptors (AhR), promoting transcription of SNAI2 (Slug),45 an E-Cadherin repressor protein.46 Furthermore, the negative correlation of ICAM-1 and E-Cadherin was consistent with the functions of each molecule. Zhao et al.47 has also shown that reduced expression of E-Cadherin was associated with increased expression of ICAM-1 in mice models of breast cancer.\n\nTamoxifen, the most established hormone therapy for breast cancer, is an estrogen receptor antagonist that operates in its active metabolite, hydroxytamoxifen, in breast cancer.48 This therapy decreased ICAM-1 expression, and increased E-Cadherin expression in DMBA-induced mouse models compared to NC, as seen in Figures 2 and 3. This finding is consistent with the results of Sun et al.48 who discovered that Tamoxifen administration can reduce the Toll-like receptor 4 (TLR4)/NFkB-mediated inflammatory response, resulting in a reduction in ICAM-1 expression. This process might potentially account for the rise in E-Cadherin following Tamoxifen administration. As previously stated, NFkB mediates E-Cadherin repression,44 therefore, inhibiting this pathway will increase E-Cadherin expression. Furthermore, Tamoxifen could prevent the activation of Slug and Snail, the E-Cadherin protein inhibitors, by inhibiting Transforming Growth Factor Beta (TGF-β)/Smad, thus enhancing E-Cadherin expression.49\n\nIn this study, three LE groups: adjuvant, curative, and preventive, had varying effects on ICAM-1 expression. At first impression, the adjuvant group appeared to have excellent outcomes since it was substantially different from NC, preventive, and curative groups, as seen in Figure 2. This demonstrates that combining LE with Tamoxifen can dramatically lower ICAM-1 expression. However, this role may be attributed only to Tamoxifen, implying that the addition of LE had no meaningful effect on decreasing ICAM-1 expression. This was further confirmed as no significant difference between the adjuvant and PC group was found. As a result, an assessment of the effects of LE in the curative and preventive groups is essential. Figure 2 shows that the curative group did not have significant outcomes in terms of ICAM-1 expression. Zhu et al.50 reported the same result, indicating that lunasin administered to monocytes was unable to decrease ICAM-1 expression. On the other hand, the preventive group showed some intriguing findings. Figure 2 shows a substantial difference in ICAM-1 expression between the preventive group with the other groups including NC, PC, and normal groups. This indicates that, even though LE at preventive doses considerably reduced ICAM-1 expression relative to NC, it was not as low as in the normal or PC groups. Although there has not been any research yet to show the preventive effect of LE on ICAM-1 expression, these findings may be explained by lunasin's antimitotic activity. A study by Hsieh et al.51 found that lunasin had an anti-mitotic effect by suppressing mutations in a DMBA-induced mouse model. Jeong et al.52 also shown that lunasin can prevent Ras mutations by inhibiting core H3 and H4 histone acetylation. This evidence explains why LE administered preventively (before DMBA induction) was more effective than LE administered curatively (after DMBA induction) in decreasing ICAM-1 expression. This is due to LE's ability to prevent the Ras mutation induced by DMBA, therefore preventing the NFkB pathway from being potentiated, which can enhance ICAM-1 expression.\n\nThe three LE groups also exhibited distinct effects on E-Cadherin expression. The adjuvant group was able to significantly increase E-Cadherin expression as represented by the significant difference it has with both NC and curative (Figure 3). However, similar to ICAM-1, this result might be attributed to the impact of Tamoxifen alone. Contrastingly, the curative group did not demonstrate a significant increase in E-Cadherin expression. A study by Pabona et al.53 reported that the lunasin administration promoted E-Cadherin expression. However, their study is an in vitro study using synthetic lunasin, which is different from this study. The preventive group, unlike the curative group, showed a significant difference in E-Cadherin expression compared with the normal and NC group. However, this was not seen with the PC group. This suggests that administering a preventive dosage of LE in the breast cancer model was able to significantly enhance E-Cadherin expression relative to NC until it was as high as PC, but not as high as the normal group. Interestingly, unlike ICAM-1, E-Cadherin expression in the preventive group did not differ from that of the Tamoxifen group. This is possible because, as seen in Figure 5, more pathways influence E-Cadherin expression than ICAM-1. This creates increased heterogeneity in the expression of E-Cadherin, which is difficult to identify in this study. Aside from these differences, the preventive group outperformed the curative group in terms of enhancing E-Cadherin expression, compared to the findings on ICAM-1 expression. This finding could be explained by the same mechanism that occurs in ICAM-1, namely mutation-inhibiting action by LE.51,52\n\n7,12-Dimethylbenz [a] anthracene (DMBA) can cause breast cancer by inducing Ras mutations, which cause nuclear factor-kappaB (NFkB) potentiation via the Ras-RAF-MEK-ERK pathway. ICAM-1 and TWIST expression will be enhanced as a result of NFkB activation. TWIST is a transcription factor that inhibits the production of E-Cadherin. DMBA can also bind to aryl hydrocarbon receptor (AhR) and promote the transcription of Slug, an inhibitor of E-Cadherin production. Lunasin extract suppresses Ras mutations, which contribute to the prevention of breast cancer progression. As a result, NFkB potentiation does not occur, resulting in a decrease in ICAM-1 expression, and an increase in E-Cadherin expression. Tamoxifen, on the other hand, can suppress Toll-like receptors (TLR)-4 and Transforming Growth Factor Beta (TGF-β). TLR-4 suppression may also prevent NFkB potentiation. Furthermore, TGF-β inhibition will disrupt the smad/Slug and smad/Snail pathways, resulting in inhibition of E-Cadherin production.\n\nThis study has limitations, such as administrating one dose (500mg/kg BW) of the LE, therefore, the effects could not be compared in a dose-dependent manner. As a result, research with a more diversified dose is recommended. Furthermore, more study on other biomarkers, both in the same and distinct molecular pathways, is required to explore the preventive potential of LE in breast cancer.\n\n\nConclusion\n\nA preventive dose of LE was able to reduce ICAM-1 expression while increasing E-Cadherin expression. Our findings show that LE has cancer-preventive effects in a well-characterized animal model of breast cancer. Further study, incorporating more biomarkers, is required to explore the mechanism of action of this peptide on mammary carcinogenesis as well as other forms of cancer.\n\n\nData availability\n\n(Harvard Dataverse): The potential of lunasin extract for the prevention of breast cancer progression by upregulating E-Cadherin and inhibiting ICAM-1.\n\nDOI: https://doi.org/10.7910/DVN/EXUSQ2.26\n\nThis project contains the following extended data:\n\n• ICAM-1 Raw Data.tab: The ICAM-1 raw data is the result of the IHC profiler quantification.\n\n• ICAM-1 Grouping.tab: grouping the results of ICAM-1 raw data based on the treatment group (normal, negative control, positive control, adjuvant, curative, and preventive).\n\n• E-Cadherin Raw Data.tab: The result of the IHC profiler quantification.\n\n• E-Cadherin Grouping.tab: grouping the results of E-Cadherin raw data based on the treatment group (normal, negative control, positive control, adjuvant, curative, and preventive).\n\n• ICAM-1 and E-Cadherin Research Protocol.pdf: The experimental protocols were approved by the Ethics Committee of the Faculty of Medicine, University of Indonesia with protocol number KET-647/UN2.F1/ETIK/PPM.00.02/2019.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReporting guidelines\n\n(Harvard Dataverse): ARRIVE checklist for “The potential of lunasin extract for the prevention of breast cancer progression by upregulating E-Cadherin and inhibiting ICAM-1”.\n\nDOI: https://doi.org/10.7910/DVN/EZTWXY.23\n\nThis project contains the following extended data:\n\n• ARRIVE 2.0 Checklist_ICAM-1 and E-Cadherin.pdf\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor contributions\n\nKK, NKR, AMM designed the concept of this research article. KK, EW, NKR, AMM performed the methodology. KK carried out the overall reproducibility of experiments and other research outputs. Application of statistical, mathematical, computational, or other formal techniques to analyze or synthesize study data was done by EW. Conducting the research and investigation process, specifically performing the experiments, or data/evidence collection was done by EW, NKR, AMM. The resources were provided by KK, AE, HS. The Organization and management of the datasets collection, as well as writing the original draft of this article was by EW. Review & Editing was done by KK, NKR, AMM, AE, HS. Verification, of the overall reproducibility of experiments and other research outputs was performed by KK, AMM, AE, HS.",
"appendix": "Acknowledgment\n\nWe would like to thank Universitas Indonesia for supporting the research process.\n\n\nReferences\n\nGhoncheh M, Pournamdar Z, Salehiniya H: Incidence and Mortality and Epidemiology of Breast Cancer in the World. Asian Pac J Cancer Prev. 2016; 17(S3): 43–6. PubMed Abstract | Publisher 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(6): 394–424. PubMed Abstract | Publisher Full Text\n\nDi D, Chen L, Wang L, et al.: Downregulation of human intercellular adhesion molecule-1 attenuates the metastatic ability in human breast cancer cell lines. Oncol Rep. 2016; 35(3): 1541–8. PubMed Abstract | Publisher Full Text\n\nMüller V, Fuxius S, Steffens CC, et al.: Quality of life under capecitabine (Xeloda®) in patients with metastatic breast cancer: data from a german non-interventional surveillance study. 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PubMed Abstract | Publisher Full Text\n\nMolnar R, Szabo L, Tomesz A, et al.: In vivo effects of olive oil and trans-fatty acids on miR-134, miR-132, miR-124-1, miR-9-3 and mTORC1 gene expression in a DMBA-treated mouse model. PLoS One. 2021; 16(2): e0246022. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartiniani R, Di Loreto V, Di Sano C, et al.: Biological Activity of Lenalidomide and Its Underlying Therapeutic Effects in Multiple Myeloma. Adv Hematol. 2012; 2012: 842945. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSong S, Choi K, Ryu S-W, et al.: TRAIL promotes caspase-dependent pro-inflammatory responses via PKC?? activation by vascular smooth muscle cells. Cell Death Dis. 2011; 2: e223. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShanmugam M, Singh A, Baskaran N, et al.: Pro-apoptotic and anti-inflammatory potential of andrographolide during 7,12-dimethylbenz [a] anthracene induced hamster buccal pouch carcinogenesis. J Experimental Integrative Medicine. 2012; 2. Publisher Full Text\n\nAggarwal BB: Nuclear factor-κB: The enemy within. Cancer Cell. 2004; 6(3): 203–8. PubMed Abstract | Publisher Full Text\n\nGarg R, Ingle A, Maru G: Dietary turmeric modulates DMBA-induced p21ras, MAP kinases and AP-1/NF-κB pathway to alter cellular responses during hamster buccal pouch carcinogenesis. Toxicol Appl Pharmacol. 2008; 232(3): 428–39. PubMed Abstract | Publisher Full Text\n\nBian Y, Terse A, Du J, et al.: Progressive tumor formation in mice with conditional deletion of TGF-beta signaling in head and neck epithelia is associated with activation of the PI3K/Akt pathway. Cancer Res. 2009; 69(14): 5918–26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSinghai R, Patil VW, Jaiswal SR, et al.: E-Cadherin as a diagnostic biomarker in breast cancer. N Am J Med Sci. 2011; 3(5): 227–33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBelguise K, Guo S, Yang S, et al.: Green Tea Polyphenols Reverse Cooperation between c-Rel and CK2 that Induces the Aryl Hydrocarbon Receptor, Slug, and an Invasive Phenotype. Cancer Res. 2007; 67(24): 11742. PubMed Abstract | Publisher Full Text\n\nMoussa RA, Khalil EZI, Ali AI: Prognostic Role of Epithelial-Mesenchymal Transition Markers \"E-Cadherin, β-Catenin, ZEB1, ZEB2 and p63\" in Bladder Carcinoma. World J Oncol. 2019; 10(6): 199–217. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChua HL, Bhat-Nakshatri P, Clare SE, et al.: NF-κB represses E-cadherin expression and enhances epithelial to mesenchymal transition of mammary epithelial cells: potential involvement of ZEB-1 and ZEB-2. Oncogene. 2007; 26(5): 711–24. PubMed Abstract | Publisher Full Text\n\nIkuta T, Kawajiri K: Zinc finger transcription factor Slug is a novel target gene of aryl hydrocarbon receptor. Exp Cell Res. 2006; 312(18): 3585–94. PubMed Abstract | Publisher Full Text\n\nBolós V, Peinado H, Pérez-Moreno MA, et al.: The transcription factor Slug represses E-cadherin expression and induces epithelial to mesenchymal transitions: a comparison with Snail and E47 repressors. J Cell Sci. 2003; 116(Pt 3): 499–511. PubMed Abstract | Publisher Full Text\n\nZhao L, Zhao Y, He Y, et al.: miR-19b promotes breast cancer metastasis through targeting MYLIP and its related cell adhesion molecules. Oncotarget. 2017; 8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSun X, Ji C, Hu T, et al.: Tamoxifen as an effective neuroprotectant against early brain injury and learning deficits induced by subarachnoid hemorrhage: possible involvement of inflammatory signaling. J Neuroinflammation. 2013; 10: 157. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYi EY, Park SY, Jung SY, et al.: Mitochondrial dysfunction induces EMT through the TGF-β/Smad/Snail signaling pathway in Hep3B hepatocellular carcinoma cells. Int J Oncol. 2015; 47(5): 1845–53. PubMed Abstract | Publisher Full Text\n\nZhu Y, Li H, Wang X: Lunasin abrogates monocytes to endothelial cells. Mol Immunol. 2017; 92: 146–150. PubMed Abstract | Publisher Full Text\n\nHsieh CC, Hernández-Ledesma B, de Lumen BO: Soybean peptide lunasin suppresses in vitro and in vivo 7,12-dimethylbenz [a]anthracene-induced tumorigenesis. J Food Sci. 2010; 75(9): H311–6. PubMed Abstract | Publisher Full Text\n\nJeong HJ, Jeong JB, Kim DS, et al.: Inhibition of core histone acetylation by the cancer preventive peptide lunasin. J Agric Food Chem. 2007; 55(3): 632–7. PubMed Abstract | Publisher Full Text\n\nPabona JM, Dave B, Su Y, et al.: The soybean peptide lunasin promotes apoptosis of mammary epithelial cells via induction of tumor suppressor PTEN: similarities and distinct actions from soy isoflavone genistein. Genes Nutr. 2013; 8(1): 79–90. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "94586",
"date": "22 Sep 2021",
"name": "Asmi Chakraborty",
"expertise": [
"Reviewer Expertise Cancer",
"Glycobiology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 novel therapeutic molecule, lunasin, which can work synergistically with the current treatment option of Tamoxifen, in breast cancer. While the findings are exciting and merit investigation, the following points need to be addressed:\nMajor:\nInclude more details on the breast cancer type and what DMBA induces. DMBA is not spoken about before the methods. Since this is the only major experiment there needs to be more reasoning on why this was chosen. It is known in the literature that DMBA induced rat tumors are not invasive, have longer durations of latency. Hence, further justification of the model with help the reader.\n\nThe authors mention that the cost of production of LE is expensive. Is the method used by the paper a cheaper way of producing it or are the authors simply mentioning this to state that this is a potential drawback?\n\nAlthough the authors mention in the conclusion that the lack of data on dose-dependent response is a drawback, there needs to be a reason for choosing the current dosage in the study. Perhaps a reference or any other justification. This is critical.\n\nThe results need to be more elaborate. Did the authors perform any survival study on the animal groups?\n\nThere are several unestablished connections being made in the discussion. While all the pathways are valid, connecting LE to the whole carcinogenic cascade is an over-interpretation of one experiment in the paper. In my opinion, this is not appropriate and needs further experimentation to be proven. The rat tumors can be homogenized to isolate RNA and protein to further validate the claims made in the discussion. Without this validation, the authors cannot claim the statements in the discussion as it is all speculative with regards to LE.\n\nPer the previous comment Figure 5. Should be a hypothesis or future direction-related figure. These are great future directions for the study.\n\nOverall, this is a promising study that can lead to the development of synergistic treatment with current therapy for breast cancer. While further investigation is needed, this paper does offer exciting insights into the role of LE as a therapeutic molecule in breast cancer treatment.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the 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": "93820",
"date": "23 Sep 2021",
"name": "Bambang Pontjo Priosoeryanto",
"expertise": [
"Reviewer Expertise Cancer Pathology",
"Anticancer activity from natural substances"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 an interesting study about the potential of breast cancer therapeutic substance of lunasin from a natural product of soybean. The result is very clear and indicated the potential promising of lunasin to be a candidate for combating breast cancer disorder.\n\nSome points need to be addressed and clarified:\nThe work on extraction in the methods is very clear but there is no result information about the extract. Maybe it's better if there is a short piece of information about the extraction result, even if this extraction work will be published elsewhere.\n\nThere is no information on how the author chose the dose of lunasin (500 mg/BW), what is the basic reason for this choice?\n\nIt will be better if the type of cancer was also explained in the result by at least using a general hematoxylin-eosin staining method, it will enhance the understanding of the action of lunasin in the tumor type.\n\nNeed clarification in the method of IHC, concerning the counterstain. it was written that used hematoxylin-eosin (it means hematoxylin and eosin) or only hematoxylin because hematoxylin will stain nuclear, while eosin stains cytoplasm.\n\nFigure 5 as a concept of hypothetical lunasin action is a good direction idea for further study for the clarification of the actions cascade.\n\nGeneral conclusion :\nThis work is a good study in order to elaborate the lunasin activity especially as an anticancer in the breast cancer model and will have a good impact on the development of therapeutic anticancer molecules although further study is needed. Results from this study have enriched the current information about lunasin in order to better understanding the lunasin activity and its molecular mechanism.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the 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": []
},
{
"id": "93818",
"date": "11 Oct 2021",
"name": "Hardhono Susanto",
"expertise": [
"Reviewer Expertise Biomedical and Sports Medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study examines the potential of Lunasin Extract (LE) as a natural product that can inhibit breast cancer progression through the biomarker mechanism. This study used biomarkers E-Chaderin and ICAM-1 as markers in evaluating the action of LE. This study used immunohistochemistry methods for assessing these biomarkers. This study indicates that LE can inhibit breast cancer progression by increasing E-Chaderin and decreasing ICAM-1.\nSome points that need to be addressed and clarified:\nThe author needs to explain the origin of the use of LE in this study. Usually, in researching natural products, a minimum of 3 different doses will be used. If the author has conducted previous studies regarding the dose of this LE, it can be added to this study.\n\nThe method used in this research is excellent and complete. As input, the results of the extraction and characterization of LE may be attached. This could be very helpful for other researchers who want to create LE with different parameters.\n\nThe addition of Figure 5 is excellent and complete. Still, its placement in this study is more suitable as a hypothesis for further research.\n\nGeneral conclusion:\nThe content of this study has linearity with the authors’ expertise. They cite enough recent literature, clearly cited. The method contains adequate and sufficient details, e.g. sum of samples, the procedure of laboratory examination with a fit statistical method. They explain their result and discussion in good enough clearly their interpretation. The statement of the conclusion answers the aim of the study. Also, in reasonable and appropriate academic language.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-902
|
https://f1000research.com/articles/10-899/v1
|
08 Sep 21
|
{
"type": "Research Article",
"title": "Orchestration of autonomous trusted third-party banking",
"authors": [
"Saravanan Muthaiyah",
"Kalaiarasi Sonai Muthu Anbananthen",
"Nguyen Thi Phuong Lan",
"Kalaiarasi Sonai Muthu Anbananthen",
"Nguyen Thi Phuong Lan"
],
"abstract": "Background Digital transformation is changing the structure and landscape of future banking needs with much emphasis on value creation. Autonomous banking solutions must incorporate on-the-fly processing for risky transactions to create this value. In an autonomous environment, access control with role and trust delegation has been said to be highly relevant. The aim of this research is to provide an end to end working solution that will enable autonomous transaction and task processing for banking.\nMethod We illustrate the use case for task delegation with the aid of risk graphs, risk bands and finite state machines. This paper also highlights a step by step task delegation process using a risk ordering relation methodology that can be embedded into smart contracts.\nResults Task delegation with risk ordering relation is illustrated with six process owners that share immutable ledgers. Task delegation properties using Multi Agent Systems (MAS) is used to eliminate barriers for autonomous transaction processing. Secondly, the application of risk graph and risk ordering relation with reference to delegation of tasks is a novel approach that is nonexistent in RBAC.\nConclusion The novelty of this study is the logic for task delegation and task policies for autonomous execution on autonomous banking platforms akin to the idea of federated ID (Liberty Alliance).",
"keywords": [
"Autonomous banking",
"RkBAC",
"RBAC",
"task delegation",
"risk ordering relation",
"role based",
"risk band",
"risk graph"
],
"content": "Introduction\n\nDigital transformation has been changing the landscape of banking and the future of banking will be very much different from what it is today. Faced with enormous competition, consumer expectations and new business models’ banks are required to put in place process automation that will gain confidence of its customers. With much negative publicity from recent events such as Enron, Madoff Investment Securities and WorldCom, the financial sector is becoming the least trusted sector. This is constantly highlighted in the Edelman Trust Barometer report. From 2011 until 2017, among eight industries financial services that incudes baking has been reported as the least trusted. In 2011 the sector scored 37% and in 2017 it scored 54%. The percentage increase is negligible compared to the other industries as shown in Figure 1. Financial services must embrace trust in its core business model in order to overcome this negative perception. Future of banking will include autonomous systems that must ensure trust at it’s core processing. In this paper we present a Multi Agent System (MAS) approach that is based on the Blockchain technology to facilitate data exchange, loan processing, withdrawals, loan inquiry, third party transfers, wallet activation and much more.\n\nThis is to ensure customer confidence and trust is ensured1. The core of this technology ensures provenance, data integrity, auditability and trust2. The decentralized trust embedded system has been illustrated with the Trusted Third Party (TTP) principle3.\n\n\nTrust attributes\n\nTrusted systems are defined as systems that rely upon upholding or enforcing trust in relation to transaction processing, integrity, data provenance, auditability and adherence to policy. In an autonomous banking system trust attributes can also be defined as compliance, data provenance as well as true and fairness. The purpose of statutory audit is to ensure compliance and rigor for check and balance. Blockchain technology is useful in this context to enable a unified vision that is agreeable and verifiable by all entities involved in the trusted network3,4. As mentioned earlier to facilitate Tasks (t1, t2…,.tn) that refer to specific task descriptions highlighted in Table 1, we propose evaluation of Exposure Analysis (EA) and Risk Band (RB)5. The idea is to specifically incorporate trust factor into the distributed ledgers via smart contracts that will provide required governance for all transactions illustrated in Figure 2 below.\n\nIn this instance, we highlight a transaction that is shared across six process owners. The immutable ledgers will evaluate individually for each process owners i.e. 1) opening account, 2) loan approval, 3) e-wallet activation, 4) fund transfer, 5) facility check and 6) wire transfer.\n\n\nMethods\n\nIn this study, the RR, EA and EL analytical data model below was used to rank order to determine Risk Band (RB) based on ISO31000 standards. Multi Agent Systems (MAS) will execute and update RB into respective immutable ledgers shown in Figure 2.\n\nState charts or state chart diagrams can be used to define processes that are dynamic. It is used to define state changes that are triggered by events6. As depicted in Figure 3, there are thirteen states that are being triggered one after the other. Task 1 (t1) triggers task 2 (t2) until all thirteen states are completed for a particular transaction. As mentioned earlier, these tasks are transaction based such as a third-party fund transfer. Since the banking system is designed to be autonomous the MAS will coordinate the automated transaction processing without human intervention.\n\nTable 2 illustrates nine tasks with relation to banking transactions without trust delegation. Description of the tasks (T) and relative Risk Bands (RB) have also been listed. RB can be grouped into five groups of risks, 1) Low risk, 2) Low to Medium, 3) Medium risk, 4) Medium to High risk and 5) High risk. Risks are identified by RB and the risk levels are indicated numerically from 1 to 6 as shown in Figure 4. Low level of risk is indicated by RB5 and RB6 that maps to T2 (statement request) and T1 (opening account). High level of risk is indicated by RB1 that maps to T8 as well as T10. In the Figure 1 below, there are nine KYPs (t1…t9), which are tagged to company platforms available on the P2P platform.\n\nAnalysis from RA and EA calculations show that Risk band 6 (RB = 6) includes t1, t2, and t4, which are high risk platforms. Risk band 1 (RB = 1) includes t7, t8 and t9, which are relatively low risk platforms. Overall, we can compare the risk bands to show relative risks between (t1 to t9). For example, t9, will have the same level of risk as t8, which are compatible in terms of risk band. T8 refers to Loan Facility Approval and T10 refers to international foreign currency wire transfer. Comparable risks are for tasks (T6, T7 and T9) which all fall under RB2. Similarly, T1 and T3 also share the same RB which is RB5. Whereas non-comparable RBs are those such as different tiers such as T9 and T10.\n\nRisk scales for automated transaction are embedded into our proposed autonomous banking system for enabling a trust-based network. The main objective of this study is to determine access rights based on risk bands. The idea is to use risk-based assessment for better control measure and execution. Intuitively, the larger the risk, the greater the risk band and the higher the scrutiny. Before rights to access is granted, detailed access control permissions are allocated based on risk bands. However, trust delegation for transactions can also be dealt with in this methodology. This sis explained further in the next section.\n\nTrust delegation in principle refers to any task (t) where the role of approval can be delegated or transferred personnel within boundaries of process owners7.\n\nFigure 5 highlights the proposed trust based autonomous banking platform where trust delegation is included. A total of nine tasks (t1…t9), for autonomous banking is illustrated. Risk band 6 (RB6) includes high risk tasks (t1, t2 and t4). (RB1) includes low risk tasks (t7, t8 and t9). Risk band 3 (RB3) includes average risk tasks (t3, t5 and t6).\n\nFor example, if a process owner executes t9, the process owner will have the same level of risk as t8, which are compatible in terms of risk band. Any task that has a higher risk than RB = 1, more scrutiny will be applied to grant permission for that task.\n\nThis flexibility is crucial for tasks that are dynamic in the context of autonomous banking. In this manner post evaluation for the transactions can be executed this enabling risk levels to move up or down depending on the RB. Intuitively, the larger the gap between the RB, the higher the risk7. As such, Tasks t1, t2, and t4 belong to the same level of risk (RB = 6). Securing transaction threats by accessing risks associated with them can reduce likelihood of liabilities however the risk assessment process should not be ambiguous, inconsistent and have omissions. Therefore, the mathematical formulation below is necessary to add rigor to the assessment7.\n\nIn a Multi Agent System (MAS) platform for autonomous systems in this case “agents”, there is a need to have the agent systems programmed with a certain logic or algorithm so that they can execute these transactions seamlessly. As such we illustrate the following mathematical expression for developing the logic for risk ordering and risk bands. We have implemented a detailed algorithm using the Foundation of Intelligent Physical Agents (FIPA) standard shown in Figure 6.\n\n1) Subject (S) – all possible users as well as non-human entities (i.e. FSMs)\n\n2) Object (O) – entities being accessed by subject\n\n3) Operation (Op) – operation performed on object (i.e. loan processing)\n\n4) Role (R) – Capacity in which subjects access the rights to objects\n\n5) Task (T) – Operation * Object (Op * O)\n\n6) Permission (P) – Role (R) → P Task (T) (Note : P denotes power set operand)\n\n- gives a set of tasks authorized for each role (R).\n\n- task has a token and when task is over the token would expire.\n\n7) Subject Roles (SR) – Subject (S) → P Role\n\n8) PERM is a subset of Role * Task (R*T)\n\nHowever, this paper’s focus is only on developing the logic for trust delegation at this stage. More detailed transaction logic will be implemented it in the near future to accommodate transactions that are not listed in Table 2. Figure 6, illustrates autonomous banking trust delegation for task execution workflow5. The concept is based on a Multi Agent Systems (MAS) platform assumed by the functional architecture proposed by FIPA, an Agents Working Group. MAS can be thought of multitude autonomous entities, that execute processes one through seven shown below. This paper presents an implementation of an autonomous banking platform providing transparent interaction between process owners that are represented by agent systems.\n\n\nConclusion\n\nAutonomous Trusted Third-Party orchestration for banking systems must be self-auditing by its design. In order to ensure that the banking ecosystem will entail trust which will be the key to drive of its success. Technological advancements will be able to create value by quickly aggregating data which can be deployed using agent systems. In our future work we would like to investigate how control procedures can be embedded within the Blockchain technology to make autonomous banking platforms more robust.\n\n\nData availability\n\nNo data associated with this article.\n\nEthical Approval Number: EA1202021\n\nEthical approval was obtained from the research management center at the university. Researchers had to first submit the title of the project, what the author planned to do for the interviews and details of study objectives. The officer at the research management center after reviewing the documents will then issue a letter of clearance for the data collection to be carried out. The approval letter was then obtained, and the reference number of this letter is EA1202021.",
"appendix": "Author Contribution\n\nMain author: Contribution on scope of work, literature review, problem statement and trust delegation.\n\nCo-author 1: Contribution on task workflow\n\nCo-author2: Contribution on peer lending banking platforms exchanges\n\n\nAcknowledgement\n\nAll members who worked on this research have been included as authors\n\n\nReferences\n\nRaconteur: How Blockchain will disrupt the financial sector. 2019; [Accessed 15 Jul. 2019]. Reference Source\n\nSchmitz J, Leoni G: Accounting and auditing at the time of Blockchain technology: A research agenda. Australian Accounting Review. 2019; 29(2): 331–342. Publisher Full Text\n\nMuthaiyah S: Citation: Blockchain for audit provenance and trust: push factors, Value creation and challenges. International Journal of Auditing and Accounting Studies. 2019; 1(1): 13–25. Reference Source\n\nMoffitt S: The top 30 emerging technologies (2018–2028). 2019; [Accessed 15 Jul. 2019]. Reference Source\n\nMuthaiyah S: Citation: Understanding risks in Big Data Auditing. Selected Reading in Big Data Analytics and Auditing. Northern Book Center, 2020; ISBN: 81-7211-391-9pp.1-120.\n\nDammag H, Nissanke N: A mathematical framework for Safecharts. Proceedings of the 5th International Conference of Formal Engineering Methods. Singapore, 2003; 620–640. Reference Source\n\nMuthaiyah S: Propagation and delegation of rights in Access Controls. Web Services Security and E-Business. Idea Group Publishing, 2007; 328–337."
}
|
[
{
"id": "93739",
"date": "12 Oct 2021",
"name": "Indrawati Sambas",
"expertise": [
"Reviewer Expertise My area of research are technology adoption including block chain adoption in the area of finance and marketing."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think this paper is a good and important addition to the literature. I really like the conceptualization of how autonomous Trusted Third-Party orchestration for banking systems must be self-auditing by its design which I think is very important in today's banking industry. This article addresses the links between the emerging of Blockchain technology and the need for a self-auditing process in the banking industry. They explained the specific incorporation of the trust factor into the distributed ledgers via smart contracts in blockchains that enable the provision of required governance for all transactions. Ensure that the banking ecosystem will entail trust is the key to drive its success.\nImplementing the RR, EA, and EL analytical data model to determine Risk Band (RB) based on ISO31000 standards and Multi-Agent Systems (MAS) that executing and updating RB into respective immutable ledgers are excellent. This study explained how logic for task delegation and task policies for autonomous execution on autonomous banking platforms run. I do hope that the future work they will investigate how control procedures can be embedded within Blockchain technology to make autonomous banking platforms more robust.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "96362",
"date": "22 Oct 2021",
"name": "Noor Ismawati Jaafar",
"expertise": [
"Reviewer Expertise It governance",
"AIS"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general, this may be a good start to more interesting research and findings. The context and focus of the research are very interesting and have huge potential to make an impact on society's application of IT, especially in the banking environment. Although I am not very familiar with the technique used in the article, this research has its own merit and contribution to the fintech environment and the banking industry as a whole. The use of blockchain and smart ledgers is an interesting phenomenon to study. What is good about this article is the assigning of risk band in terms of the 6 common processes in the banking environment. The use of RR, EA, EL, and MAS as stated by the author makes this article worth reading and understanding. These methods used as an approach in developing the risk band enhance the strength of the article. Moreover, the issue of trust that becomes the focal point in the article has been given the attention that links between the customers and the bank.\nThe results would definitely serve as reference points for the experts like IT auditors to assess or review the banking environment in the future. By defining the risk band and exposure analysis, this article has highlighted an interesting perspective on trust in the banking industry. I would also like to touch on the task delegation and policies for autonomous execution which could be adopted in the future banking environment. This could definitely benefit the banks in terms of efficiency and better services quality to the customers. Thus, the short simplistic article presented has served as a wake-up call for operations and IT researchers to expand the study on trust issues in the financial and banking environment.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "96360",
"date": "16 Nov 2021",
"name": "Kadambini Katke",
"expertise": [
"Reviewer Expertise technology management",
"general management",
"marketing 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\n1. Industry relevant research area which can contribute towards digitization of banking services\n\n2. Paper can be improved with a few more added references to support the research findings\n3. Self-citations out of a total of seven references results in limited literature coverage.\n\n4. Research findings and flow charts are satisfactory and supports 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/10-899
|
https://f1000research.com/articles/10-251/v1
|
29 Mar 21
|
{
"type": "Research Article",
"title": "Comparison of 1480 nm and 980 nm-pumped Gallium-Erbium fiber amplifier",
"authors": [
"Siti Azlida Ibrahim",
"Amilia Mansoor",
"Tuan Ainin Sofea Tuan Mohd Marzuki",
"Nasr Y. M. Omar",
"Hairul Azhar Abdul Rashid",
"Amilia Mansoor",
"Tuan Ainin Sofea Tuan Mohd Marzuki",
"Nasr Y. M. Omar",
"Hairul Azhar Abdul Rashid"
],
"abstract": "Background: One way to reduce the length of the gain medium in Erbium-Doped Fiber Amplifier (EDFA) is by doping the fiber core with a high concentration of Erbium. However, this method caused ion clustering effects, which limits the EDFA’s efficiency. In this research, the use of Gallium as a new co-dopant in erbium-doped silica fiber is explored. Methods: The new fiber, namely Gallium co-doped Erbium fiber (Ga-EDF), is used as a gain medium in an optical fiber amplifier setup. A 2-meter length of the Ga-EDF fiber was used in a single pass configuration with a forward pumping scheme at 150 mW pump power. The Ga-EDF amplifier's gain and noise figure while pumping at 980 nm and 1480 nm were compared. The amplifier's performance was evaluated as the input signal power varied between -30 dBm to 3 dB, over the wavelength range of 1520 nm to 1580 nm. Results: The 980 nm-pumped Ga-EDF amplifier achieved the maximum small-signal gain of 22.45 dB and the corresponding noise figure of 5.71 dB at the input signal wavelength of 1535 nm. Meanwhile, the 1480 nm-pumped Ga-EDF amplifier attained the maximum small-signal gain of 20.83 dB and the corresponding noise figure of 5.09 dB at the input signal wavelength of 1550 nm. At the input signal power below -20 dBm and the wavelength range 1520 nm to 1547 nm, the Ga-EDF performs better when pumped at 980 nm. Their performance is comparable at the input signal wavelength range between 1547 nm to 1580 nm. At the input signal power above -20 dBm, the 1480 nm-pumped Ga-EDF outperformed the 980 nm-pumped amplifier. Conclusions: The overall performance indicates that the gain saturation point of the 1480 nm-pumped amplifier is higher than the 980 nm-pumped.",
"keywords": [
"optical fiber",
"fiber amplifier",
"Erbium",
"Gallium"
],
"content": "Introduction\n\nSince its invention in 1987, Erbium-doped fiber amplifiers (EDFAs) have become the most crucial optical communication device in enabling the high-speed long-haul optical fiber communications system. The essential characteristics of EDFAs include the high optical gain in the C-band and L-band, high saturation output power, low noise figure, wide gain bandwidth, independent of bit rate, and insensitivity to polarization effects. Research in designing a compact, highly efficient EDFA is still ongoing. The optical fiber core is highly doped with Erbium ions to achieve high gain using a short gain medium. However, a high concentration of Erbium causes the clustering effect, which causes pair induced quenching and degrades the EDFA's performance. The clustering problem can be reduced by increasing the Erbium solubility in silica during the fiber fabrication process. The Erbium solubility can be improved by introducing a co-dopant such as Aluminium (Al) in the silica fiber (Myslinski et al., 1997). Since Gallium belongs to the same group of elements in the periodic table as Al, it is expected that its chemical properties will be somewhat similar to Al. The properties of Gallium oxide (Ga2O3) as a glass-forming oxide and potential index riser make it more suitable as a co-dopant.\n\nGallium co-doped Erbium fiber (Ga-EDF) was fabricated using modified chemical vapor deposition (MCVD) with a solution doping method to study its properties and potentials as a gain medium of a compact optical fiber amplifier (Dissanayake et al., 2015). The Erbium concentration in the fabricated Ga-EDF was approximately 2008 ppm. The core and cladding diameters were 9 µm and 125 µm, making it easy to splice to a standard single mode fiber. Recently, Ga-EDF's use as the gain medium in 860 femtoseconds mode-lock fiber laser has improved its performance (Zazali et al., 2019).\n\nFor EDFA with a high Erbium concentration, a 980 nm pumping scheme is more efficient than a 1480 nm pumping scheme (Kimura & Nakazawa, 1993). However, a recent study showed that an amplifier made of a gain medium that is highly doped with Erbium and co-dopants, namely Hafnium and Bismuth, achieved higher gain using a 1480 nm pump (Almukhtar et al., 2019). It shows that the co-dopants play a crucial role in determining the fiber amplifier's most suitable pump wavelength. Recently, we reported on an amplifier with a single-pass configuration using a 2 m length of the Ga-EDF as a gain medium with a 980 nm forward pumping scheme (Marzuki et al., 2020).\n\nThis research aims to characterize and compare the performance of the Ga-EDF amplifier pumped at two different wavelengths, which are 980 nm and 1480 nm. This paper aims to discuss pump wavelengths' influence on the Ga-EDF amplifier's gain and noise figure at small-signal input and large-signal input.\n\nThe optical signal amplification process at different wavelengths in EDFA is best described using the three-level energy level model, as shown in Figure 1.\n\nIn an optical fiber amplifier, pumping is a process to excite Er3+ ions from the ground state to the upper energy level to cause population inversion. Pumping at 980 nm in EDFA is also known as indirect pumping, will excite the ions from the ground state 4I15/2 to the upper energy level 4I11/2. Since the upper energy level is not stable, the ions will rapidly decay to the metastable state energy level 4I13/2. This process is nonradiative, in which the energy is dissipated as heat. The ions' lifetime at the upper-state 4I11/2 in EDFA is very short, approximately 1µs. The ions lifetime at the metastable state 4I13/2 is much longer than the upper-state, typically around 10 ms. As a result, the continuous pumping process causes the accumulation of ions at the metastable state, and finally, the population inversion is attained. When the photons of the input signal enter the fiber, it causes the ions at the metastable state 4I13/2 to decay to the ground state 4I15/2 while releasing energy in the form of photons of the same phase and wavelengths. This radiative relaxation process amplifies the input signal, also known as the stimulated emission process. Erbium ions E+3's energy bands enable the amplification of signals in the C band wavelength range (Desurvire, 2002).\n\nPumping at 1480 nm excites the ions from the ground state 4I15/2 directly to the metastable state 4I13/2. It provides a better power conversion efficiency in silica-based EDFA than the 980 nm pump (Naji et al., 2011). However, higher pump power is needed using 1480 nm compared to a 980 nm pump to achieve the same small-signal gain level. The noise figure of EDFA pumped at 1480 nm is also higher than the 980 nm for a specific small-signal gain (Pedersen et al., 1992). The absorption band of 4I15/2 → 4I13/2 is quite broad. So, the pump laser wavelength does not need to be carefully selected. However, the overlapping of absorption and emission band causes incomplete population inversion, which causes unavoidable noise (Miniscalco, 1991). The 1480 nm pump signal can travel over a longer distance in the silica optical fiber without a significant loss compared to the 980 nm signal. Therefore, a 1480 nm pump is preferred for remotely pumped amplifiers, such as in submarine applications.\n\nThe amplified spontaneous emission (ASE) characteristic of a fiber amplifier is an essential factor that needs to be considered in designing an amplifier. Spontaneous emission happens when the ions at the excited state decay to the ground state and emit photons spontaneously. The spontaneously emitted photons then generate more photons as they propagate in the fiber. These photons add to the input signal as background noise, known as ASE noise. ASE behavior depends on the pump wavelength. The same fiber pumped at different wavelengths will show different ASE characteristics. The ASE also depends on the dopant composition. Pumping a YttErbium-Erbium doped fiber at 940 nm has been observed to suppressed the ASE (Booker et al., 2018). In this work, the ASE characteristics of Ga-EDF, forward pumping at 980 nm and 1480 nm, will be compared. Furthermore, ASE's influence on the Ga-EDF amplifier's gain and noise figure will also be analyzed.\n\nOne of the critical performance characteristics for an optical fiber amplifier is the power conversion efficiency, which is the ratio between the output signal power over the input pump power. A few dissipative processes reduce the power conversion efficiency of the EDFA, namely multiphonon emission, excited-stateaAbsorption (ESA), and cooperative up-conversion. Multiphonon emission results in nonradiative relaxation, where no photons are generated. ESA is also a dissipative process where the ion is excited from the metastable state to a higher state through absorption of a pump or signal photon. Another dissipative process is the ion-ion interaction known as cooperative up-conversion (Miniscalco, 1991). The cooperative up-conversion happens when two Erbium ions at the metastable state 4I13/2 exchange energy, which cause one ion to be excited to upper state 4I19/2, and another ion would decay to the ground state 4I15/2, without photon emission (An et al., 1998). This process causes concentration quenching, limiting Erbium's concentration in the EDFA. Erbium's low solubility in silica, which causes clustering, is the cooperative up-conversion's primary source. The suggested concentration for Erbium in silica is below 100 ppm for optimum amplifier efficiency (Digonnet, 2001). Hence, a long gain medium is needed to achieve a specific gain, creating a bulky footprint EDFA.\n\nIn designing a compact fiber amplifier using a short gain medium, many efforts were made to minimize the concentration quenching effect. One of the effective methods to increase Erbium solubility is by adding Aluminum to the silica host. Using 8000 ppm Aluminum and 8900 ppm Erbium, a 50 cm long EDFA has been found to achieve 24 dB gain with a pump power of 60 mW (Kimura & Nakazawa, 1993). The ion clustering effect can also be reduced by adding other rare earth co-dopants such as Ytterbium and Lanthanum (Baker et al., 2019). A small-signal gain of 36.6 dB has been achieved using 1 m length Hafnium Bismuth EDF with 12500 wt ppm Erbium in the double-pass configuration (Almukhtar et al., 2019). A 1 m amplifier made of zirconia-yttria-alumina-baria silica host achieved a flat small-signal gain of 25 dB (Duarte et al., 2019). In chalcogenide glass fiber, Gallium has been used to prevent clusterings (Digonnet, 2001). The solubility of rare-earth ions in the chalcogenide glass was increased with the presence of Gallium. Researchers at our research center conducted the first attempt to use Gallium as a co-dopant in a silica host by fabricating the Ga-EDF fiber using the MCVD and solution doping method (Dissanayake et al., 2015). The absorbance, fluorescence lifetime, and ASE were characterized (Dissanayake, 2015). However, no analysis was done on the amplifier's performance at different pump wavelengths.\n\nWe continued the research to study the Ga-EDF detail characteristics. We recently demonstrated an amplifier with a small-signal gain of 22.45 dB using a 2 m Ga-EDF in a single-pass configuration (Marzuki et al., 2020). Figure 2 shows the absorption spectra for the Ga-EDF reported by Dissanayake et al. (2015). The spectra indicate that the Ga-EDF absorption is high at the standard pump wavelengths, 980 nm and 1480 nm. In this paper, the two pump wavelengths' influence on this amplifier's performance will be presented.\n\nThis figure has been reproduced with the permission from Dissanayake (2015).\n\n\nMethods\n\nBefore the amplifier's gain and noise figure characterizations, the Ga-EDF's ASE spectra pumped at both pump wavelengths was measured. The experimental setup for the characterization of ASE spectra is illustrated in Figure 3.\n\nWDM=wavelength division multiplexing coupler module; OSA=optical spectrum analyser.\n\nA Lumics 980 nm 14-pin Butterfly LD powered by a Newport current and temperature controller (model 8000; Newport, Irvine, CA), together with a Lightel 980 /1550 nm wavelength division multiplexing (WDM) coupler module, was connected to the input end of the Er/Ga fiber. The Ga-EDF fiber's output end was connected to a Yokogawa ANDO AQ6370C Optical Spectrum Analyser (OSA) to measure the ASE spectra. The forward pump power was set to 150 mW before the measurement, and the OSA resolution was set to 0.2 nm. The experiment was repeated using Keopsys Continuous Erbium Broadband Source and a 1480/1550 nm WDM module to pump the Ga-EDF fiber at 1480 nm.\n\nFigure 4 shows the single-pass forward pumping optical fiber amplifier's experimental setup, with the 2 m length of Ga-EDF as the gain medium. The Ga-EDF was fabricated in-house using MCVD with the solution doping method, as described in Dissanayake (2015). The fiber core and cladding diameters are 9 µm and 125 µm, respectively. The cut-off wavelength for single-mode operation is 1.4 µm. ANDO 4321 C-band Tunable Laser Source (TLS) generates the input signal in the wavelength range of 1520 nm to 1580 nm, with the input signal power varied between -30 dBm to 3 dBm. An isolator was inserted between the TLS and WDM coupler to prevent the back-reflected signal from damaging the TLS. Lumics 14-pin Butterfly Laser Diode (LD) (Lumics, Berlin, Germany) was used as the pump laser at 980 nm. Keopsys 1480 nm Pump Source was used for 1480 nm pumping. The Newport current and temperature controller model 8000 controlled the 14-pin butterfly 980nm LD pumping the Ga-EDF at a maximum power of 150 mW. A 980/1550 nm WDM module was used to couple both input and pump signals into the Ga-EDF. The Yokogawa AQ6370D OSA with a resolution of 0.05 nm was used to measure the amplified signal across the wavelength range of 1500 nm to 1600 nm. The gain and noise figure was analyzed for the small-signal input power (-30 dBm) and large-signal input power (3 dBm).\n\nTLS= Tunable Laser Source, WDM=wavelength division multiplexing coupler module, OSA=optical spectrum analyser.\n\nThe summary of the experimental parameters used in this research is listed in Table 1.\n\nGa-EDF=Gallium co-doped Erbium fiber, OSA=optical spectrum analyser, ASE=amplified spontaneous emission.\n\n\nResults and discussion\n\nThe ASE spectra of the Ga-EDF amplifier are shown in Figure 5 (Ibrahim et al., 2021). The amplitude of ASE was higher at 980 nm pumping because of a higher absorption at 980 nm than 1480 nm in the Ga-EDF, as characterized by Dissanayake et al. (2015). The absorption was 25 dB/m at 980 nm and 14 dB/m at 1480 nm. Higher absorption causes a higher population inversion to occur with the 980 nm pumping. From the measurement done by Dissanayake et al. (2015), the Ga-EDF fiber's fluorescence lifetime was 6.02 ms and 6.06 ms for 980 nm pump and 1480 nm pump, respectively. The shorter lifetime also contributes to the higher ASE at 980 nm pumping. As a result, the 980 nm-pumped amplifier's ASE amplitude was higher for the whole range of the measured signal wavelengths. The 980 nm-pumped amplifier has a peak ASE power of -16 dBm at 1535 nm, 11 dB higher than the 1480 nm-pumped signal. The two peaks (at 1535 nm and 1553 nm) represent the photons emission caused by the ions transition between the sub energy levels of the 4I13/2 metastable state and the 4I15/2 ground state. The peak wavelength of 1535 nm might be the Gallium co-dopant attribute in this fiber, which differs from the peak wavelength for EDF with other co-dopants.\n\nThe comparison of the 980 nm and 1480 nm-pumped Ga-EDF amplifier small-signal gains and the noise figures are shown in Figure 6. The input signal power was set to -30 dBm. The pump power was maintained at 150 mW for both pumping wavelengths. Overall, the 980-nm pumped amplifier achieved better small-signal gain than the 1480-nm pumped amplifier, with the maximum gain of 22 dB at 1535 nm input signal wavelength. At the shorter wavelength range (1520 – 1547 nm), the 980 nm-pumped amplifier outperformed the 1480 nm-pumped amplifier, with the highest gain difference of 6 dB. At the longer wavelength range (1548 – 1580 nm), no significant difference in gain between the two pumping schemes was seen, except that the gain for 1480 nm pumping was slightly higher at the wavelength range of 1547 nm to 1565 nm, with the highest gain difference of only 0.85 dB at 1550nm. The input signal wavelength for the peak gain was related to the ASE spectra in Figure 5. The maximum gain occurs at the same input signal wavelength in the ASE spectra because it directly correlates with the ASE power. When the amplifier was forward pumped at the 980 nm wavelength, the peak gain occurred at 1535 nm, similar to the ASE peak spectra wavelength, as depicted in Figure 5. Similarly, when pumped at the 1480 nm wavelength, the peak gain occurred at 1550 nm, following its ASE spectra. The noise figure shown in Figure 6 shows that the 980-nm pumped amplifier exhibited better performance than the 1480-nm pumped amplifier at the shorter wavelength range between 1520 nm to 1545 nm. The higher noise level at the shorter wavelength is typical in EDFA due to the signal's reabsorption by the Erbium ions in the 4I15/2 state manifold. The reabsorption rate might be higher for the 1480-nm pumped amplifier due to a similar 4I13/2 metastable state lifetime.\n\nThe Ga-EDF amplifiers' performance in amplifying large signal was investigated by setting the input power to 3 dBm. The pump power of both pumping wavelengths was maintained at 150 mW. The Ga-EDF gain and noise figure when the input signal power was set to 3 dBm is shown in Figure 7. The gain at large input signal is lower than the small-signal due to gain saturation. Contrary to the small-signal characteristics, the amplifier performed better when pumped at 1480 nm for large input signals at a longer wavelength between 1528 nm to 1580 nm. The possible reason that 1480 nm-pumped outperform the 980 nm-pumped amplifiers at large input signal was the longer fluorescence lifetime. The lifetime for the photons at metastable state when pumped at 1480 nm was 0.66% longer than the photons pumped at 980 nm, as reported by (Dissanayake, 2015). Since pumping at 1480 nm is a direct pumping with a longer lifetime, more ions are accumulated at metastable states and contribute to the stimulated emissions. The 1480 nm-pumped amplifier outperformed the 980 nm-pumped both in terms of gain and noise figure. The highest achievable gain by the 1480 nm-pumped amplifier was 9 dB at the input signal wavelength of 1560 nm, with a corresponding noise figure of 4.5 dB. The 980 nm-pumped amplifier achieved a maximum gain of 6 dB with a noise figure of 9 dB at 1565 nm input signal wavelength.\n\nFigure 8 shows the gain and noise figure versus the input signal power for the amplifiers at the input signal wavelength of 1535 nm and 1550 nm. At high input power, the amplifier gave better performance with 1480 nm pumping than 980 nm pumping. It shows that the gain saturation point at 1480 nm pumping was higher than at 980 nm pumping. At the input signal wavelength of 1535 nm, the gain reduced drastically as the input power increased. Both pumpings result in the same trend. At the input signal wavelength of 1550 nm, the gain reduction was not as drastic as 1535 nm. It shows that the photons emission at 1535 nm was higher than 1550 nm only in the small-signal region. Above the input signal power of -20 dBm, operating at the 1550 nm signal performed better in both gain and noise figure than 1535 nm, at both pump wavelengths. The noise figure for the 980 nm-pumped amplifier was higher than the 1480 nm-pumped at all input signal power, except at -30 dBm input signal power at 1535 nm. The noise figure correlated to the ASE spectra is shown in Figure 5. The higher ASE in the 980 nm-pumped amplifier contributed to the higher noise. An obvious disadvantage of operating at 1535 nm is the high noise figure at both pump wavelengths. Even though the small-signal gain was maximum at 1535 nm input signal, the performance degraded severely as the input signal power increased. Therefore, it can be concluded that the Ga-EDF amplifier is best to be operated at the input signal of 1550 nm.\n\n\nConclusion and further research\n\nIn this study, the gain and noise figure characteristics of the Ga-EDF amplifier pumping at 1480 nm and 980 nm wavelengths were compared. The amplifier was set up in a single pass configuration with the forward pumping scheme. The maximum gain of 22.45 dB was achieved at 1535 nm by the 980 nm-pumped Ga-EDF. However, looking at the overall performance, the 980 nm-pumped Ga-EDF only outperformed the 1480 nm-pumped Ga-EDF at the small-signal input at the wavelength range 1520 nm to 1547 nm. Both pumping's small-signal gains were comparable at the input signal wavelength range between 1547 nm to 1580 nm. Above -20 dBm input signal power, the 1480 nm-pumped Ga-EDF achieved a higher gain and lower noise figure than the 980 nm-pumped. It indicates that the gain saturation point at 1480 nm pumping is higher than at 980 nm pumping in the Ga-EDF amplifier. The 980 nm-pumped amplifier was severely affected by the ASE noise, especially at the high input signal power. Considering the overall performance, operating the amplifier at 1550 nm is better than at 1535 nm, except in the case of input power below -20 dBm. The Ga-EDF amplifier's investigation using a double-pass configuration can be considered to achieve a higher gain in the future. The use of Ga-EDF as a gain medium in a high-power laser also could be investigated.\n\n\nData availability\n\nFigshare: ASE, gain and noise figure of Gallium-Erbum doped fiber amplifier at the C- band. https://doi.org/10.6084/m9.figshare.14213582.v1 (Ibrahim et al., 2021).\n\nThis project contains the following underlying data:\n\n- ASE Spectra of the Ga-EDF pumped at 980 nm and 1480 nm.csv\n\n- Gain and noise figure versus input signal power obtained at a pump wavelength 980 nm.csv\n\n- Gain and noise figure versus input signal power obtained at a pump wavelength 1480 nm.csv\n\n- Large signal gain and noise figure of the Ga-EDF amplifier at the input signal power of 3 dBm.csv\n\n- Small signal gain and noise figure of the Ga-EDF amplifier at the input signal power of -30 dBm.csv\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "References\n\nAlmukhtar AA, Al-Azzawi AA, Cheng XS, et al.: The effect of 980 nm and 1480 nm pumping on the performance of newly Hafnium Bismuth Erbium-doped fiber amplifier. J Phys Conf Ser. 2019; 1151(1): 012013. Publisher Full Text\n\nAn HL, Pun EY, Liu HD, et al.: Effects of ion clusters on the performance of a heavily doped Erbium-doped fiber laser. Opt Lett. 1998; 23(15): 1197–9. PubMed Abstract | Publisher Full Text\n\nBaker CC, Burdett A, Friebele EJ, et al.: Rare earth co-doping for increased efficiency of resonantly pumped Er-fiber lasers. Opt Mater Express. 2019; 9(3): 1041–1048. Publisher Full Text\n\nBooker P, Caspary R, Neumann J, et al.: Pump wavelength dependence of ASE and SBS in single-frequency EYDFAs. Opt Lett. 2018; 43(19): 4647–4650. PubMed Abstract | Publisher Full Text\n\nDesurvire E: Erbium-doped Fiber Amplifiers: Principles and Applications. Columbia U. New Jersey: Wiley Interscience. 2002. Reference Source\n\nDigonnet MJF: Rare-Earth-Doped Fiber Lasers and Amplifiers. Stanford U. New York: Marcel Dekker. 2001. Publisher Full Text\n\nDissanayake KPW: Design and Performance Analysis of Rare-Earth Doped Fibres with Modified Silica Host. Multimedia University. 2015; 56–03: 108. Reference Source\n\nDissanayake KPW, Abdul-Rashid HA, Safaei A, et al.: Fabrication and characterization of a Gallium co-doped Erbium optical fiber. Proceedings of ICP 2014 - 5th International Conference on Photonics. 2015; 113–115. Publisher Full Text\n\nDuarte J, Paul MC, Das S, et al.: Optical amplification performance of Erbium doped zirconia-yttria-alumina-baria silica fiber [Invited]. Opt Mater Express. 2019; 9(6): 2652–2661. Publisher Full Text\n\nIbrahim SA, Mansoor A, Tuan Mohd Marzuki TAS, et al.: ASE, gain and noise figure of Gallium-Erbium doped fiber amplifier at the C- band. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14213582.v1\n\nKimura Y, Nakazawa M: Gain characteristics of Erbium-doped fiber amplifiers with high Erbium concentration. Jpn J Appl Phys. 1993; 32(3R): 1120–1125. Publisher Full Text\n\nMarzuki TAS, Mansoor A, Rashid HAA, et al.: Gallium-Erbium Fiber Amplifier. In 2020 IEEE 8th International Conference on Photonics, ICP. 2020. Publisher Full Text\n\nMiniscalco WJ: Erbium-Doped Glasses for Fiber Amplifiers at 1500 nm. J Lightwave Technol. 1991; 9(2): 234–250. Publisher Full Text\n\nMyslinski P, Nguyen D, Chrostowski J: Effects of concentration on the performance of Erbium-doped fiber amplifiers. J Lightwave Technol. 1997; 15(1): 112–120. Publisher Full Text\n\nNaji AW, Hamida BA, Cheng XS, et al.: Review of Erbium-doped fiber amplifier. International Journal of Physical Sciences. 2011; 6(20): 4674–4689. Reference Source\n\nPedersen B, Thompson BA, Zemon S, et al.: Power Requirements for Erbium-Doped Fiber Amplifiers Pumped in the 800, 980, and 1480 nm Bands. IEEE Photonics Technol Lett. 1992; 4(1): 46–49. Publisher Full Text\n\nZazali NA, Latifa AA, Lau KY, et al.: 860 femtoseconds mode-locked fiber laser by Gallium co-doped erbium fiber (Ga-EDF). Results in Physics. 2019; 15: 102644. Publisher Full Text"
}
|
[
{
"id": "82436",
"date": "06 Apr 2021",
"name": "Colin C. Baker",
"expertise": [
"Reviewer Expertise Synthesis and characterization of rare earth doped silica fibers"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 was my understanding that this is a paper was meant to explore the benefit of Ga co-doping of EDF. However, there is no comparison with an erbium doped fiber without gallium co-doping. It seems that results and analysis should be done with a comparison of an erbium doped fiber of nearly identical concentration without gallium in order to ascertain its benefits or at least a mention of the differences with the co-dopant. It is also stated that Ga2O3 is a better co-dopant than aluminum but there is no information to back that up. This paper is then essentially concerned with a comparison of pumping at 980 nm vs. 1480 nm, which has been studied extensively by many authors. Very little information is given about the fiber itself. I had to go to the previous reference to learn more about the properties of the fiber, such as the ratio of Ga to Er (very important), and its NA, etc... There I learned that the fiber also contains phosphorous. What is its role here? Please check for errors. In the abstract its says signal powers from -30dBm to 3dB, it should say ...to 3dBm.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7097",
"date": "08 Sep 2021",
"name": "Siti Azlida Ibrahim",
"role": "Author Response",
"response": "A comparison with an erbium-doped fiber without Gallium co-dopant is added in the discussion section (paragraph 3). The comparison was made with an erbium-doped fiber with nearly identical erbium concentration and fiber length. This work is not intended to compare aluminum co-dopant and Gallium co-dopant. The aluminum as a co-dopant is mentioned as a justification to use Gallium. The word “more” in the last sentence of paragraph 1 was removed to avoid confusion. The fiber properties were added in the second paragraph of the Introduction part, including Ga:Er ratio, the NA, and the cut-off wavelength. During the fabrication, phosphorous is added to increase the pore size of the deposited silica soot, hence increase the incorporation of dopants. It will also reduce the required sintering and collapse temperatures. For this preform case, it does not have any effect on the optical properties of the fiber. Correction made in the abstract (dB changed to dBm)."
}
]
},
{
"id": "82439",
"date": "05 May 2021",
"name": "Abdollah Malakzadeh Fard Khangheshlaghi",
"expertise": [
"Reviewer Expertise fiber optics",
"fiber sensor",
"FBG",
"distributed fiber sensors",
"THz generation",
"Ultrashort pulse 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\nI reviewed the article “Comparison of 1480 nm and 980 nm-pumped Gallium-Erbium fiber amplifier”. These are my questions for the authors: However the comparison between the two pump lasers in the medium is a necessity and attractive,\nThe comparison is for a fixed length. Does this have a physical reason?\n\nThe power is limited to 150mW. Why did the authors not use higher power lasers?\n\nThe setup benefits a single pass one directional pumping? Why forward directional pumping? Why not backward or bidirectional pumping?\n\nIn figure 6, what is the error bar in the graphs? It seems there is almost no difference in noise figure or small signal gain values of pumping with both wavelengths in large ranges of the spectra. Is such insensitivity for the gain length or the co-dopant (Ga) magnitude?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7098",
"date": "08 Sep 2021",
"name": "Siti Azlida Ibrahim",
"role": "Author Response",
"response": "The comparison is made for the optimum length at a maximum gain. The optimum length was found using the cut-back method. In the reference, Marzuki et al., 2020, the amplifier's performance with different lengths has been discussed. 150 mW is the maximum pump power available at the lab. The forward directional configuration was chosen as it is the simplest configuration of a fiber amplifier which we felt is enough to show the applicability of the fiber. Since the experiment was conducted at a relatively low pump power, the difference is not significant due to limited gain length. As mentioned in the reference Marzuki et al., 2020, a longer gain medium does not produce a higher gain output at 150mW pump power."
}
]
}
] | 1
|
https://f1000research.com/articles/10-251
|
https://f1000research.com/articles/10-898/v1
|
07 Sep 21
|
{
"type": "Research Article",
"title": "Therapy for patients with asymptomatic and mild cases of COVID-19 in Indonesia",
"authors": [
"Joni Wahyuhadi",
"Erwin Astha Triyono",
"Christijogo Soemartono Waloejo",
"Agus Harianto",
"Halim Priyahau Jaya",
"Fauqa Arinil Aulia",
"Nalendra Djaya Iswara",
"M. Arif Harianto",
"Krisna Murti",
"Sriyono Sriyono",
"Ninis Herlina Kiranasari",
"Nurarifah Destianizar Ali",
"Michael Austin Pradipta Lusida",
"Claudia Herda Asyari",
"Friedrich Rabin Situmorang",
"Nabilah Nabilah",
"Muhammad Reza Arifianto",
"Langgeng Agung Waskito",
"Makhyan Jibril Al Farabi",
"Christijogo Soemartono Waloejo",
"Agus Harianto",
"Halim Priyahau Jaya",
"Fauqa Arinil Aulia",
"Nalendra Djaya Iswara",
"M. Arif Harianto",
"Krisna Murti",
"Sriyono Sriyono",
"Ninis Herlina Kiranasari",
"Nurarifah Destianizar Ali",
"Michael Austin Pradipta Lusida",
"Claudia Herda Asyari",
"Friedrich Rabin Situmorang",
"Nabilah Nabilah",
"Muhammad Reza Arifianto",
"Langgeng Agung Waskito"
],
"abstract": "Background Though coronavirus disease (COVID-19) has been designated as a global pandemic, its nature as a viral infection means that it is essentially a self-limiting disease. We studied the application of symptomatic, isolation, relaxation, nutrition and observation (SIRNO) therapy in patients with asymptomatic and mild symptoms of COVID-19 at a rescue hospital in Indonesia.\n\nMethods This is a retrospective cohort study involving 2122 patients who were admitted to Indrapura Field Hospital in Surabaya from 28 May 2020 to 20 September 2020. We analyzed demographic data, clinical signs and symptoms, laboratory data, therapy and clinical outcomes.\n\nResult The total sample of 2122 patients consisted of 1403 male patients (66.12%), and 719 female patients (33.88 %). The most common age range was 26-45 years, at 52.54% (1115 patients). The clinical symptoms of 1121 patients (52.8%) were asymptomatic, 977 patients (46%) had mild symptoms, and 24 patients (0.1%) had moderate symptoms. All patients received the SIRNO therapy method. From a total of 2122 patients, 1930 patients (90.9%) were cured, 181 patients (8.5%) are still being treated, seven patients (0.03%) were referred for indications of desaturation (SpO2 <94%), and four patients (0.01%) were moved to a referral hospital. Until 20 September 2020, the final date studied, there were no patient deaths.\n\nConclusion The SIRNO method provides excellent results in the management of COVID-19 at a rescue hospital for patients with asymptomatic and mild symptoms. Economic pharmacological research can initiate a follow-up study in order to objectively measure the effectiveness and efficiency of SIRNO treatment methods in patients with asymptomatic, mild symptoms of COVID-19, and the small number of 24 patients (0,.1%) with moderate symptoms.",
"keywords": [
"Symptomatic",
"Isolation",
"Relaxation",
"Nutrition",
"Observation",
"COVID-19"
],
"content": "Introduction\n\nCoronavirus disease (COVID-19) is a global public health issue that was confirmed as a pandemic in March 2020. Defined by the World Health Organization (WHO), COVID-19 is caused by a new coronavirus called the 2019-novel coronavirus (2019-nCoV)1. However, the International Committee on Taxonomy of Viruses named the novel coronavirus as \"Severe Acute Respiratory Syndrome Coronavirus 2\" (SARS-CoV-2)2.\n\nOn September 21, 2020, a total of 30,675,675 confirmed COVID-19 cases were reported in more than 216 countries, including 954,417 deaths, resulting in a mortality rate of 3.1%. In Indonesia, the total number of cases was 248,852 with a death rate of 9,677, while in East Java the total number of cases was 40,708 (16.35%) with a mortality rate of 7.28 %, or 2,695 patients3. As the number of COVID-19 sufferers in some countries continues to increase, as well as the deaths resulting from it, epidemiological studies are very important in order to determine the source of transmission and devise effective and efficient therapeutic methods4. Although the understanding of COVID-19 epidemiology continues to develop, it is assumed that SARS-CoV-2 is primarily transmitted through droplets and close contact with a person that is carrying the virus4 and the likelihood of death strongly depends on the methods of therapy and comorbidities found in patients.\n\nCOVID-19 has a very wide clinical output, from asymptomatic to severe and critical symptoms; more than 75% cases are asymptomatic cases5. Among those symptomatic patients, clinical presentations of this include fever, non-productive cough, dyspnea, myalgia, fatigue, normal or decreased leukocytes count, and radiography evidence of pneumonia6. Severe complications can include organ dysfunction, including shock, acute respiratory distress syndrome (ARDS), acute heart injury and acute kidney injury. These manifestations may continue and lead to death7. The WHO recommended therapies for asymptomatic and mild symptomatic COVID-19 cases are symptomatic, isolation, and observation, related to complaints as well as the monitoring of vital signs and the progress of the disease. In addition, highly nutritional therapy8 and relaxation are also needed in the form of light exercise, communication with fellow patients, a psychological approach and calming of the patient with spiritual lectures and studies into religion, as well as a relaxed atmosphere in the hospital9. This approach was based on the nature of viral infection which is a self-limiting disease. Viruses that enter the body will be countered by our body's defense system, either naturally via non-specific defences, or specific antibodies.\n\nIf the body's non-specific defenses are unable to prevent the virus, then the virus will enter the cell, damage the cell and replicate itself. Antiviral drugs specifically for SARS-COV-2 are still in clinical trials, the administration of antiviral side effects damages the body's cells, so the type, time and dosage of its administration must be precise. In addition the effectiveness of virusidal against the virus that causes COVID-19 has not yet been empirically proven. A review of the economic pharmacology also needs to be considered, the efficiency and effectiveness of therapy is key to the success of the therapy method10.\n\nKogabwilhan II Indrapuara Field Hospital is a specialized hospital that treats COVID-19 patients, which is confirmed by swab results with positive PCR (polymerase chain reaction) examination infected with SARS-COV-2. The hospital was established for the treatment and isolation of COVID-19 patients without symptoms and with mild symptoms, in an effort to support COVID-19 services in existing referral hospitals. The initiator of the establishment of Indrapuara Field Hospital was the COVID-19 Control Task Force of East Java Province, with financing from the National Disaster centre and fully supported by the Provincial Government of East Java, military regional command V Brawijaya, East Java regional police, the Ministry of Health and the Commander of Joint Command Region II.\n\nThe purpose of this study is to describe application of symptomatic, isolation, relaxation, nutrition, and observation (SIRNO) therapy for asymptomatic and mild symptomatic patients at rescue field hospital.\n\n\nMethods\n\nThis study is a retrospective cohort study of COVID-19 patients who were admitted at Kogabwilhan II Indrapura Field Hospital from 28 May 2020 to 20 September 2020 in Surabaya, East Java Indonesia. This date range was chosen as the opening date of service of the Indrapura Field Hospital for COVID-19 patients. The obtained data was downloaded from the hospital electronic medical records, including demographic data, clinical signs and symptoms, laboratory data, therapy and clinical outcomes (24).\n\nAll patients with COVID-19 enrolled in this study diagnosed according to the guidelines for diagnostic criteria from Clinical management of COVID-19: interim guidance (World Health Organization, 27 May 2020). All patients suffered from the infection of SARS-CoV-2, ascertained in the laboratory (the results of RT-PCR [reverse-transcription polymerase chain reaction] specific for SARS-CoV-2 was positive). Diagnosis of mild case patients is made based on the criteria of symptomatic patients and meets the definition of COVID-19 cases without evidence of viral pneumonia or hypoxia, and moderate cases of patients with clinical symptoms of pneumonia (fever, cough, dyspnea, rapid breathing) but no sign of severe pneumonia, including SpO2 ≥ 90% in the air of the room. All patients treated in Indrapura field hospital according to the criteria constitute the sample of the study.\n\nData demographic characteristics of patients were obtained with form collection from the electronic medical record. The collected information included age, gender, occupation, and domicile.\n\nThe patients’ clinical data were data related to current and past patient medical history. Current signs and symptoms were fever, cough, shortness of breath, fatigue, anorexia, muscle pain, headache, chills, nausea and vomiting, diarrhea, and confusion. Patients’ past history included hypertension, heart disease, diabetes, obesity, chronic obstructive pulmonary disease, liver disease. Serial vital signs included blood pressure, pulse, respiratory rate, body temperature, oxygen saturation, and body mass index. The date of onset of the disease is defined as the day when symptoms are first known. Determination of COVID-19 positivity was based on RT-PCR SARS-CoV-2 from naso/oropharyngeal swabs which were collected on the day of admission and evaluated when patients were discharged. Clinical outcome data, including recovery rates, length of treatment, referred cases and death cases, were also analyzed in this study.\n\nSymptomatic by providing therapy according to the complaints felt by the patient, such as the administration of antipyretics, anti diarrhea, decongestan, antitussive and so on.\n\nIsolation by dividing into red zones for patients, which are not mixed between patients and service providers. The room includes a bed space, space for rest and a field for outdoor activities, as well as a garden.\n\nRelaxation by doing gymnastics activities on the field, as well as deep breathing exercises. In addition, there are karaoke activities while still using masks and keeping distance, and regular spiritual and religious lectures and stress management.\n\nNutrition provided is adjusted to the patient's caloric needs and comorbidity. The type of food provided should also meet the balance of macro nutritional needs such as carbohydrates, proteins, fats, vitamins, and minerals.\n\nObservations are divided into three shifts, each shift will enter the isolation zone for 3 hours to observe the patient's vital signs, complaints and progress. During observation, patients can also consult both physical and mental complaints such as sleep difficulty and restlessness. Patients can also contact the care team at any time online.\n\nAll patients are not given antiviral therapy or antibiotics.\n\nStatistical analysis was performed using SPSS Version 24. All continuous data is presented as a mean ± standard deviation (SD) or median ± interquartile range (IQR). Categorical data is presented as numbers and percentages.\n\nThe study protocol was approved by the Ethics Committee of Dr. Soetomo Teaching Hospital (Surabaya, Indonesia), and Universitas Airlangga Faculty of Medicine (Surabaya, Indonesia). All participants have provided written consent for the usage of their data for research purposes.\n\n\nResults\n\nFrom the research period of 28 May to 20 September 2020, a total of 2122 patients were found to fit the research criteria. Of these, 1403 patients (66.12%) were men, with the most common age range of study subjects being 26–45 years of age at 52.54% (1115 patients), while 27.33% were 46–65 years, 17.58% were 12–25 years , 1.51% were 6–11 years and 1.03% were over 65 years. In total, 1656 patients were treated without comorbidities (78%) and 466 patients had comorbidities (21.9%). The most common comorbidities were hypertension, at 286 patients (13.47%), diabetes mellitus at 84 patients (3.95%), while 59 patients (2.78%) were obese. A small number of patients also had various comorbidities such as bronchial asthma, hypertensive heart disease, and coronary heart disease. In terms of patient occupation demographics, 946 patients (44.58%) worked as a private employee, followed by 219 patients (10.3%) as military and police, 130 patients (6.1%) as civil servants, and 73 patients (3.4%) as medical personnel, with details of 68 nurses (3.20%), four doctors (0.18%), and one midwife (0.04%) (Table 1).\n\nCHD: Coronary Heart Disease; HIV: Human Immunodeficiency Virus.\n\nOf the COVID-19 patients that were treated at Indrapura field hospital, there were 1121 patients (52.8%) without complaint, 977 patients (46%) with mild symptoms, and 24 patients (0.1%) with moderate symptoms. The most common symptoms of COVID-19 were coughing in 325 patients (15.3%), followed by a cold in 132 patients (6.2%), anosmia in 110 patients (5.1%), fever in 93 patients (4.3%), nausea in 47 patients (2.2%), headaches in 46 patients (2.1%), and shortness of breath in 39 patients (1.8%). There were also other symptoms that patients complained about such as abdominal pain and diarrhea in 38 patients (1.7%) (Table 2).\n\nRT-PCR SARS-CoV-2: Reverse-Transcriptase Polymerase Chain Reaction Severe Acute Respiratory Syndrome Coronavirus 2\n\nAll RT-PCR SARS-CoV-2 swab results were positive for patients treated at Indrapura field hospital. Recovered patients are patients with missing or mildly tolerated clinical symptoms after treatment without symptomatic drugs, and for whom swabs have been negative as much as two times. After leaving the hospital, 181 patients (8.5%) gave feedback related to post-treatment re-swab examination. Of these 181 patients, there were 52 patients (28.7%) who re-examined after exiting the Indrapura field hospital, while 129 patients (71.3%) did not do the re-swab. A total of 19 patients (37.3%) did the re-examination after more than 15 days of returning home, followed by eight patients (15.3%) on the 14th day, and the rest did the examination on the 6th day. Of the 52 patients who did the re-swab, we found 43 patients (82.8%) with negative results, and 9 patients (17.2%) with positive results (Table 2).\n\nAll patients treated in Indrapura field hospital received SIRNO therapy which was symptomatic (such as antitussive, expectorant, antipyretic, decongestan, bronchodilator), and involved isolation, relaxation, nutrition, and observation. In addition, patients also received therapy for comorbidities. Until 20 September 2020, 1907 patients (89.87%) received multivitamin therapy (Becefort), 337 patients (15.8%) received N-acetyl cystein therapy 200mg (NAC), 227 patients (10.6%) received decongestant therapy (such as Tremenza and Flutrop), 171 patients (8%) received paracetamol, and 97 patients (4.5%) received lorazepam for anxiety disorders. For hypertensive comorbid therapy, 197 patients (9.28%) received Amlodipine therapy 10mg and 190 patients (8.95%) received Amlodipine 5mg, while 26 patients (1.2%) received candesartan therapy 16mg and 21 patients (0.98%) received Candesartan 8mg. Patients with comorbid diabetes (as many as 37 patients, or 1.74%) received metformin therapy 500mg, Glimepiride therapy 2mg was received by 43 patients (2%), and 16 patients (0.75%) received insulin (Apidra, Novorapid, and Levemir). All patients in Indrapura field hospital had no antiviral therapy, nor corticosteroids (Table 3).\n\nFrom a total of 2122 patients, 1930 patients (90.9%) were cured, and 181 patients (8.5%) are still being treated. There were seven patients (0.03%) referred for indications of desaturation (SpO2 <94%), and four patients (0.01%) moved to a referral hospital. No patient died or returned home on their own request (0%). The highest number of patients treated in the Indrapura field hospital based on average length of stay (LOS) was in the group with a LOS of less than 7 days, which was 1399 patients in total (72.48%), followed by the group with a LOS of 8–14 days with 417 patients (21.6%), the group with a LOS of 15–21 days with 91 patients (4.71%), and the group with a LOS of 22–28 with 20 patients (1.04%). Additionally, three patients (0.15%) were treated with a LOS of more than 28 days (Table 3).\n\n\nDiscussion\n\nCOVID-19 has been reported to have caused the deaths of more than one million people, and the nature of viral infection remains a concern of many medical doctors worldwide. As for the asymptomatic and mild symptom cases, isolation and supportive therapy is the recommended approach11. The clinical outcome was mainly affected by patient comorbidities, including old age, chronic metabolic diseases, obesity and long term viral exposure12. Our data showed various medical comorbidities, with the most common being hypertension and diabetes mellitus. In addition, occupation-based analysis showed most patients were private employees, followed by military and police and civil servants. These occupations were occupations with high risk for contact with other people and high risk for COVID-19 infection3.\n\nIn this study, there were 1238 patients without complaint (58.3%), 325 patients complained of coughing (15.3%), followed by 132 flu patients (6.2%), 110 anosmia patients (5.1%), and 93 fever patients (4.3%). Complaints of nausea, headache, tightness, abdominal pain, and diarrhea were less common. Gastrointestinal complaints were not found in COVID-19 patients in this study. Based on previous research by Ge et al. in 2019, we conducted retrospective research on confirmed patients for 10 months and obtained clinical manifestations of patients infected with SARS-CoV-2, ranging from mild non-specific symptoms to severe pneumonia with damage to organ function13 Common symptoms are fever (77.4–98.6%), cough (59.4–81.8%), fatigue (38.1–69.6%), dyspepsia (3.2–55.0%), myalgia (11.1–34.8%), sputum production (28.2–56.5%), and headaches (6.5–33.9%)13. Sore throat, rinorhea, chest pain, hemoptysis, conjunctiva congestion, diarrhea, nausea, and vomiting were less frequent14. One study showed that 39.6% of the 140 confirmed COVID-19 patients had gastrointestinal symptoms, and 10.1% of patients experienced gastrointestinal discomfort at the onset13. SARS-CoV-2, SARS-CoV, and MERS-CoV (Middle East respiratory syndrome coronavirus) infections have many similar clinical symptoms, including fever, cough, myalgia, and dyspnea15. However, patients with SARS and MERS had more gastrointestinal symptoms (about a third) than COVID-19 patients16.\n\nThe latest guidelines for the treatment of COVID-19 patients indicate that suspected and confirmed cases should be treated in isolated hospitals with effective isolation and protection conditions17. As for asymptomatic and mild COVID-19 cases, the WHO recommends that COVID-19 patients are given symptomatic treatments such as antipyretics for fever and pain, adequate nutrition and appropriate rehydration7. In this study, it was found that all patients treated at Indrapura field hospital did not receive antiviral therapy. The procedures were provided in the form of isolation, observation, and supportive therapy, symptomatic therapy, multivitamins, nutrition, therapies for comorbidities and randomized control trials such as amplodipine for hypertension, then therapy to reduce symptoms such as N-acetyl cystein (NAC), decongestants, and paracetamol. Indeed, there were several anti-viral drugs available for treating COVID-19 patients. Of the three clinical cohort studies, oseltamivir was used for antiviral therapy in 35.8% of patients, 89.9% of patients, and 92.7% of patients18. Another study involved 99 COVID-19 patients, of which 76% received antiviral treatment, including oseltamivir, ganciclovir, and lopinavir and ritonavir tablets, with the duration of antiviral treatment being 3–14 days. Although oseltamivir was widely used in early cohort studies, its effectiveness in treating COVID-19 has not been so clear13. To date, there is no evidence to recommend any specific anti-COVID-19 treatment. Large-scale RCT (randomized controlled trial) COVID-19 drugs are still ongoing. The current use of chloroquine, hydroxychloroquine, oseltamivir, lopinavir/ritonavir, favipiravir, and remdesivir in COVID-19 management is currently based on small-scale clinical studies, which are not enough to draw strong conclusions about its efficacy and safety. Based on clinical pharmacological reviews, the decision to use this drug during the COVID-19 pandemic should consider its potential benefits and risks for patients, as the drug is likely to be effective, available and affordable, with the lowest risk to patients and the public19. Therefore, the administration of antivirals is not recommended for infections with no symptoms. To date, isolation and close observation are still considered as better options for asymptomatic patients20.\n\nWith this procedure, in this study, the obtained clinical outcome is 1399 patients (72.48%) with a LOS of less than 7 days, followed by 417 patients (21.6%) with a LOS of 8–14 days, 91 patients (4.71%) with a LOS of 15–21 days, 20 patients (1.04%) with a LOS of 22–28 days, and three patients (0.15%) were treated with a LOS of more than 28 days. In addition, eight patients were referred for clinical worsening indications, two patients moved hospitals, and one patient was in self-isolation. After leaving the hospital, there were 181 patients (8.5%) which gave feedback related to post-treatment re-swab examination. Of these 181 patients, there were 52 patients (28.7%) who were re-examined after exiting the Indrapura field hospital, while 129 patients (71.3%) did not do the re-swab. A total of 19 patients (37.3%) did re-examination after more than 15 days of returning home, followed by eight patients (15.3%) on the 14th day, and the rest did the examination on the sixth day. Of the 52 patients who did the re-swab, we found 43 patients (82.8%) with negative results, and nine patients (17.2%) with positive results.\n\nThere were several limitations to this study. Firstly, the included subjects in this study were asymptomatic and mild symptom patients without any comparison between the treated and untreated groups, hence we could not generate a good conclusion. Secondly, this study only covers one location with mostly Javanese patients. Since Indonesia does not only consist of Javanese people, a multi-center study involving more patients will give a more comprehensive understanding of the management of COVID-19 patients in Indonesia.\n\n\nConclusion\n\nThe conclusion of this study is that SIRNO method provides excellent output in the management of COVID-19 at Indrapura field hospital. Economic pharmacological research can perform a follow-up study in order to objectively measure the effectiveness and efficiency of SIRNO treatment methods in asymptomatic and mild symptomatic infections of COVID-19.",
"appendix": "Data availability\n\nFigshare: Demographic Information Indrapura Field Hospital Surabaya, Indonesia 2122.xlsx. https://doi.org/10.6084/m9.figshare.14412464.v221\n\nThe project contains the following underlying data:\n\nDemographic Information Indrapura Field Hospital Surabaya, Indonesia 2122.xlsx (This is part of the article Therapy for Asymptomatic and Mild Cases of COVID-19 Patients in Indonesia)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe full data are not publicly available due to restrictions for ethical reasons, as the information could compromise the privacy of research participants. The datasets used and/or analysed during the current study are available from the corresponding author (Erwin Astha Triyono, erwintriyono@yahoo.com) on reasonable request.\n\n\nReferences\n\nJin A, Yan B, Hua W, et al.: Clinical characteristics of patients diagnosed with COVID-19 in Beijing. Biosaf Health. 2020; 2(2): 104–111. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGorbalenya A, Baker S, Baric R, et al.: Severe acute respiratory syndrome-related coronavirus : The species and its viruses - a statement of the Coronavirus Study Group. Nat Microbiol. 2020.\n\nPerhimpunan Dokter Spesialis Penyakit Dalam Indonesia (PAPDI), Perhimpunan Dokter Spesialis Kardiovaskular Indonesia (PERKI), (PDPI) PDPI, Perhimpunan Dokter Anestisiologi dan Terapi Intensif Indonesia (PERDATIN), Ikatan Dokter Anak Indonesia (IDAI): Pedoman Tatalaksana Covid-19. 2nd ed. 2020. Reference Source\n\nWu JT, Leung K, Leung GM: Nowcasting and forecasting the potential domestic and international spread of the 2019-nCoV outbreak originating in Wuhan, China: a modelling study. Lancet. 2020; 395(10225): 689–97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJayaweera M, Perera H, Gunawardana B, et al.: Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy. Environ Res. 2020; 188: 109819. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuang C, Wang Y, Li X, et al.: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; 395(10223): 497–506. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGao Z, Xu Y, Sun C, et al.: A systematic review of asymptomatic infections with COVID-19. J Microbiol Immunol Infect. 2021; 54(1): 12–16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrugliera L, Spina A, Castellazzi P, et al.: Nutritional management of COVID-19 patients in a rehabilitation unit. Eur J Clin Nutr. 2020; 74(6): 860–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu K, Chen Y, Wu D, et al.: Effects of progressive muscle relaxation on anxiety and sleep quality in patients with COVID-19. Complement Ther Clin Pract. 2020; 39: 101132. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoh J, Shah SU, Chua PEY, et al.: Epidemiological and Clinical Characteristics of Cases During the Early Phase of COVID-19 Pandemic: A Systematic Review and Meta-Analysis. Front Med (Lausanne). 2020; 7: 295. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLotfi M, Hamblin MR, Rezaei N: Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company’s public news and information. Clin Chim Acta. 2020; 508: 254–66.\n\nWORLD HEALTH ORGANIZATION (WHO): Support for Rehabilitation after COVID-19-Related Illness. 2020; 22. Reference Source\n\nGe H, Wang X, Yuan X, et al.: The epidemiology and clinical information about COVID-19. Eur J Clin Microbiol Infect Dis. 2020; 39(6): 1011–1019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang P, Ding Y, Xu Z, et al.: Epidemiological and clinical features of COVID-19 patients with and without pneumonia in Beijing, China. medRxiv. 2020; 2020.02.28.20028068. Publisher Full Text\n\nWang D, Hu B, Hu C, et al.: Clinical Characteristics of 138 Hospitalized Patients with 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA - J Am Med Assoc. 2020; 323(11): 1061–1069. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Wit E, van Doremalen N, Falzarano D, et al.: SARS and MERS: Recent insights into emerging coronaviruses. Nat Rev Microbiol. Nature Publishing Group; 2016; 14(8): 523–34. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZumla A, Hui DS, Perlman S: Middle East respiratory syndrome. Lancet. Lancet Publishing Group; 2015; 386(9997): 995–1007. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOzamiz-Etxebarria N, María MDS, Munitis AE, et al.: Reduction of COVID-19 Anxiety Levels Through Relaxation Techniques: A Study Carried Out in Northern Spain on a Sample of Young University Students. Front Psychol. 2020; 11: 2038. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen N, Zhou M, Dong X, et al.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020; 395(10223): 507–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInstiaty, Darmayani IGAAPS, Marzuki JE, et al.: Antiviral treatment of COVID-19: a clinical pharmacology narrative review. Med J Indones. 2020; 29(3). Publisher Full Text\n\nJoni W: Demographic Information Indrapura Field Hospital Surabaya, Indonesia 2122.xlsx. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14412464.v2"
}
|
[
{
"id": "95974",
"date": "04 Oct 2021",
"name": "Zhongheng Zhang",
"expertise": [
"Reviewer Expertise Critical care",
"sepsis",
"ARDS"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is descriptive and there is no comparative analysis, thus the results cannot draw conclusions that are indicative of effectiveness. These mild patients can recover even without hospital admission. The most important treatment for those in isolation is to prevent the spread of the disease.\n\nCan you also report the duration of RT-PCR positive for those patients? I am interested in whether the treatment can shorten the duration of virus clearance.\n\nSince all patients are managed with the SIRNO method, the effectiveness cannot be explored. Are there any components of the bundle that is different between patients? Some special interventions can benefit subgroups of patients.\n\nThe SIRNO method is too general that it cannot be explored in an academic paper.\n\n\"If the body's non-specific defenses are unable to prevent the virus, then the virus will enter the cell, damage the cell and replicate itself.\": This paragraph seems irrelevant to the current study.\n\nIt is strange, why not treat these patients by isolating them at home, especially for those with no symptoms?\n\nStatistical inference can be performed to make some causal links. For example, whether differences in SIRNO components can have different impacts on the length of hospital stay. Hong et al., 20191 explore the risk factors for prolonged length of stay for COVID-19. Length of hospital stay is an important outcome for these patients because of limited medical resources during the pandemic outbreak. The SIRNO method included many component interventions, since there is evidence on the use of oxygen therapy for COVID-192 it should be explored individually for its effectiveness for COVID-19.\n\nIs the work 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? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "94781",
"date": "22 Dec 2021",
"name": "Kurnia Fitri Jamil",
"expertise": [
"Reviewer Expertise Internist",
"Tropical Diseases and Infectious Consultant",
"Professor in Internal 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 suggestions that we can give to the manuscript are:\nThe grammatical errors in the text were quite large in number. Authors need to send the manuscript for proofreading and correction.\n\nAs highlighted by the authors, the time of the study was short.\n\nIn my opinion, some of the information provided in the Introduction section is more suitable to be included in the Discussion instead. A lengthy introduction compared to the Discussion might give an impression that available studies in the literature on this matter is more than adequate in contributing the information without the need of the current study.\n\nIt is better if the authors can provide more updates or additional facts that can be obtained from this study compared to what has already been published in the literature.\n\nI suggest comparing the SIRNO method with other therapeutic parameters, but which have similar objectivity, not only in Asia, which can strengthen the results of the study.\n\nReferences: Correct or full citation for reference numbers 2, 21.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7900",
"date": "28 Feb 2022",
"name": "Joni Wahyuhadi",
"role": "Author Response",
"response": "Thank you very much for your feedback, attached below are my responses The grammatical errors in the text were quite large in number. Authors need to send the manuscript for proofreading and correction.-> we will revise the grammatical error, thanks for the feedback As highlighted by the authors, the time of the study was short.-> yes exactly, the study was conducted in a short time In my opinion, some of the information provided in the Introduction section is more suitable to be included in the Discussion instead. A lengthy introduction compared to the Discussion might give an impression that available studies in the literature on this matter is more than adequate in contributing the information without the need of the current study.-> we will try to reduce the lengthy discussion in the introduction It is better if the authors can provide more updates or additional facts that can be obtained from this study compared to what has already been published in the literature.-> We will add this part into the discussion I suggest comparing the SIRNO method with other therapeutic parameters, but which have similar objectivity, not only in Asia, which can strengthen the results of the study.-> We will also add this part in the discussion References: Correct or full citation for reference numbers 2, 21. Thanks, we will revise it soon Best regards and many thanks for your review"
}
]
}
] | 1
|
https://f1000research.com/articles/10-898
|
https://f1000research.com/articles/9-321/v1
|
04 May 20
|
{
"type": "Research Article",
"title": "Using pens as an incentive for questionnaire return in an orthopaedic trial: an embedded randomised controlled retention trial",
"authors": [
"Alex S. Mitchell",
"Liz Cook",
"Alexandra Dean",
"Caroline Fairhurst",
"Matthew Northgraves",
"David J. Torgerson",
"Mike Reed",
"Liz Cook",
"Alexandra Dean",
"Caroline Fairhurst",
"Matthew Northgraves",
"David J. Torgerson",
"Mike Reed"
],
"abstract": "Background: We did a ‘study within a trial’ (SWAT), evaluating the effectiveness of the inclusion of a pen with a postal questionnaire, compared to no pen being included, on the retention rate in a large orthopaedic trial. Methods: The SWAT was embedded in the KReBS trial. The primary outcome was the proportion of 12-month questionnaires returned. Secondary outcomes were the proportion of questionnaires completed and time to questionnaire return. Binary data were analysed using logistic regression and time to return using Cox proportional hazards regression. Odds ratios (OR) and hazard ratios (HR) are presented, with associated 95% confidence intervals and p-values. Results: In total, 2306 participants were randomised into the SWAT. In the pen group, 1020/1146 (89.0%) of participants returned a questionnaire, compared to 982/1147 (85.6%) in the no pen group. The absolute difference in questionnaire return rate was 3.4% (95% CI: 0.7% to 6.1%; p=0.01). There were statistically significant differences in questionnaire return rate (OR 1.34; 95% CI: 1.04 to 1.72; p=0.02), questionnaire completion rate (OR 1.39; 95% CI: 1.10 to 1.76; p<0.01) and time to questionnaire return (HR 1.16; 95% CI: 1.06 to 1.27; p<0.01) favouring the pen group. Conclusion: This SWAT adds to the growing evidence base for whether pens are effective as an incentive for retention, and indicates their potential effectiveness. Registration: KReBS trial registered on 20 February 2019, ID ISRCTN87127065; SWAT registered on 1 April 2019, ID SWAT92.",
"keywords": [
"SWAT",
"Study Within A Trial",
"attrition",
"follow-up"
],
"content": "Introduction\n\nRecruitment and retention of participants have been identified as serious issues for randomised controlled trials (RCTs)1,2.\n\nIncentives, both monetary and non-monetary, are used by UK clinical trials units as part of recruitment and retention strategies3. In particular, the use of pens has recently been evaluated as a non-monetary incentive for recruitment4, while in 2016, Bell et al. assessed whether pens were effective in improving retention5. The study by Bell and colleagues indicated that the inclusion of a pen with postal follow-up questionnaires may increase return rates; however, the authors stated that the results are uncertain and that further research is needed.\n\nIn response to this uncertainty, we did a ‘study within a trial’ (SWAT) evaluating the effectiveness of the inclusion of a pen with a postal questionnaire, compared to no pen being included, on the retention rate in a large orthopaedic trial.\n\n\nMethods\n\nThis paper details the methods and results of a SWAT embedded within the prospectively registered KReBS RCT (ISRCTN87127065). KReBS evaluated the effectiveness of a two-layer compression bandage compared with a standard wool and crepe bandage applied post-operatively on patient-reported outcomes in total knee replacement patients6.\n\nThe SWAT was conducted in 26 NHS hospital trust sites and was implemented after the start of KReBS follow-up. All KReBS participants were eligible for this SWAT provided they were not deceased or withdrawn from follow-up before being due to be sent their 12-month follow-up postal questionnaire.\n\nParticipants in the SWAT intervention group received a pen (branded with the York Trials Unit and University of York logos) with their 12-month questionnaire. All SWAT participants received pre-planned retention strategies within KReBS.\n\nThe primary outcome was the proportion of participants who returned a 12-month questionnaire. Secondary outcomes were proportion of participants who completed the questionnaire and time to questionnaire return. A questionnaire was considered complete if the participant had answered 11 or more questions of the 12-item host trial primary outcome, the Oxford Knee Score7.\n\nSince this was an embedded trial, the sample size was determined by the number of participants in the main KReBS trial6, which aimed to recruit 2600 participants.\n\nParticipants were randomised into the SWAT in two batches, using a 1:1 allocation ratio, in a single large block the size of the batch. The allocation schedule for each batch was generated by a statistician at York Trials Unit using Stata v158.\n\nParticipants were not informed of their explicit participation in the SWAT, but due to the nature of the intervention could not be blinded to receipt (or not) of a pen with their questionnaire. Similarly, it was not possible to blind research staff to SWAT allocation.\n\nThe SWAT was incorporated into the host trial protocol and approved as part of Substantial Amendment 2 by the Research Ethics Committee North East – Newcastle and North Tyneside on 13/04/2018. As the SWAT was deemed to be low risk, and to avoid disappointment for participants who did not receive the additional incentive, informed consent was not obtained for participation in this SWAT.\n\nAnalyses were carried out using Stata v16.09. A diagram detailing the flow of participants through the SWAT is provided, and baseline characteristics are presented by SWAT allocation. Outcomes are summarised descriptively. Statistical tests were two-sided, used a 5% significance level, and were done on an intention to treat basis. All analyses (except the calculation of the absolute difference in return rate) used mixed effects, adjusting for SWAT allocation and host trial allocation as fixed effects and trial site as a random effect. The absolute difference in return rates was estimated using the two-sample test of proportions. Relevant parameter estimates are presented with associated 95% confidence intervals (CI) and p-values.\n\nThe proportion of participants who returned a 12-month questionnaire was analysed using logistic regression. Questionnaire completion was analysed in the same manner.\n\nTime to questionnaire return was analysed using a Cox proportional hazards shared frailty model. Participants who did not return a questionnaire were censored at 90 days.\n\n\nResults\n\nIn total, 2335 participants were recruited into the KReBS trial and 2306 were randomised into the SWAT (Figure 1). The average age was 69.0 years and 55.2% were female (Table 1). A further 15 participants died or withdrew following randomisation and as a result, 1146 participants in the pen group, and 1147 in the no pen group, were sent a 12-month questionnaire and were included in the analysis.\n\nIn the pen group, 1020 (89.0%) of participants returned a questionnaire, compared to 982 (85.6%) in the no pen group (Table 2). The absolute difference in return rate was 3.4% (95% CI: 0.7% to 6.1%; p=0.01). There was a statistically significant difference between the groups in the likelihood of returning a questionnaire (OR 1.35; 95% CI: 1.05 to 1.73; p=0.02), and also in the likelihood of returning a complete questionnaire (OR 1.39; 95% CI: 1.10 to 1.76; p<0.01). In addition, there was evidence of a reduction in time to return in favour of the pen group (HR 1.16; 95% CI: 1.06 to 1.27; p<0.01). See Underlying data for full, individual-level data10.\n\n\nDiscussion\n\nThere is strong evidence that the use of a pen as a non-monetary incentive in the KReBS trial increased the proportion of questionnaires returned and completed, and also decreased the time to return. The decrease in time to return provides support to the findings of Bell et al.5. However, completion rate was calculated as a proportion of all SWAT participants rather than all SWAT participants who returned a questionnaire, and as a result questionnaire completion was highly correlated with questionnaire return. On the other hand, the large sample size of this SWAT means the results can be generalised to other orthopaedic trials.\n\n\nConclusion\n\nThis SWAT adds to the growing evidence base for whether pens are effective as an incentive for retention and indicates their potential effectiveness.\n\n\nData availability\n\nOpen Science Framework: Underlying data and CONSORT checklist for Using pens as an incentive for questionnaire return in an orthopaedic trial: an embedded randomised controlled retention trial. https://doi.org/10.17605/OSF.IO/BEPN310.\n\nThis project contains the underlying data in CSV, SAS and V8XPT formats, alongside a data key.\n\nOpen Science Framework: CONSORT checklist for ‘Using pens as an incentive for questionnaire return in an orthopaedic trial: an embedded randomised controlled retention trial’. https://doi.org/10.17605/OSF.IO/BEPN310.\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\nHewitt CE, Kumaravel B, Dumville JC, et al.: Assessing the impact of attrition in randomized controlled trials. J Clin Epidemiol. 2010; 63(11): 1264–1270. PubMed Abstract | Publisher Full Text\n\nTudur Smith C, Hickey H, Clarke M, et al.: The trials methodological research agenda: results from a priority setting exercise. Trials. 2014; 15: 32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBower P, Brueton V, Gamble C, et al.: Interventions to improve recruitment and retention in clinical trials: a survey and workshop to assess current practice and future priorities. Trials. 2014; 15: 399. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWhiteside K, Flett L, Mitchell A, et al.: Using pens as an incentive for trial recruitment of older adults: An embedded randomised controlled trial [version 1; peer review: 2 approved]. F1000Res. 2019; 8: 315. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBell K, Clark L, Fairhurst C, et al.: Enclosing a pen reduced time to response to questionnaire mailings. J Clin Epidemiol. 2016; 74: 144–150. PubMed Abstract | Publisher Full Text\n\nCook L, Northgraves MJ, Fairhurst C, et al.: Knee Replacement Bandaging Study (KReBS) evaluating the effect of a two-layer compression bandage system on knee function following total knee arthroplasty: study protocol for a randomised controlled trial. Trials. 2019; 20(1): 261. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDawson J, Fitzpatrick R, Carr A, et al.: Questionnaire on the perceptions of patients about total hip replacement. J Bone Joint Surg Br. 1996; 78(2): 185–190. PubMed Abstract | Publisher Full Text\n\nStataCorp: Stata Statistical Software: Release 15. College Station, TX: StataCorp LLC, 2015.\n\nStataCorp: Stata Statistical Software: Release 16. College Station, TX: StataCorp LLC, 2019. Reference Source\n\nMitchell A, Cook L, Dean A, et al.: Underlying data and CONSORT checklist for Using pens as an incentive for questionnaire return in an orthopaedic trial: an embedded randomised controlled retention trial. 2020. http://www.doi.org/10.17605/OSF.IO/BEPN3"
}
|
[
{
"id": "63133",
"date": "07 May 2020",
"name": "Frances Shiely",
"expertise": [
"Reviewer Expertise clinical trial methodology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 This was a SWAT within the KReBS trial. The purpose of the SWAT was to evaluate the effectiveness of the inclusion of a pen with a postal questionnaire, compared to no pen being included, on the retention rate in a large orthopaedic trial. The authors conclude that pens are potentially effective as an incentive for retention.\n\nAbstract The background section needs to be amended as your SWAT did not evaluate retention in clinical trials. Likewise, the conclusion is not supported. Please see the comments on the conclusion section below.\nIntroduction Section In the introduction section, you mention the Bell et al. study and state that the authors say the results are uncertain, and in response to this you conducted your study. However, say what the reason for the uncertainty is. It would be helpful to give support to the necessity for your research study to include the shortcomings of Bell et al. Please amend.\nMethods Section Intervention All SWAT participants received pre-planned retention strategies within KReBS. This sentence is left hanging there with no further explanation. What were these retention strategies? When you say all SWAT participants received these retention strategies, do you mean the SWAT comparator group also? IF so, why is this sentence under the “intervention” heading? It implies that you are speaking about the intervention group only. Perhaps you’d be better saying both SWAT intervention and SWAT comparator groups received pre-planned retention strategies if that is what you meant. Please qualify. Outcomes I question the selection of the secondary outcome, the proportion of participants who completed the questionnaire. In reality, if someone begins, whether it’s the York CTU pen or their own, what does the supply of the York pen have to do with the completion of the questionnaire? You then go on in your results to state that questionnaire completion was highly correlated with questionnaire return. How useful is this measure then? I would like to see the questionnaire completion rate removed as a focus of this SWAT. It additionally detracts from your main findings.\n\nRandomisation What do you mean by two batches, and why were there two batches?\n\nConclusion Your conclusion is not supported by your results. Your conclusion should be that pens are effective as an incentive for returning questionnaires in postal studies, and also effective at increasing the time to return. You did not measure retention, as this was a postal questionnaire and not a follow-up of the patients at the centre. It’s a stretch to extrapolate that filling out a questionnaire and returning it is a measure of retention in a clinical trial. I would be interested to know how many of those that received the pen return to the CTU for the main trial for their next appointment. Please modify your conclusions.\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 source data required\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "5548",
"date": "28 May 2020",
"name": "Alex Mitchell",
"role": "Author Response",
"response": "We would like to thank the reviewer for the helpful comments and the interest shown in our paper. We hope that our responses are satisfactory. Please note that we will update the article in response to the points raised after we have received comments from additional reviewers.The background section needs to be amended as your SWAT did not evaluate retention in clinical trials. Likewise, the conclusion is not supported. Please see the comments on the conclusion section below.Please see the response to your final point.In the introduction section, you mention the Bell et al. study and state that the authors say the results are uncertain, and in response to this you conducted your study. However, say what the reason for the uncertainty is. It would be helpful to give support to the necessity for your research study to include the shortcomings of Bell et al. Please amend.The results from Bell et al. were uncertain in that the primary outcome of questionnaire return was of borderline statistical significance, and the authors indicated that research across a range of participant groups was required.All SWAT participants received pre-planned retention strategies within KReBS. This sentence is left hanging there with no further explanation. What were these retention strategies? When you say all SWAT participants received these retention strategies, do you mean the SWAT comparator group also? IF so, why is this sentence under the “intervention” heading? It implies that you are speaking about the intervention group only. Perhaps you’d be better saying both SWAT intervention and SWAT comparator groups received pre-planned retention strategies if that is what you meant. Please qualify.Thank you for making this point. We can confirm that SWAT participants in both the intervention and comparator groups received pre-planned retention strategies. Participants were sent a reminder letter and a further copy of the questionnaire if they had not returned a completed copy 4 weeks after sending. If there was still no response following the postal reminder, participants were contacted by telephone to obtain the patient reported outcomes. I question the selection of the secondary outcome, the proportion of participants who completed the questionnaire. In reality, if someone begins, whether it’s the York CTU pen or their own, what does the supply of the York pen have to do with the completion of the questionnaire?You then go on in your results to state that questionnaire completion was highly correlated with questionnaire return. How useful is this measure then? I would like to see the questionnaire completion rate removed as a focus of this SWAT. It additionally detracts from your main findings.We accept your point that the theory of how the inclusion of a pen influences completion rates is not immediately obvious. If a participant were to use their own pen, they may have had to spend some time trying to find one. This may lead to the participant becoming frustrated with the questionnaire, and thus decrease the probability of them completing it correctly. We hoped that by including a pen with the questionnaire, we would make the process easier for the participant. We disagree that the completion rate should be removed as an outcome as this was pre-specified in the published KReBS protocol. While we agree with your point on its limitations, we have already outlined these in the discussion section, and believe this is a more scientifically sound approach than removing it from the paper.What do you mean by two batches, and why were there two batches?This SWAT was embedded at the 12 month time point and was only intended to include participants who had not died or expressly withdrawn from data collection up to this point. It was not logistically feasible to randomise participants in real time just before they were sent the questionnaire, and yet by randomising participants into the SWAT too early we risked participants withdrawing from the trial before they were sent the 12 month questionnaire. We balanced minimising the time between randomisation into the SWAT and being sent the questionnaire, and the resources required to randomise participants, by choosing to randomise two large sets (‘batches’) of participants. Shortly before the first participant was due to be sent their 12 month questionnaire we randomised participants into the SWAT (i.e. the study statistician was sent a list of participant ids to allocate to receive a pen or not), then any remaining participants were included in the second batch later on. Your conclusion is not supported by your results. Your conclusion should be that pens are effective as an incentive for returning questionnaires in postal studies, and also effective at increasing the time to return. You did not measure retention, as this was a postal questionnaire and not a follow-up of the patients at the centre. It’s a stretch to extrapolate that filling out a questionnaire and returning it is a measure of retention in a clinical trial. I would be interested to know how many of those that received the pen return to the CTU for the main trial for their next appointment. Please modify your conclusions.Thank you for this comment, however we think we are justified in retaining use of the term ‘retention’ in the context of this trial. There were no clinic or YTU follow up appointments in the KReBS trial; it exclusively used postal follow up questionnaire to obtain outcome data. The primary outcome in KReBS was the participant reported Oxford Knee Score collected at 12 months. Therefore, we used a broader definition of retention i.e. the return of outcome data via any means. We believe this blog post by Shaun Treweek and Katie Gillies shows that this is in line with the definition of retention used in the SWAT community (https://blogs.biomedcentral.com/on-medicine/2017/09/01/trial-retention-its-time-for-cinderella-to-go-to-the-ball/ )."
}
]
}
] | 1
|
https://f1000research.com/articles/9-321
|
https://f1000research.com/articles/10-897/v1
|
07 Sep 21
|
{
"type": "Opinion Article",
"title": "Perspectives on automated composition of workflows in the life sciences",
"authors": [
"Anna-Lena Lamprecht",
"Magnus Palmblad",
"Jon Ison",
"Veit Schwämmle",
"Mohammad Sadnan Al Manir",
"Ilkay Altintas",
"Christopher J. O. Baker",
"Ammar Ben Hadj Amor",
"Salvador Capella-Gutierrez",
"Paulos Charonyktakis",
"Michael R. Crusoe",
"Yolanda Gil",
"Carole Goble",
"Timothy J. Griffin",
"Paul Groth",
"Hans Ienasescu",
"Pratik Jagtap",
"Matúš Kalaš",
"Vedran Kasalica",
"Alireza Khanteymoori",
"Tobias Kuhn",
"Hailiang Mei",
"Hervé Ménager",
"Steffen Möller",
"Robin A. Richardson",
"Vincent Robert",
"Stian Soiland-Reyes",
"Robert Stevens",
"Szoke Szaniszlo",
"Suzan Verberne",
"Aswin Verhoeven",
"Katherine Wolstencroft",
"Mohammad Sadnan Al Manir",
"Ilkay Altintas",
"Christopher J. O. Baker",
"Ammar Ben Hadj Amor",
"Salvador Capella-Gutierrez",
"Paulos Charonyktakis",
"Michael R. Crusoe",
"Yolanda Gil",
"Carole Goble",
"Timothy J. Griffin",
"Paul Groth",
"Hans Ienasescu",
"Pratik Jagtap",
"Matúš Kalaš",
"Vedran Kasalica",
"Alireza Khanteymoori",
"Tobias Kuhn",
"Hailiang Mei",
"Hervé Ménager",
"Steffen Möller",
"Robin A. Richardson",
"Vincent Robert",
"Stian Soiland-Reyes",
"Robert Stevens",
"Szoke Szaniszlo",
"Suzan Verberne",
"Aswin Verhoeven",
"Katherine Wolstencroft"
],
"abstract": "Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.",
"keywords": [
"scientific workflows",
"computational pipelines",
"automated workflow composition",
"semantic domain modelling",
"workflow benchmarking",
"bioinformatics",
"life sciences"
],
"content": "Introduction\n\nComputational pipelines, commonly referred to as scientific workflows*, play a key role in modern life science research.1–3 Analyses must be tailored to highly complex biological data by successive application of different algorithms and routines to maximize biological insight. Hence, scientists regularly use sophisticated workflows, composed from several software tools and data resources, for tailored data analysis processes. The highly dynamic eScience software ecosystem, which continuously sees new tools emerging, new reference data being provided and computational infrastructure improving, provides the basis for new and innovative workflows. Once developed, workflows are rarely considered stable, but are regularly adapted and reimplemented to meet the latest state of the art.\n\nFor more than two decades, dedicated scientific workflow management systems4–9 have been developed to support researchers at the different stages of the workflow development life cycle.10 There is a flourishing ecosystem around these systems, including software-oriented ontologies,11–16 tool registries with rich metadata and functional annotations,12,17–19 containerization technologies,20,21 workflow management and execution frameworks,7,22–25 workflow repositories,26–29 workflow exchange formats,30 and more.31 Importantly, with the use of workflows in large scale data science and machine learning systems32–36 there has been a large increase in the interest in composing and executing workflows at scale.37 These developments bring the long-standing vision of automated workflow composition38 - the use of algorithms to perform the often tedious, time-consuming, limited and error-prone workflow development process - within reach.\n\nTo biologists there is a latent fear to have chosen the wrong computational paths for the analysis of their data, which could cause problems during the peer review, and in the worst case misdirect the data interpretation and invalidate downstream experiments. While human expert knowledge is an indispensable factor for validating and curating computational workflows, their automated assembly can significantly reduce the effort of getting from novel ideas to production and mainstream application, and at the same time help to increase scientific quality, reliability, and robustness. In fact, benefits of (partially) automated workflow development are manifold and include:\n\n• Minimal technicalities in software composition. Manual workflow construction can be a tedious process. It requires the workflow developer to get familiar with the individual tools, sort out the compatibility of their input/output data formats, and connect them correctly to perform the intended process. An automated composer would not only save valuable research time, but also reduce errors.\n\n• Exhaustive exploration of data-analytical possibilities. Given the abundance of bioinformatics tools available today, it is impossible for a human to consider all possible combinations that could be relevant for their problem. Indeed, scientists often resort to the tools and workflows with which they are familiar, at the risk of missing better suited or more effective pipelines for their problem. Assisted or even automated workflow composition would systematically and comprehensively explore the workflows that are possible with the available tools, and could also rank the possible workflows based on specific user requirements, such as runtime, compute requirements, underlying database usage, etc. This would enable new scientific findings by discovering well or better performing workflows that researchers would not have thought of themselves.\n\n• Generating ensembles of workflows. When using workflows to test biological hypotheses, automated workflow composition enables us to generate ensembles of orthogonal workflows combining different tools and services seizing on different aspects of the data (for example, algorithms that concentrate on different subsets of the raw data). This idea has been proposed by Gil et al.39 and is not epistemologically novel. As Hempel summarized over half a century ago, “The confirmation of a hypothesis depends not only on the quantity of the favorable evidence available, but also on its variety: the greater the variety, the stronger the resulting support”.40 As a single, linear, workflow is typically unable to collect all available evidence and parallelization is not always an option, workflow ensembles can provide additional confidence in rejecting null hypotheses.\n\n• Repairing workflows by tool substitution. Within a strictly and semantically well-defined context, alternative, semantically equivalent tools or services may be fully automatically substituted when the default is deprecated or unavailable. In a less well-defined setting, the workflow developer might still be semantically guided towards possible alternatives and receive suggestions for sensible replacement tools. Ideally, the resulting workflows would also be tested automatically, to check if they produce the same or similar output as the old workflow on available benchmarking data. Workflows that can be automatically repaired in this way are inherently more robust and viable.\n\n• Optimizing workflow output. Workflow topology, components as well as parameters can be optimized in an integrated workflow composition and benchmarking framework. This can be used, for example, to maximize output, e.g. identified proteins in a proteomics experiment, or minimize some computational resource, e.g. memory or CPU time. Specific properties of a data set might influence such optimization adapting the methods not only to the data type but also the data itself.\n\n• Ensuring the methodological quality of workflows. Automated composition can ensure that data is correctly used within components (e.g. training and test data are properly used in machine learning). Likewise, it can prevent errors in parameter setting as well as combinations of components.\n\nIn this article we report on the state of the art of automated workflow development in the life sciences, discuss current and future challenges and develop perspectives for the coming years. The report is based on discussions during a Lorentz Center workshop (held at the Lorentz Center in Leiden, Netherlands, from 9-13 March 2020) dedicated to this topic41 (workshop program available in Extended data115), with the authors as participants. In the section Workflow life cycle we outline a “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling (section Semantic domain modelling), automation in workflow development (section Automation in workflow development), and workflow assessment (section Workflow assessment). In the Roadmap section, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. Finally, the Conclusion section wraps up the discussion.\n\n\nWorkflow life cycle\n\nThe development of scientific workflows is an involved, multistep, and often iterative process. The schematic process in Figure 1 captures the “big picture” that emerged from the discussions at the Lorentz Center workshop. It extends earlier descriptions of the scientific workflow life cycle,42–44 and will provide guidance for the discussion of automation approaches in the remainder of this article. The life cycle distinguishes six principal stages:\n\n1. The scientific question to answer, or the hypothesis to test. It guides the subsequent exploration of suitable analysis methods, as well as for the choice of data, methods, tools, platforms, and interpretation of results.\n\n2. The conceptual workflow, as a sketch of the methodical steps that the workflow should perform on data from a specific experiment type, from a domain-specific perspective. It is the result of exploring possible analysis methods for the scientific question/hypothesis and the data at hand. It can be formalized, for example as a Concept Map,45,46 but often it will only take the form of a paper or mental sketch. Nevertheless, it is an important stage in the workflow development process.\n\n3. The abstract workflow, describing sequences of computational tools that implement the conceptual workflow. It is the result of composing individual tools into workflows, taking into account the compatibility of their input/output types and other kinds of static information. An abstract workflow is not yet (fully) configured, however, and thus not readily executable.\n\n4. The concrete workflow, as the fully implemented, fully configured and readily executable stage. It is the result of instantiating an abstract workflow with the relevant data and parameters.\n\n5. The production workflow, deployed and ready for (re) use by other parties. It is the result of benchmarking different variations of a workflow in order to arrive at a tested and robust version for wider use.\n\n6. Finally, the scientific results that emerge from executing the workflow with the research data. They are interpreted by the domain scientists, and ideally shared with others in a manner that promotes reproducibility and transparency. This often leads to new scientific questions or hypotheses, to be addressed by another workflow.\n\nIn practice, these stages are often not so clearly distinguishable. They can be interleaved, skipped, and taken in a different order than the life cycle suggests. A non-exhaustive list of examples includes:\n\n• A workflow developer might not produce an (explicit) conceptual sketch of the workflow before starting to explore and compose tools, but rather do so in one go.\n\n• Trying to compose an abstract workflow might reveal that the research question/hypothesis and/or the conceptual workflow need to be refined.\n\n• Many popular workflow management systems, such as Galaxy,7,57 handle both composition and instantiation simultaneously and combine abstract and concrete workflows in one formalism. Typically, they also allow for workflow execution for both benchmarking and production purposes, thus covering additional stages in the life cycle.\n\n• A benchmarked workflow might be used to generate results, but is never actually deployed for reuse by others.\n\n• Existing workflows from repositories like myExperiment,28,29 Dockstore47 or the WorkflowHub26 can be reused at different stages, preceding stages in the principal life cycle to be either skipped or shortened.\n\n• Popular production workflows, such as those provided by the Bioinformatics Core Facility48 are routinely used by researchers in a close execution -> results -> interpretation -> execution sub-cycle.\n\n• Specific data and study properties pre-determine workflow components by prior knowledge about tool performance.\n\nThe figure also indicates the importance of literature, data, domain ontologies and tool registries and workflow repositories. They provide the basis for exploring, composing, implementing, running, evaluating, sharing, and reusing computational pipelines, and are thus central to the whole workflow life cycle. In fact, they are the enablers of many of the “shortcuts” outlined above.\n\nFinally, the figure distinguishes two principal roles in the workflow life cycle: 1) the workflow user, here represented by a wet-lab biologist, who has research questions and data for which they use computational tools and workflows to obtain results, and 2) the workflow developers, here represented by a technology-oriented bioinformatician, who has the skills to develop and provide computational workflows for their colleague’s data analysis problems. While there are obviously individuals who perform both roles, there is an increasing specialization happening in the field of scientific workflows, with research software engineers skilled in workflow technologies emerging as a professional profile in its own right.49\n\n\nSemantic domain modelling\n\nIn the context of scientific workflow development, the semantic domain model is (formalized) knowledge about the technical entities within a domain. It includes domain ontologies as controlled vocabularies for annotating entities with metadata, and registries and repositories of annotated data, tools and workflows. For the purpose of automating (parts of) the workflow construction process, tools and their functional annotations are of particular importance. Possible connections of individual tools are in the first place determined based on the annotated input/output data types and formats.\n\nThe eScience community, and especially the life science circles, were early adopters of semantic technologies. For example, driven by the myGrid project in the UK, the myGrid Ontology16 was an early initiative of a software-oriented ontology designed to facilitate bioinformatics service discovery, and the BioCatalogue18,19 was one of the first domain-specific web service registries, providing a curated collection of semantically annotated bioinformatics services. Around the same time in the same context, myExperiment28,29 emerged as one of the first repositories for scientific workflows, allowing users to upload, describe, annotate and share their computational pipelines. As a successor to myExperiment, EOSC-Life has now established the FAIR Computational Workflow registry WorkflowHub.50 Whereas myExperiment treated workflows as data objects, WorkflowHub recognises them as software objects with dependencies and other properties.\n\nOver the last decade, these early ideas, approaches and platforms have evolved further, and are now increasingly being adopted by the life science and wider eScience communities.\n\nThree important, contemporary and active semantic domain modelling platforms are EDAM/bio.tools, OntoSoft and SADI. They support the production and dissemination of semantic software descriptions that help to make these tools more FAIR (Findable, Accessible, Interoperable and Reusable).51–53\n\nEDAM and bio.tools\n\nThe EDAM ontology of bioinformatics terms14 and the bio.tools registry54,17 have become the primary resources for semantic software annotation in the European life sciences community. EDAM provides a controlled vocabulary for the annotation of computational tools with relevant bioinformatics topics, performed operations, as well as type and format of the input and output data. The bio.tools registry uses EDAM for the fine-grained semantic description of tools and their functionality according to a pragmatic model defined in the biotoolsSchema.55 The annotations facilitate the discovery of individual tools, and the assessment of their (inter) operability such as their combination into workflows. The development of both EDAM and bio.tools is driven and supported by the broader community.\n\nbio.tools is part of the ELIXIR Tools Platform and becomes increasingly connected with its other services such as BioContainers,56 Galaxy,7,57 BioConda,58 WorkflowHub26 and OpenEBench,59 as well as external services like Debian Med.60 This will form a centralised, transparent ecosystem of information about tools and services in the life sciences. Here, EDAM serves as a common language to connect and enrich extensive software dossiers.\n\nOntoSoft\n\nThe OntoSoft ontology20,21 has been designed as an ontology for scientific software metadata. OntoSoft allows for the description of software. This includes understanding how to access and update that software, how to execute it, how to use it, and information on who supports the software. The OntoSoft ontology is the basis for the design of the user interface in the OntoSoft portal, the organization of the underlying knowledge base, and the integration with other software repositories. Although OntoSoft is currently focused on earth sciences applications, providing geoscientists in the NSF EarthCube project61 with an intelligent system to share and reuse code, its principles are equally applicable in other domains.\n\nOntoSoft-VFF (Ontology for Software Version, Function and Functionality)62 extends OntoSoft. It stores semantic software metadata needed to manage workflow evolution and updates, suitable to help scientists to find and select the right tools to implement given workflow steps, explore alternative tools to use in their workflows, and keep track of tool and workflow changes. Similarly, OntoSoft is the basis for OKG-Soft,63 an open knowledge graph that describes scientific software in a machine-readable manner and supports the FAIR principles for software.\n\nSADI registries\n\nSADI (Semantic Automated Discovery and Integration)64 is a framework for creating Semantic Web Services and a design pattern for the formal description of the service interfaces. Services are described by an ontology that defines I/O class names, predicates and service names with a unique URL. The ontology specifies an explicit relationship (semantic predicate) describing the functionality of a service between the I/O, for example “getDrugNamebyDocument”.65 The service descriptions are collected in a SADI registry. From there, SADI Services can be readily discovered and composed into workflows, as all services consume and generate RDF (syntactic interoperability) and thus the output of one SADI service can be directly consumed by any other SADI service. Through the provisioning of Semantic Web services on top of relational databases for semantic querying, SADI facilitates both data-as-a-service and algorithms-as-a-service. Recently Valet SADI66 was developed as a service generator for assisting the technically involved authoring of SADI Web Services. Designed as middleware, SADI is not accessed directly, but through specialized query engines (see section SHARE & HYDRA).\n\nSemantic domain modelling is hard.67 Especially in highly collaborative community efforts like EDAM/bio.tools, OntoSoft and SADI, it is important to realize that the controlled vocabulary defined by the domain ontology constitutes a kind of social contract that all tool annotators must understand and respect. Using the same interpretations of the terms defined by the ontology is crucial for the meaningfulness and consistency of the domain model.\n\nTo be useful for practical application, ontologies have to be designed for a clear purpose. In the context of workflow composition, it needs to be defined, for example, if the ontology is supposed to help the (manual) search for and/or the automated composition of computational tools, and if it targets the creation of informatically, bioinformatically and/or biologically valid workflows. Furthermore, the ontology needs to use an adequate level of detail, neither too simple nor too complex, to avoid overgeneralization as well as overfitting. These challenges are both technological and social, with the latter typically being harder to address. This was also reflected by the discussion of semantic domain modelling during the Lorentz workshop, with the use of EDAM and bio.tools as guiding examples.\n\nScope\n\nIn the case of bio.tools, the EDAM ontology and the biotoolsSchema provide a technical basis and general direction for the annotation of bioinformatics tools in the registry. However, they leave room for interpretation, calling for clarification. What kinds of tools are in scope, and what exactly should be included in their annotation?\n\nContent: The bio.tools Curators Guide46 defines the scope of relevant tools as “application software with well-defined data processing functions (inputs, outputs and operations)”. This clearly includes, for example, command-line tools for sequence alignment, or web services for database searches. For other workflow building blocks this is less clear. On the one hand, workflows often require the inclusion of “shims”,68,69 small formatting or conversion tasks between the actual data processing steps. They are often not considered tools in their own right, but are indispensable for interoperability. Automated workflow composers as well as human workflow developers would hence benefit from their availability in the registry, and it would prevent a lot of reinvented wheels. While these are strong arguments for the inclusion of shims in bio.tools, there is also a certain risk of fragmentation and overloading the registry with trivial functionality that needs to be managed. On the other hand, workflows can also be considered tools that can be used in (other) workflows. From the perspective of a tools registry it is desirable to include them as “black boxes” providing certain functionality as a service. The inner workings can be visible in a workflow repository like the WorkflowHub, similar to the source code of other computational tools being available in a repository like GitHub.\n\nSimilarly, clear guidelines are needed for meaningful annotation of tool suites and multifunctional tools. The bio.tools Curators Guide recommends registering tool suites as such (the biotoolsSchema foresees a tool type “Suite”), but to also add separate entries for the individual tools to capture their functionality clearly. An example is the SAMtools suite70 and its members, such as samtools_sort https://bio.tools/samtools_sortand samtools_slice_bam. Multimodal tools with different functions should be annotated with multiple specific functions (as supported by the biotoolsSchema) rather than trying to cover all modes of operations in one generic annotation.\n\nAnnotation: The biotoolsSchema includes various kinds of attributes that can be used for tool annotation. The bio.tools Curators Guide46 provides guidance for tool annotators and describes which information must, should, should not, and must not be included. For automated workflow composition, the annotation of tool function (performed operation, data type and format of inputs and outputs, execution command) is essential. In practice annotators often face ambiguous situations, such as:\n\n• Tool inputs can be distinguished into payload data and configuration parameters. For example, a set of sequences to be aligned is payload data, and a gap penalty value is a parameter for an alignment tool. This distinction is however not always clear. For example, a substitution matrix used by the algorithm as a parameter but provided as an additional input file could be placed in either of the categories. Currently tool annotation in bio.tools mostly focuses on the annotation of payload input (for pragmatic reasons such as conciseness and limitation of complexity), but for full automated workflow construction information about the parameters to be configured would also be required.\n\n• The biotoolsSchema readily distinguishes between the type (kind of content, domain perspective) and the format (representation, technical perspective) of input and output data. For example, an “RNA sequence” is a type, and “FASTA” is one of the possible formats in which it can be represented. This distinction is however not always easy to make. The IUPAC International Chemical Identifier (InChI),71 for example, is classified as a format in EDAM, but it could also be viewed as a type of data. The domain ontology should have clear criteria for the classification of such formats, and ideally make sure that all formats included are connected to at least one type of data (and vice versa) to enable meaningful tool annotation.\n\n• Composite data formats contain different parts, where a specific tool might only use one or some of them. For example, RetroPath 2.072 works with InChI identifiers that are available from one column of a CSV file. Currently it is not clear how these would be modeled in the ontology and annotated in the registry in the best way. Possible solutions might include a combination of reusing approaches such as the structured metadata for CSV and other tabular data73 and providing corresponding, ideally automatically generated, shim libraries.\n\nClearly, the domain ontology needs to provide a vocabulary that supports the required annotations and the desired level of granularity. As the needs change, also the ontology has to evolve. EDAM is indeed continually evolving based on input from the bioinformatics and, in particular, the bio.tools community. It is for example well developed for the proteomics domain, due to recent work on (automated) workflow composition and benchmarking.\n\nQuality\n\nThe quality of automatically composed workflows critically depends on the quality of the domain ontology and tool annotations (“garbage in, garbage out”).74,75 Hence it is important that all tool annotations consistently adhere to the curation guidelines that capture the defined scope and annotation conventions. Consequently, if annotations are too vague or imprecise, automatic composition will likely generate incorrect or nonsensical workflows. If they are overly specific or narrow, possible workflows might be overlooked due to overfitting. This sounds simple, but is difficult in practice. It requires not only a thorough understanding of the curation guidelines and annotation conventions, but also expert-level knowledge in the application domain of the tools, and ideally practical experience of using them. Variations in the stringency of rules for the annotation being followed have direct effects on the interpretability of queries to the system.\n\nNote that the semantics of the annotation is typically limited to a positive tagging, that is, no negative statements as in “not performing indexing” can be expressed, and there are no set operations like intersections or exclusions. When also allowing negative statements, or exceptions to a universal quantifier, this easily leads to semantically incorrect workflows merely by omission. Thus, negative statements or set operations shift responsibilities for correctness to the maintainers of higher-level resources like ontologies. This poses a challenge to synchronize the development of catalogs and ontologies as their granularity in biological expressiveness needs to match the decision making of users for the applicability of scientific tools for a given problem. With a larger amount of scrutiny on the ontologies than on individual catalog entries, this may support stringency and help overall quality.\n\nThe quality problem is aggravated when there is a need to annotate large numbers of tools (at the time of writing, for example, bio.tools comprises almost 19,000 entries). Ideas to scale up annotation rates include text-mining of annotation information from the tool’s documentation pages, deriving annotations from other repositories (such as the Galaxy Toolshed76), and the automation of semantic description of tools and services via propagation from tried-and-tested workflows.77 While enabling the inclusion of more tools in a shorter time, such automated approaches do not guarantee a consistent high-quality annotation of tools. Therefore, automatically annotated tools should be checked for a minimal level of curation quality before being made available for automated workflow composition.\n\nA community registry like bio.tools needs to find a balance between being open to contributions and curating entries for quality control. At the end of the day the (manual) curation work invested needs to reflect the actual usage, i.e. frequently used tools justify greater curation efforts. Curators need adequate training to become able to deliver high-quality annotations. While desirable, it is unrealistic to assume that this is feasible to provide to everybody who might (potentially) contribute. A pragmatic way out might be to mark curated entries to distinguish them from unchecked ones, for instance with a tag or badge denoting that the functional tool annotation was checked and the tool is suitable to be used by automated workflow composers. This could be combined with procedures to develop consensus annotations for widely used tools by a group of experts, which can then serve as landmark or even “gold standard” examples for tool annotation. Furthermore, technical monitoring of tools, continuously performed by e.g. OpenEBench,59 could provide up-to-date information about tool status and availability. In any case these mechanisms should be defined in a governance model, together with the processes for maintaining and updating the entries in the registry.\n\nFinally, it is not only tools that develop, but also their metadata in the registries. Inconsistencies can easily lead to errors or unsatisfactory performance of automatically composed workflows. Manual verification is likely to fall short, especially since registries take a passive stance towards tools’ updates. With good reference workflows and benchmarking data available, however, workflows could be tested automatically as a joint quality control for the tools and their semantic descriptions in the registry. One may anticipate that such an automated quality assurance even prepares for workflow optimization.\n\nIncentives\n\nThe success of registries like bio.tools depends on community contributions, which is predicated upon the motivation of tool users and developers. There are several incentives for potential contributors. For example, for tool developers, rich annotation of their software will increase its findability and comprehension, and thus its potential to be (re-)used individually or within a workflow. This in turn can improve the impact and eventual citations of the software. Improved tooling (intuitive user interface, annotation help, very-well defined metadata schemas) that integrates well with the tool development infrastructure can help to lower the threshold to tool registration and annotation. Registering tools in a community is also in line with recent practice guides like the “Four simple recommendations to encourage best practices in research software”78 and the “Five Recommendations for FAIR Research Software”,53 which are increasingly attracting the attention of organizations and project-funding agencies. Similarly, publishers might require the registration of tools in a community registry as a condition to accept papers that are describing or using the software, providing additional enforcement. A related problem is the incentives for updating registry entries when the respected tool has changed (updates, new versions, new features).\n\nIdeally, the problem would be solved through “knowledge acquisition by stealth”: sneaking in metadata curation steps in people’s normal routines, and e.g. scrape them from available documentation or with smart tools that integrally capture the semantics from the start, so that people do not feel like having to do something extra. This is an appealing but complex long-term goal, however, which requires consideration of the entire lifecycle of tool and workflow development.\n\n\nAutomation in workflow development\n\nThe possibilities for automation in the multi-stage workflow development process are manifold and range from assistance in specific phases to full automation. The most likely basic form of assistance, the possibility to search for available components with keywords or filter criteria, is a common feature of visual and interactive workflow management systems. More sophisticated is the assistance through context-dependent suggestions, which can take the form of guided workflow construction. An early example here is the ontology-driven assisted web service composition facilitated by BioMoby,79 which was integrated in the Taverna workflow system to guide workflow construction.80 Further down in the workflow life cycle, automated service configuration can assist the user to set parameters and get the workflow ready for execution. Automated service substitution aims to replace unavailable or otherwise deprecated tools by semantically equivalent but operating ones, to repair a workflow and make it executable again. Related, automated shim suggestion is intended to introduce mere technical steps (such as reformattings or format conversions) between the actual data analysis tools. One of the most intriguing forms of automation in workflow development is the automated anticipation, or exploration, of entire new workflows. Systems like Magallanes81,82 and PROPHETS,83,84 for example, have already demonstrated about a decade ago that AI planning and program synthesis techniques can be applied in pursuit of this goal.\n\nAt the Lorentz workshop, the following four current and active approaches to automation in the workflow design process were presented and discussed in greater detail.\n\nThe tool recommender system in Galaxy\n\nGalaxy7,57 is a popular web-based platform for high-throughput sequencing data and other big data analyses. Researchers can use it to share data and analyze them by running workflows. Workflows can be imported (shared workflows), extracted from history, or built manually. With more than 2,000 tools available in Galaxy, users need guidance during workflow construction. Therefore, a recommendation system has been developed to suggest possible next tools in a workflow under construction.85 The recommender system uses an approach based on deep learning. The idea is to learn possible tool combinations from existing workflows, and use this knowledge to suggest tools for new workflows. The model is trained on tool sequences that are extracted from workflows. A Recurrent Neural Network with gated recurrent units (RNN-GRU)86 is used, with tool usage as weights. The recommender system uses the trained model to predict possible next tools, ranking them by a score that is provided by the model and indicates the prevalence of the respective combination.\n\nWorkflow INstance Generation and Selection (WINGS)\n\nWINGS6,39,87 is a semantic workflow system that assists scientists with the design of computational experiments. A unique feature of WINGS is its high-level semantic workflow representations that are automatically configured and customized into executable workflow instances. Therefore, WINGS employs workflow reasoning algorithms that use constraint-based planning. The constraints can reference both workflow constituents (steps, data, parameters) and metadata of input datasets, and are used to customize a workflow to a given dataset. For example, a constraint could require that the alignment step and the assembly step in a bioinformatics pipeline are done with the same reference genome. Such constraints capture domain expertise about workflows (as purpose-specific combinations of tools) that goes beyond what the metadata of the individual tools can express.\n\nAnother interesting feature of WINGS with regard to automation is that it allows for the use of abstract (in terms of our Figure 1: conceptual) steps in the workflow, which can be implemented by different tools or sub-workflows. For example, PeptideSearch is a method that is performed by the tools X! Tandem,112 MSGF+113 and Myrimatch.114 The implementations can flexibly be chosen and exchanged, making it easy to quickly generate and compare workflow variants, for example to assess the robustness of the method or to take part in benchmarking challenges.88\n\nThe Automated Pipeline Explorer (APE)\n\nAPE89 is a command-line tool and application programming interface (API) for the exploration of possible workflows in large collections of semantically annotated tools. Input for APE is a high-level workflow specification that captures the user’s intents. It includes the available input data (type and format), the desired output data (type and format), and possibly additional constraints (such as tools to use or to avoid). For example, a proteomics workflow might be specified (using EDAM terms) as taking “Mass spectrum” in “Thermo RAW” format as input, producing an “Amino acid index” http://edamontology.org/data_1501in any format (see here), and using a “Retention time prediction” operation in the analysis. When applied to bio.tools, APE finds several workflows that meet this specification.\n\nThe exploration algorithm in APE is a variant of LTL-guided program synthesis, implemented as bounded search through iterative deepening.90,91 The domain model (ontology and tool annotations as provided by EDAM and bio.tools) and workflow specification are encoded as a SAT instance (a propositional Boolean formula in conjunctive normal form), and given to a SAT solver to find a satisfying assignment of variables. The SAT solutions are translated back into actual workflows, which can be transformed further into, for example, executable shell scripts, CWL workflows or other representations.\n\nSHARE & HYDRA\n\nSHARE92 and HYDRA93–95 are specialized query engines to work with SADI registries. They receive user input in the form of SPARQL queries and use the registry as a knowledge base for automated workflow composition, matching the query to thousands of services (Data as a Service (DaaS)/Application as a Service (AaaS)). Concretely, a SADI query engine maps triple patterns from the WHERE clause of a SPARQL query to indexed SADI properties in the registry. In particular it checks the I/O descriptions to ensure compatibility between services. In doing so it discovers SADI Web Services capable (when combined in a workflow) of generating the required triples. Finally the query engine plans and orchestrates a workflow with calls to RESTful web services, integrating service outputs locally in RDF.\n\nWhile SHARE supports the construction of the queries through a textual mechanism called SPARQL Assist, HYDRA also provides a keyword-based and graphical interface. Moreover, HYDRA performs reasoning on an input SPARQL query with respect to ontologies, leveraging the service registry to identify service calls may help answering the query. Iteratively, data returned from service calls triggers new registry calls to identify further relevant service calls. Through this incremental workflow extension, answers are produced incrementally with the user in the loop. The process terminates when all service calls have been made and all available answers have been produced.\n\nThe four approaches sketched above introduce automation to different phases of the workflow development life cycle, thus complementing each other. In the following we discuss cross-cutting aspects of automation in different phases of the life cycle.\n\nTarget audience\n\nThe different approaches clearly fit different user profiles and are intended to serve different target audiences. It seems useful to broadly distinguish between biologists as workflow users and bioinformaticians as workflow developers (obviously there are people who qualify for both roles). Many biologists simply want answers to their (biological) questions. They want to be able to find software solutions for their computational problems that they can trust, that have been tested and evaluated, that are reliable and that will run. They are not interested in the technical details of tools, workflows or even their construction processes. Despite the increasing integration of (bio) informatics education in life science curricula, this is not likely to change much. Hence this group of users is a target audience for production workflows as end results of the workflow development process. The development of workflows is in the hands of tech-savvy bioinformaticians. Within this large group, it seems that the “workflow engineer” emerges as its own professional profile. They compose, curate, evaluate and deploy workflows for specific bioinformatics problems, and make them ready for the actual end users.\n\nOf the automation approaches sketched above, HYDRA is the only one that directly and explicitly targets a workflow end user. This is made possible by the careful service curation that enables the direct execution of the workflows composed for the queries. The other approaches are better suited to support workflow developers in different phases of the construction process. APE is most suited to supporting workflow exploration and composition in an early phase, acting as a “route planner” that automatically explores and generates new possibilities of workflows for an abstractly described problem. The obtained “recipes” can then be developed further into concrete and executable workflows. The Galaxy tool recommender also targets the early, still exploratory phases of workflow construction, but based on a concrete workflow under construction. WINGS takes an abstract/template workflow as the basis, and then takes care of automatically instantiating it to obtain a concrete and executable workflow. Interestingly, to the best of our knowledge, the existing approaches do not cover automated workflow benchmarking yet, which will however be essential for bringing automatically created workflows to the production stage.\n\nApplicability and trust\n\nAll approaches have in common that their applicability depends on the quality of the underlying knowledge base or semantic domain model (cf. Section Semantic domain modelling). Generally, a somewhat lower quality seems to be tolerable for assisted workflow composition, as the developer can correct or discard suggestions based on their domain knowledge. This is the case, for example, when using a tool recommender system, like that in Galaxy, where the user can at any point decide whether or not to follow the recommendation. Semi-automated approaches like in APE and WINGS require higher-quality semantic annotations, but as the workflow developer still has the possibility to check and revise the workflow before execution, they can tolerate medium-quality annotations to some extent, Complete automation is possible for specific application areas or use cases with well-defined domain knowledge and high-quality annotations. As the required curation efforts are substantial, it is not realistic to achieve this in a generic framework. HYDRA instances, for example, are set up for well-defined application areas and invest in a rigorous semantic annotation of the provided Web Services. As a result, end users can use HYDRA to query for and directly execute workflows. Another good example for complete automation in a well-defined scope is Automated Machine Learning (AutoML),35 where machine learning models are generated automatically given a start and end point.\n\nConversely, the higher the degree of automation, the more the user needs to decide whether to blindly trust the outcome, or conduct checks to verify its plausibility and correctness. This is again connected to the quality of the knowledge base/semantic domain model, but also has to do with the degree of involved “blackbox” behaviour. For example, a HYDRA workflow is not easily validated before execution (as it is directly executed during construction), but the recorded provenance data make it possible to inspect and assess the performed computations afterwards. In contrast, the Galaxy tool recommender leaves the control about selecting workflow steps to the user, but requires trust in the quality of its recommendations. As they are machine-learned from tool combinations in existing workflows, there is likely a bias towards frequently used and against less used and new tools. Further metrics and criteria to base recommendations on are of course possible (such as a functional similarity index, compatibility, citation index or novelty), but in any case they should be made transparent to the user and create awareness for possible biases.\n\nAbstract Workflows\n\nDifferent levels of abstraction are key to differentiating the phases of the workflow development life cycle and assess the potential for automation (Figure 1). Indeed, automation in the development process usually means automated concretization. The process starts with a domain-level problem description as an initial idea, and then phase by phase boils it down to a concrete implementation, until a production workflow brings it back to the domain level and end user.\n\nThe term abstract workflow has been used with different meanings.38 In the executable Common Workflow Language (CWL),30 for example, it is possible to define a workflow with step/tool implementations (e.g. Docker containers) or with abstract placeholder operations; in either case the workflow defines and connects all workflow steps and their parameters. In CWL an abstract workflow can thus be classified as containing one or more placeholder operations; note however that CWL engines may still permit partial workflow execution for the concrete steps.\n\nIn CWL such abstract operations can still refer to a concrete tool that should be used when implementing the workflow for execution (omitting details such as command line), or to a class of possible tools (e.g. by using an EDAM operation term). In WorkflowHub, CWL is used as the canonical workflow description for workflows where possible, alongside the native workflow description: for example a Galaxy workflow for Climate analysis that is expressed in Abstract CWL.96 In WINGS, an abstract workflow is even more generic and flexible, allowing not only for abstract operations, but also for missing steps that are filled in during workflow elaboration.\n\nHere we separate the notions of conceptual and abstract workflows (cf. Fig. 1): We define a conceptual workflow to be a sketch of a data analysis pipeline, similar to a concept map,45,46 that describes the process in domain-level but implementation-independent terms, for instance using operation and data terms from the EDAM ontology. Next to that, we define an abstract workflow to be a template that describes complete sequences of computational tools, but that is not yet fully configured and executable. Such conceptual and abstract workflows make it possible to focus on the workflow steps without complexities such as parameter settings, execution or data sets. They are also convenient for enabling search (both for users and automation) and comparisons with other workflows, thus providing a suitable exchange level and intersection point for different stakeholders and communities. They can be the target (e.g. the result of workflow exploration with APE) as well as the input (e.g. a starting template for workflow elaboration with WINGS) for automated composition approaches.\n\nFurthermore, abstract workflows can be obtained by automated abstraction from (collections of) concrete workflow instances.97-99 They are useful for better describing, understanding and evaluating workflows, and for preserving the essence of computational pipelines in automatically generated method sections also when the executable instances of the workflow decay.98 They can therefore provide a way to document workflows in a FAIR way.50-52\n\n\nWorkflow assessment\n\nThe abundance of computational tools available in today’s eScience ecosystem leads to an enormous number of possible workflows. With automated composition approaches these can be more easily accessed and generated. There is a problem of identifying and selecting the “best” (whatever that means in the concrete case and context) alternatives among various options at different stages of the workflow development process: Which methods should be chosen given the available data and the analysis goals? Which individual tools should be given preference over others? Which combinations of tools to favor over others? Which workflow candidates to select for implementation? Which workflows to bring into productive use?\n\nTo enable automated composers to make informed choices, tools and workflows need to be compared with well-defined meaningful criteria. To structure the discussion of possible criteria and selection strategies, we follow the traditional distinction between static (based on information that is available without execution of the workflow) and dynamic (based on workflow execution) analysis.\n\nStatic analysis is performed on the “source code” of the workflow (may be in a classical scripting language or a specific workflow formalism) without actually executing it, treating the individual tools as black-box building blocks that have particular (static) properties. As such, static analysis mostly concerns the early stages of the workflow development life cycle, where the workflow developer (human or machine) can use available information about individual tools and tool combinations to explore possible workflows and the tools to implement them. Arguably, static analysis is often less meaningful than the results obtained through actual execution, but provides a powerful way for pre-screening the capability of a workflow. In addition, in many cases it is simply not possible to implement and execute all possible workflows in order to choose between options. Hence it is important to leverage what can be said about tools and workflows without executing them. Which information can be used to compare and (pre-)select individual tools and entire workflows at this stage? What would we like to see in a workflow before we run it? What can (possibly) be provided by tool registries and workflow repositories?\n\nThere are many qualities and merits to consider, but there seem to be three categories of information relevant at this stage, on which we elaborate in the following: technical parameters, domain-specific considerations, and community influence (summarized in Table 1).\n\n\n\n• Basic tool information (such as license, version, recent updates)\n\n• (Theoretical) compatibility of tools based on their functional annotation\n\n• (Practical) compatibility of tools based on their use in existing workflows\n\n• Tool statistics like number of runs, number of users, speed, reliability, etc.\n\n• Service monitoring information about availability, uptime, downtime, runtime, etc.\n\n• Number of shims (format converters) needed in the workflow\n\n• Data format flexibility (generic vs. tailored)\n\n• Data-flow properties (such as live and dead variables) of the workflow\n\n• Control-flow properties (such as cyclomatic complexity, parallelization potential)\n\n• Tool and workflow FAIRness metrics\n\n\n\n• Subject-specific unique or essential features of tools that the workflow needs and relation to a typical concept map in the domain\n\n• Establishment of tools (known quality metrics, well-understood configuration). Usage in commonly used workflows and known compatibilities by actual usage\n\n• Novelty of tools (new functionalities, potential for novel results, adaptation to new data types)\n\n• Similarity to existing concrete or abstract workflows (see above), workflow motifs\n\n• Type and format of produced results. Potential for direct comparison with output from other workflows\n\n• Availability of common quality control, benchmarks and benchmarking data\n\n\n\n• Reception in the domain literature (citations, altmetrics, praise and criticism)\n\n• Reputation, someone or something being “famous”\n\n• Trends, currently popular technologies\n\n• User comments and ratings (reflecting, e.g., adequacy, understandability, usability)\n\n• Trust in developers and/or providers\n\nTechnical Parameters\n\nTechnical parameters of individual tools and their combinations are relevant to their operation in the context of a composite workflow. These include a whole range of properties, as indicated in Table 1. It is worth noting here that several of these properties (for static analysis at design time of the workflow) are in fact based on prior dynamic analysis of individual tools or other workflows on different levels of abstraction. This underscores the relevance of systematic dynamic analysis of scientific tools and workflows, discussed further below. For use in (automated) workflow composition, we assume the availability of such information in a tool registry like bio.tools, as additional metadata in the tool annotations. Ideally, such metadata would also be collected “by stealth” through the major community platforms, and provided to tool registries in a standard format. Similarly, an archive of historical workflow traces would be useful, which could provide representative data about prior use of tools and their combinations.\n\nDomain-specific considerations\n\nWhile technical parameters are important to consider for operational workflows, they need to be complemented with domain-specific considerations to obtain scientifically meaningful results. Examples of domain-specific considerations in (automated) workflow composition are given in Table 1.\n\nCommunity influence\n\nFinally, community dynamics also influence which tools and workflows are considered preferable. Examples are given in Table 1. While these influences are probably stronger for human workflow developers, also automated composers rely on community-provided information and are thus not agnostic to the corresponding biases.\n\nDynamic analysis refers to assessment based on execution, and naturally mostly concerns workflows at the later stages of the life cycle, when they are configured, executable and can be applied to actual data and produce results. We simply distinguish between plain executability, basic validation and systematic benchmarking in the following. Note that the focus of the discussion during the workshop was on benchmarking.\n\nExecutability\n\nExecutability is probably the most basic and at the same time the most important property of a computational tool or workflow. Only execution will show if the workflow actually works, if the individual tools are compatible in practice (and not only on the annotation level), and if all components have been configured correctly. In practice, it is not uncommon that this executability is applied as the only criterion: If it works and produces results at all, it is considered good enough. If it does not work, one can either try to fix it (requiring understanding why it fails) or discard it. With automated composition and workflow repositories on the rise, which give easier access to alternative workflows for the same problem, the latter is becoming an increasingly viable option.\n\nValidation\n\nBetween mere executability and systematic benchmarking there is an area of workflow assessment that we here call validation. It is about critically assessing the behaviour of the workflow. Is the workflow doing what it is supposed to do? Can the results be true? Note that this notion of validation is related to, but not the same as testing, which is a separate issue for scientific software.100–102 In scientific practice, validation is often done by the workflow developer through execution of (parts of) workflows and inspection of results to see if they look as expected. Ideally, a “testing set of mind” would be taken and, for example, the workflow be tried with data that is outside of the supported range to see if/how it crashes or gives incorrect results. Such assessment can be cumbersome and challenging as it requires knowledge of both the tool functions and the applied data.\n\nIn more formal terms, we may classify these concerns into validation, verification, sensitivity analysis and uncertainty quantification (UQ) of a workflow (or workflow instance), with the canonical use of these terms being found in.103 These terms, and the distinction between them, are found more often in discussions of computational models used in physics and engineering,104,105 but the concepts are relevant to (and may be adapted to) the general scientific workflows covered in this article.\n\nIn simple terms, validation asks if what we want to do is correct; verification asks if our implementation is doing what we think it is doing; and uncertainty quantification asks about how sensitive our results are, for example, to uncertainty in the initial inputs. More concretely, validation refers to the accuracy of the theoretical approach we are trying to implement (the mathematical model or analysis procedure) and is measured by agreement with 'reality' e.g. comparing predictions with experimental results. Verification is a much broader term, encompassing various assessments of the correctness of the implementation itself - is execution of my workflow or code reproducing the theoretical approach I think it is? Finally, uncertainty quantification is an enormous field in its own right, and there are many levels at which it may be introduced to a workflow, from modification of individual steps (most intrusive) through to repeatedly sampling the entire workflow as a 'black box' (least intrusive, e.g. see reference.106\n\nWhile only a subset of the above may be relevant to any given workflow, a scientific workflow in general will be subject to all three concerns. Adoption of automated workflow composition tools in the wider scientific community will likely come with demands for rigorous checks of correctness, and a range of definitions thereof.\n\nBenchmarking\n\nWhen done systematically, the dynamic analysis of computational tools and workflows is also known as benchmarking.59 In the scientific workflow development life cycle (Figure 1) benchmarking helps to determine which workflow versions or instances will be put into production for large-scale use by third parties. It assumes that the workflows are executable and validated. Generally, benchmarking can be performed with regard to scientific (e.g. analysis quality), technical (e.g. runtime performance, robustness) and usability (e.g. ease of reuse) aspects. Ideally, benchmarking uses publicly available (gold, silver, or artificial/synthetic) reference datasets. Benchmarking can be performed in a single lab (often done for benchmarking on specific aspects) or by a community of researchers (advantageous to avoid bias, often done for common and shared challenges). Due to their composite nature, workflows are generally more fragile than individual tools, which is also relevant for their benchmarking. For instance, benchmarking can help to identify problematic tools or non-interoperable tool combinations.\n\nOpenEBench59 provides a platform for community-based benchmarking of bioinformatics resources. Its scientific benchmarking component provides a virtual research environment in which individual researchers or scientific communities can share data, tools, workflows and metrics for their benchmarking challenges. The virtual research environment supports the execution of automated metrics generation workflows, and the comparison of different resources’ benchmarking results. In addition, OpenEBench has a technical monitoring component, which automatically checks basic technical properties of the registered resources, and updates the OpenEBench entry on a daily basis. Information captured here includes, for example, the availability of documentation, uptime/access time of remote resources, and the number of citations on corresponding publications. Currently metrics for the FAIR software principles52 are being developed, which will also be integrated in OpenEBench’s technical monitoring component.\n\nAlthough we discussed separately static and dynamic workflow analysis, it is clear that in practice they are used together, often interleaved. Workflow developers would combine a first few tools, then execute to see what happens, and from there adapt and extend the workflow. Automated approaches to workflow development should follow this pattern, and assist the workflow developer in this incremental, checkpoint-rich style of development, rather than aiming for complete start-to-end automation. In the following we discuss three major, cross-cutting aspects of workflow assessment further: the question of what is “best”, the idea of a fitness function to measure to what extent a workflow meets its purpose, and a “great bake-off” perspective on automated composition and systematic benchmarking.\n\nThe “best”\n\nSomewhat didactically, we started off the discussion about workflow assessment with the aim of looking for the “best” possible workflows. However, obviously it is highly context-dependent and often unclear what this means. With the large number of candidates potentially generated by automated composition, it is often more sensible to cull nonsensical workflows rather than trying to find the very best. Doing this with the most coarse-grained criteria will ideally lead to a significantly reduced list of options that is amenable to more fine-grained analysis and evaluation. Nevertheless, the question of what kind of workflows to prefer remains context-specific. It seems advisable to explicate concrete use cases and personas to get a better understanding of relevant situations, perspectives, and requirements. Some spontaneous ideas from the workshop are summarized in Figure 2.\n\nDemands for configurability are ordered from low (top) to total (bottom). All participants need a publication-ready description of the provenance of their findings for perfect reproducibility. Not on the list is Rob the Routinier, who keeps doing his stuff just the way he did it for the last ten years.\n\nObviously these use cases and personas need to be worked out much further and only cover a part of the possible scenarios, but they clearly show that the meaning of “best” workflow spans a wide range of interpretations.\n\nFitness function\n\nAnother way to think about the problem of workflow assessment is designing a fitness function in an evolutionary computing approach or reward function in reinforcement learning.107 Thus, the goal is to try to learn or optimize a particular workflow given the required output. Such an optimization lens could be useful for applying advances in machine learning or evolutionary computing to workflow composition. Thus, the aim would be to devise functions to evaluate how “fit for purpose” workflows are, given a goal like, for example, a certain benchmark. Such a function should consider functional (biological) as well as performance (computational) metrics, such as:\n\n• Biological ground truth, what is known biologically\n\n• Robustness to a non-specialist user, and to evolving technical requirements (execution architecture)\n\n• Performance, reliability, reproducibility\n\n• Tool compatibility, tool popularity\n\n• Ratings from users who have employed workflows that are presented as possibilities (akin to looking at the ratings of a product on Amazon.com when making a purchase)\n\n• How unique is the combination of tools.\n\nA critical challenge for adopting this approach is the translation of the rich information both about workflows and surrounding biological knowledge into structures amenable to these optimization frameworks.\n\nGreat Bake-Off\n\nWe found it an appealing perspective to think about workflow assessment in the context of automated composition as a ‘Great Bake-Off’: carry out a pre-selection of automatically generated alternative workflows with low-effort assessment methods, and then let the remaining candidates compete against each other through rigorous benchmarking, in order to finally determine the workflow(s) to use in production. This process should include all areas of benchmarking (i.e., scientific, technical, and usability), though possibly with varying weighting depending on context. A similar strategy has for example successfully been taken by Automated Machine Learning (AutoML)35 for the automated generation of machine learning models.\n\nGenerally, technical benchmarking is comparatively easy and objective, while scientific and usability benchmarking are quite involved, less objective and more subject to bias. They require expert knowledge and ideally many different test data sets and metrics provided by different people. Critical assessments using unpublished data with ground truth may be a reliable means to get quality benchmarking information from the communities. This can also include the creation of synthetic benchmarking data sets in case no suitable real data is available. Synthetic data might furthermore deliberately contain noise or wrong items, to test if workflows are robust or able to detect unsuitable data quality.\n\nObviously, for a ‘Great Bake-Off’ there needs to be a decision or agreement on the metrics used to determine the “best”. For wide acceptance, they need to be informative and domain-specific, but also community-supported. These community approaches should be objectively executed without including the tool and workflow developers. Unfortunately, such endeavours are rare at the time being.\n\n\nRoadmap\n\nThe Lorentz workshop aimed at developing a common perspective on future directions for automated composition of workflow in the life sciences. Ideas were collected in the discussion during the whole week, but the last workshop day was devoted to formulating concrete action items for the coming years. Generally speaking, the overall goal of these actions is to bring the different individual pieces discussed in the workshop together in a (more) coherent framework. We deliberately focused on actions for the next five years, acknowledging that we, in our thinking, need to distinguish between the short-term practical possibilities from long-term speculations and the things that might be achieved only over decades. In the following we outline such future directions for foundations, tooling and infrastructure, community and applications of automated workflow composition in the life sciences.\n\nAchieving broad application of automated workflow composition depends on solid foundations, including a common understanding of its scope and purpose as well as community-approved definitions and standards that support these aims (see Table 2).\n\nThe lack of clearly defined use cases was a recurring theme during the workshop discussions. While all approaches and methods make implicit assumptions about the usage scenarios and user groups they target, this is hardly spelled out explicitly. Their elucidation (using established methods from software requirements engineering) is a priority and will form a solid basis for future joint efforts. For example, a user who has some data and a desired endpoint, wondering how to possibly get there, might benefit from a “PipelineSketcher” that can automatically propose suitable sequences of (conceptual) operations. Another user might want to take an existing concrete workflow and get suggestions for new tools, which could be given by a “RoboAdvisor”.\n\nAnother important area of foundational work is the definition and development of lacking standards and methods, such as universal workflow identifiers and methods for meaningful workflow comparison. Furthermore, several promising, but so far little developed ideas wait to be explored further. Examples include the use of workflow provenance traces as a knowledge base for heuristic improvements of automated composition, methods for automating the benchmarking or workflows, and the concept of “knowledge acquisition by stealth”.\n\nDeveloping and maintaining effective tooling and infrastructure for automated composition of workflows is hard. The workflow discussions highlighted several challenges of the current software ecosystem, in particular related to missing functionality, insufficient compatibility and interoperability, usability and convenience. Accordingly, the list of actions on tooling and infrastructure grew very easily (see Table 3).\n\nThe concept and technology of nanopublications108 could possibly have a role in contributing to solutions to the above points. Nanopublications are small snippets of provenance-aware semantic representations, which can among other things be used to represent workflows, workflow steps, and the data they consume and produce. An ecosystem of tools and services around nanopublications has recently emerged that allows for decentralized and robust interaction with such semantic representations, which could now be harnessed for automated workflow composition.\n\nClearly, the field faces a trade-off between a limited workforce and many wishes, underscoring the need for well-defined use cases and prioritized requirements (see above) and community involvement (see below).\n\nCommunity is known to be key, and not surprisingly several actions were proposed in relation to community building and involving the community in further development. Several future steps can benefit from existing communities and connect to ongoing initiatives, making them feasible in the medium term. Table 4 shows some of the concrete actions proposed.\n\nAt the beginning of the workshop several workflow applications from the fields of genomics, proteomics, proteogenomics, metabolomics, metaomics, scientometrics and text mining were presented to set the scene. After all, such applications should drive the developments, and they will mercilessly put methods, tools and infrastructure to the test. Several applications of the available workflow composition frameworks were sketched by the participants, some more domain-oriented and some more tool-oriented, but all with the potential of creating valuable insights for further developments (see Table 5).\n\nCurrently the coverage in ontologies and maturity of tool annotations vary considerably between life science domains, with genomics and more recently proteomics having received more attention. As success stories from adjacent fields are so important in encouraging joint efforts and widening adoption, we see future efforts focused on providing high-quality tool curations with concomitant ontology updates in specific fields, such as metagenomics, metaproteomics, metabolomics, epidemiology or biomedical imaging.\n\n\nConclusion\n\nIn this report we have summarized the salient points from five days of intense scientific discourse ranging from fine-grained technical details to very broad thematic topics. Naturally, not everything that was discussed in the workshop could be included here. Despite similar ideas and efforts having struggled to find widespread application in the past, the attendees left the workshop with renewed confidence and optimism that we are at least considerably closer now, having clearly identified what development of community standards, ontologies and annotations is still needed to achieve broad adoption of automated workflow composition techniques across the life sciences.\n\nIn the time between the workshop and finalizing this report, several things have happened. For example, bio.tools received a number of new features, and continues to grow. The WorkflowHub has been released and is now in productive use. Along with this, the Bioschemas Computational Workflow Profile,109 a schema.org-based specification for describing a computational workflow, has been defined. It is used by the WorkflowHub to mark up its entries and as the description of a workflow in the Workflow-RO-Crate,110 the interchange packaging format which is a specialisation of the RO-Crate packaging format,111 also based on schema.org. This enables workflows and associated components to be exchanged between the WorkflowHub, workflow management systems like Galaxy, Snakemake and Nextflow and their repositories, and workflow utilities like OpenEBench and LifeMonitor. Given its schema.org web markup basis, workflows marked up using the profile are readily accessible to search engines. Furthermore, case studies have been started, project proposals written, and further papers published.\n\nWhile some of these developments were in some form anticipated at the workshop, others emerged from ongoing developments and urgent needs. Perhaps this is representative for a field that strives to push and challenge the frontiers of life science infrastructure. After all, the value of automated workflow composition lies in the unexpected.\n\n\nData availability\n\nNo underlying data are associated with this article.\n\nOpen Science Framework: Lorentz Center Workshop: Automated Workflow Composition in the Life Sciences. https://doi.org/10.17605/OSF.IO/A5EJ7.115\n\nThis project contains the following extended data:\n\n- Executive Summary.pdf (short post-workshop summary)\n\n- Workflow Poster.jpg (workshop poster)\n\n- Workshop Program.pdf (workshop agenda)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nIn early March 2020, just in time before the Covid-19 pandemic disrupted life as we knew it, 36 researchers from 10 different countries and specializations ranging from biomedicine to computer science met at the Lorentz Center in Leiden (Netherlands) for a weeklong workshop on automated composition of workflows in the life sciences. They worked towards a common level of understanding and joint research agenda that is summarized by this paper. We compliment all participants for their valuable contributions during the workshop keynotes, technical talks, breakout discussions and hackathons.\n\nIn particular, we thank Jennifer Harrow, Rohola Hosseini, Rajaram Kaliyaperumal, Mateusz Kuzak, Melchior du Lac, David Lähnemann, Miriam Paya Milans and Marco Roos for their input to the discussions and collaborative notes that laid the foundations for this manuscript.\n\nSpecial thanks go to the Lorentz Center staff who went above and beyond their duties to make the workshop a success.\n\nThe figures in the illustrations were created using BioRender.com.\n\n\nReferences\n\nPerkel JM: That’s the way we flow. Computational pipelines turn raw data into reproducible scientific knowledge. Nature. 2019; 573: 149–150. Publisher Full Text\n\nAtkinson M, Gesing S, Montagnat J, et al.: Scientific workflows: Past, present and future. Future Gener. Comput. Syst. 2017; 75: 216–227. 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New York, NY, USA: Association for Computing Machinery; 2017; pp. 565–576. Publisher Full Text\n\nGarijo D, Gil Y, Corcho O: Abstract, link, publish, exploit: An end to end framework for workflow sharing. Future Gener. Comput. Syst. 2017; 75: 271–283. Publisher Full Text\n\nKanewala U, Bieman JM: Testing scientific software: A systematic literature review. Inf. Softw. Technol. 2014; 56: 1219–1232. Publisher Full Text\n\nHeaton D, Carver JC: Claims about the use of software engineering practices in science: A systematic literature review. Inf. Softw. Technol. 2015; 67: 207–219. Publisher Full Text\n\nJohanson A, Hasselbring W: Software Engineering for Computational Science: Past, Present. Future. Comput. Sci. Eng. 2018; 20: 90–109. Publisher Full Text\n\nOberkampf WL, Roy CJ: Verification and Validation in Scientific Computing.Cambridge; Cambridge University Press; 2010. Publisher Full Text\n\nGroen D, Arabnejad H, Jancauskas V, et al.: VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations. Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 2021; 379, 20200221. Publisher Full Text\n\nCoveney PV, Groen D, Hoekstra AG: Reliability and reproducibility in computational science: implementing validation, verification and uncertainty quantification in silico. Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 2021; 379: 20200409. Publisher Full Text\n\nZimoń M, Elisseev V, Sawko R, et al.: Uncertainty quantification-as-a-service. In: Proceedings of the 28th Annual International Conference on Computer Science and Software Engineering. USA: IBM Corp.; 2018; pp. 331–337.\n\nDrugan MM: Reinforcement learning versus evolutionary computation: A survey on hybrid algorithms. Swarm Evol. Comput. 2019; 44: 228–246. Publisher Full Text\n\nKuhn T, Meroño-Peñuela A, Malic A, et al.: Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data. In: 2018 IEEE 14th International Conference on e-Science (e-Science). 2018; pp. 83–92. Publisher Full Text\n\nBioschemas - 1.0 Release (09 March 2021) . Last accessed 2021/09/01. Reference Source\n\nWorkflow RO-Crate (DRAFT). Last accessed 2021/03/08. Reference Source\n\nEoghan ÓC, Carole G, Peter S, et al.: A lightweight approach to research object data packaging. Bioinformatics Open Source Conference (BOSC). Basel, Switzerland: ISMB/ECCB 2019; 2019. Publisher Full Text\n\nCraig R, Beavis RC: TANDEM: matching proteins with tandem mass spectra. Bioinformatics. 12 June 2004; Volume 20, Issue 9, Pages 1466–1467. Publisher Full Text\n\nGranholm V, Kim S, José CFN, et al.: J Proteome Res. 2014; 13 (2), 890–897. Publisher Full Text\n\nDavid LT, Christopher G, Fernando, et al.: J Proteome Res. 2007; 6(2): 654–661. Publisher Full Text\n\nLamprecht A, Palmblad M, Ison J, et al.: Lorentz Center Workshop: Automated Workflow Composition in the Life Sciences; 2021, August 16. Publisher Full Text\n\n\nFootnotes\n\n* We use the terms “pipeline” and “workflow” interchangeably here. Another common, more differentiating view is that pipelines are purely computational and as such a subset of the more general notion of workflows, which can also involve a human element."
}
|
[
{
"id": "94267",
"date": "19 Oct 2021",
"name": "Pinar Alper",
"expertise": [
"Reviewer Expertise scientific workflows",
"provenance",
"data 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\nThe paper is the final report from a 2020 workshop on automated workflow development in life sciences.\nThis is overall a well written paper, which, scope-wise, is framed by the discussions of the workshop rather than being an exhaustive state-of-the-art paper on semantic workflow development techniques. The paper is lengthy and covers many topics in a partly explored research space in scientific workflows, it requires multiple reads to have an overall viewpoint.\nThe contributions of the paper are the following:\nA scientific workflow lifecycle outlining the various activities and artefacts in stages of the lifecycle. I think this is the strongest contribution of the paper. It acts as a map for authors to place various past and future research.\n\nA survey of current technologies and practices that directly or indirectly support workflow composition. This is not an exhaustive survey reporting research and techniques in workflow composition, instead focuses on what is currently working and available to life science researchers.\n\nA set of future directions on research and technology development to enable automated workflow composition across the lifecycle.\n\nThe paper reports on a stimulating topic and can act a kick starter for the next era of research on the intersection of semantic technologies and scientific workflows.\n\nSuggestions for improvements:\nThe paper does not utilise section numbers which makes reading difficult. If the journal format allows I’d recommend the use of numbering.\n\nAbstract reads “Recent technological advances have returned …” What are those? Give one example in the abstract.\n\nIn the introduction you do not mention explicitly the bioinformatician but say “To biologists there is a latent fear to have chosen …” and later mention “human expert knowledge” which I guess refers to the bioinformatician. So I gather automated composition will ultimately assist the bioinformatician. Without such clarification the paragraph reads as if biologists due to their “latent fear of making a mistake” will consult “automated assembly”. I believe that is an overly optimistic statement without any reference to any surveys or observations on biologists’ and bioinformaticians’ expectations or experience with workflows. During peer-review scientists are held _accountable_ for their analytical methods and in this paragraph it is not justified with any references how an automated decision made by composition software increases trustworthiness of the method.\n\nThe introduction states the ”developments bring the long standing vision of automated composition … within reach”. Here 1-2 sentences, will be helpful, that summarise to date how much progress has been made on this vision (a very brief summary of page 11 essentially).\n\nThe paper often cites multiple papers to refer to the same system or approach. Taverna, Galaxy, myExperiment, Biocatalogue, Ontosoft, Magallenes, Prophets are all cited with refs to multiple papers. While this is useful to have an overview of all papers, it would help the reader if you cited the definitive or the more relevant papers for these systems. If both citations are needed then footnotes will be helpful on what different can be found in each particular paper for one system. Tightening up the citations could also help creating space for citations of past workflow systems which have addressed assisted workflow composition e.g. Vistrails or perhaps references to any useful reviews (if exist) on the topic.\n\nStatic analysis of scientific workflows* (an area that has received limited attention), is closely tied to data and control flow constructs in workflow languages and provenance. Static analysis (re: technical parameters) can tell whether resulting provenance traces from a workflow would provide granular traceability or not. This may as well be another technical parameter aiding automated composition.\n\nStatic analysis over workflows re: domain-specific characteristics has so far been done to understand, compare and contrast various scientific domains and their use of workflows **. Findings from such studies may help in refine “domain-specific considerations”.\n\n* Alper P, Belhajjame K, Goble C: Static analysis of Taverna workflows to predict provenance patterns. Future Generation Computer Systems. 2017; 75: 310-329\n** Garijo D, Alper P, Belhajjame K, Corcho O, et al.: Common motifs in scientific workflows: An empirical analysis. Future Generation Computer Systems. 2014; 36: 338-351\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "96797",
"date": "05 Nov 2021",
"name": "Rafael Ferreira da Silva",
"expertise": [
"Reviewer Expertise scientific workflows",
"distributed computing",
"modeling and simulation of distributed systems",
"parallel computing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents a summary of the discussions and findings from a Lorentz Center workshop organized in March 2020, with the focus on automated workflow development in the life sciences.\nOverall, the paper is well written and presents a community view on the current state-of-the-art, challenges, and perspectives for research efforts. Another key contribution of the paper is the development of a schematic process of the scientific workflow life cycle, which is comprised of six principal stages, each with their associated artifacts. Although a survey of state-of-the-art technologies is not the goal of the paper, it still provides a reasonable amount of background information.\nOn the downside, the paper could better articulate which properties are inherent to each of the aforementioned stages, and organize the discussions around them.\nSpecific comments:\nI would recommend authors to identify common properties for the set of tools described in the paper. The current text alludes to individual tool functionalities but does not clearly discuss their common ground / specificities.\n\nIt is not clear to me how \"workflow benchmarks\" are defined. At some moments I see them as \"reference workflows\" for validating the workflow structure and data, while at other sections I see them as performance drivers. It might be good to provide an actual definition of the term, or even separate them (as they seem to measure different properties).\n\nThe proposed future work (foundations, tooling and infrastructure, community, and applications) could leverage several ongoing efforts from the scientific workflows community such as in [1, 2, 3].\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-897
|
https://f1000research.com/articles/10-895/v1
|
07 Sep 21
|
{
"type": "Research Article",
"title": "Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya",
"authors": [
"Fuzia Elfituri Muftah Eltariki",
"Kartikeya Tiwari",
"Mohammed Abdelfatah Alhoot",
"Fuzia Elfituri Muftah Eltariki"
],
"abstract": "Background: A large number of undiscovered fungal species still exist on earth, which can be useful for bioprospecting, particularly for single cell oil (SCO) production. Mortierella is one of the significant genera in this field and contains about hundred species. Moreover, M. alpina is the main single cell oil producer at commercial scale under this genus. Methods: Soil samples from four unique locations of North-East Libya were collected for the isolation of oleaginous Mortierella alpina strains by a serial dilution method. Morphological identification was carried out using light microscopy (Olympus, Japan) and genetic diversity of the isolated Mortierella alpina strains was assessed using conserved internal transcribed spacer (ITS) gene sequences available on the NCBI GenBank database for the confirmation of novelty. The nucleotide sequences reported in this study have been deposited at GenBank (accession no. MZ298831:MZ298835). The MultAlin program was used to align the sequences of closely related strains. The DNA sequences were analyzed for phylogenetic relationships by molecular evolutionary genetic analysis using MEGA X software consisting of Clustal_X v.2.1 for multiple sequence alignment. The neighbour-joining tree was constructed using the Kimura 2-parameter substitution model. Results: The present research study confirms four oleaginous fungal isolates from Libyan soil. These isolates (barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) were discovered and reported for the first time from diverse soil samples of district Aljabal Al-Akhdar in North-East Libya and fall in the class: Zygomycetes; order: Mortierellales. Conclusions: Four oleaginous fungal isolates barcoded as MSU-101, MSU-201, MSU-401 and MSU-501 were identified and confirmed by morphological and molecular analysis. These fungal isolates showed highest similarity with Mortierella alpina species and can be potentialistic single cell oil producers. Thus, the present research study provides insight to the unseen fungal diversity and contributes to more comprehensive Mortierella alpina reference collections worldwide.",
"keywords": [
"Single cell oil",
"Mortierella alpina",
"Potato dextrose agar",
"Sporangiospore",
"Mortierellales"
],
"content": "Introduction\n\nEdible oils produced by oleaginous microorganisms are named as single cell oils (SCO). Most of these oil accumulating microorganisms are species of yeast and fungi. The comprehensive nuclear ribosomal deoxyribonucleic acid (DNA) molecular phylogeny analysis reported that the order Mortierellales contains nearly 100 described species and the Mortierellaceae family contains about 13 genera. M. alpina is one of the main single cell oil producing species/arachidonic acid producing at commercial scale under Mortierella genus. (Coemans 1863; Hibbett et al. 2007; Hoffman et al. 2013; Spatafora et al. 2016; Wagner et al. 2013). Wang et al. (2011) described the M. alpina genome scale reconstructed metabolic model for higher production of arachidonic acid at industrial scale. Scientists are in continuous search for the new species/novel strains and trying hard to crack the reconstruction genome code to exploit these species, so that the arachidonic acid production can be simplified and commercialized with an improved protocol (Shin et al. 1994; Rhie et al. 2002; Rhie and Park 2001; Ha et al. 2004).\n\nOleaginous fungi especially Mortierella species are ubiquitous, saprophytic and belong to zygomycetes class. The polyunsaturated fatty acids (PUFA) production potential makes these fungi unique and significant to oil producing industries. Modern internal transcribed spacer based taxonomical classification (Kirk 1997; Linnemann 1941; Degawa and Gams 2004; Ariyawansa et al. 2015) categorizes the Mortierella genus into seven groups: selenospora and parvispora”, “verticillata-humillis”, “lignicola”, “mutabillis, globulifera and angusta”, “strangulate and wolfii”, “alpina and polycephala”, and “gamsii”.\n\nDuring our studies on Libyan Mortierellaceous fungi, we have isolated many diverse species. Surprisingly, four species of Mortierella we have encountered in Libya have not yet been reported. To our knowledge, this is the first report on these oleaginous fungal species from this country.\n\n\nMethods\n\nThis study was carried out in December 2017. In total, four different locations viz. Marawah, Albayda, Faydiyah and Suluntah located in district Aljabal Al-Akhdar, North-East Libya were chosen as shown in Table 1. In total, a 10 g rhizosphere soil sample from each location was collected in sterilized polybags and transported to the microbiology laboratory of Management and Science University, Shah Alam, Malaysia and stored at 4°C for further processing.\n\nThe fungal isolation was carried out by a conventional serial dilution technique in which 1 g of soil was mixed with 9 mL of sterile distilled water and shaken for 15 min at 25°C; serial dilutions ranging from 10−1 to 10−4 were made. An aliquot of 0.1 mL from each dilution was transferred to potato dextrose agar supplemented with 100 μg chloramphenicol/mL antibiotic and incubated at 25°C for 3–7 days.\n\nMorphological features of the fungus were observed on potato dextrose agar (PDA) medium after one-point inoculation in 9-cm petri dishes and incubation at 25°C for 5-7 days (Hyde et al. 2016). The samples were inoculated with the help of a sterilized inoculation needle by center point inoculation on the PDA media containing petri dishes. All methods were performed at the laminar air flow by maintaining all aseptic conditions to avoid any kind of contamination using standard protocol described by Lee et al. (2017). The Petri dishes were sealed by parafilm and incubated for 5-7 days at 25°C in the dark for the growth of novel fungal species. All four distinct isolated fungal species were kept on plastic Petri dishes (9 cm diameter). These plates were observed on daily basis and their morphological characteristics viz. colony appearance, pigmentation, growth pattern, colony colour (front and reverse), colony diameters were documented. Individual colonies of fungi that showed varying morphologies were picked up and identified by mycokeys 3.0 version. The morphological features of four fungal isolates were compared with distinguished monographs precisely with II Subgenus: Mortierella; 2. Section ALPINA Linnem. Mucorineen-Gatt. Mortierella: 35. 1941 monograph (Gams 1977) to assess the novelty as shown in Table 2.\n\nComparison of morphological and cultural characteristics of fungal isolates obtained in this research study with reference, Mortierella alpinaa.\n\na Source of reference: Gams W. (1977) and Nagy et al. (2011).\n\nDirect microscopic identification was performed by using distilled water (wet mount technique) in which, a clean glass slide was labelled in the middle portion by marker and a drop of sterilized distilled water was put in on the marked middle portion, aerial spores and vegetative hyphae of the fungal isolate taken with the help of sterilized inoculation needle and distributed evenly within the water drop. Subsequently the glass coverslip was carefully added on the preparation in such a way that there was no air bubble formed. Same procedure was applied with lactophenol solution for identification of distinguished structures and prepared slides were examined under a light microscope at 40× magnification (Model: SZX16 Olympus, Japan). The sporangiophore, sporangium and sporangiospores, shape and size, developmental pattern, mature and immature sporangiospores, intercalary chlamydospore were measured and documented (White et al. 1990). Pure cultures of four fungal isolates were preserved and maintained (Fully grown barcoded fungal cultures after 5 days incubation at 25°C) in PDA slant tubes and stored in 20% glycerol at –80°C in a cold chamber of the university microbiology laboratory. Later, all four cultures were barcoded as MSU-101, MSU-201, MSU-401 and MSU-501 and deposited at MSU Culture Collection Center, Management and Science University, Shah Alam, Selangor, Malaysia.\n\nTotal genomic DNA (gDNA) was extracted according to the standardized protocol (Tamura et al. 2013). ITS and rDNA conserved regions were amplified using ITS4 (5′-GGAAGTAAAAGTCGTAACAAGG-3′) and ITS1 (5′-TCCTCCGCTTATTGATATGC-3′)\n\nTotal genomic DNA (gDNA) was extracted directly from the mycelia of fungal isolates, using Genomic DNA reparation Kit (KIT-1200-50: Fungal DNA Barcoding Kit, Apical Scientific Sdn Bhd Malaysia, following the manufacturer’s instructions). Step by step protocol of gDNA isolation includes 1. 500 μL of Fungal Lysis Buffer added into 1.5 mL micro-centrifuge tube that contains the 1 cm agar cube of pure fungal culture. 2. 3 μL of Proteinase K solution added. Vortex to mix and spin down briefly. 3. The tubes were incubated at 56° C for overnight and centrifuged the lysate at 14,000 to 16,000×g for 10 minutes. 4. Transferred ~500 μL of supernatant to a new 1.5 mL micro-centrifuge tube, which contains 500 μL of isopropanol. The tube was inverted several times to mix gently. 6. Centrifuged at 14,000 to 16,000×g for 10 min and the supernatant was discarded. 7. 1 mL of 70% ethanol was added, centrifuged again at 14,000 to 16,000×g for 5 min and the supernatant was discarded. 8. The pallet was air dried for 3 min, resuspended with 50 μL TE Buffer and incubated at 56°C for < 1 hr. 9. Optical density (OD) was measured reading using spectrophotometer (Thermo Scientific, USA) and the nucleic acid was diluted to 15 to 25ng/μL and 2 μL of diluted nucleic acid was used as DNA template for PCR. 10. PCR mix was prepared according to manufacturer’s instructions and 2 μL of DNA template was added with each 23 μL of PCR mix into 0.2 mL tube or 96-well plate. 11. PCR cycle protocol was run on thermocycler and ~700bp PCR products were checked on 1% agarose gel (First Base NGS KIT, Malaysia) and sequenced by ABI3100 sequencer. 12. After the sequencing results were ready, the reads were trimmed off with quality value (QV) < 20, after that the forward and reverse sequencing results were aligned. 13. The obtained sequences were compared against the earlier submitted NCBI database using the BLAST algorithm (Kimura 1980) to verify the percentage of identity corresponding to the analysed species (Table 2). 13. The fungal sequences were aligned using Clustal_X v.2.1 and neighbour joining based phylogenetic tree was constructed using Mega (molecular evolutionary genetic analysis) X software version 16.04.4 (with unity desktop, ANALYZE mode; Tamura et al. 2013) to observe the grouping of obtained novel fungal species sequences (Kimura 1980; Nagy et al. 2011; Chien et al. 1974).\n\n\nResults and discussion\n\nOn the basis of morphological and cultural characteristics, the fungal isolates were confirmed and belong to Mortierella genus. Colonies of oleaginous fungal isolates after seven days of incubation at 25°C on PDA, were sporulating, fast growing, producing a concentric pattern, had flower-shaped radial growth, and were yellowish to whitish in color as depicted in Figure 1 (Eltariki, Tiwari, & Alhoot, 2021). The detailed descriptions of morphological characteristics such as sporangiophores, sporangium, sporangiospores with reference M. alpina (ATCC 32222; CBS 528.72) isolate are given in Table 3 and Figure 2. Distinguishing prominent features between four fungal isolates (Barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) were growth pattern, margin and colour of the colony on PDA medium in front and back side as shown in Figure 1, which requires further investigation. Thus, these four novel isolates were examined for molecular characterization and genetic diversity.\n\n(A) MSU-101 colonies on PDA front and back view. (B) MSU-201 colonies on PDA front and back view. (C) MSU-401 colonies on PDA front and back view. (D) MSU-501 colonies on PDA front and back view.\n\n(A) Meiospore of MSU-101 isolate. (B) Immature sporangia from branched sporangiophore of MSU-101. (C) Intercalary chlamydospore of MSU-101 isolate. (D) Hyaline and ovoid sporangia, MSU-201 isolate. (E) Developing sporangia on single sporangiophore, MSU-201 isolate. (F) Immature young sporangia on highly branched sporangiophore, MSU-201. (G) Immature young sporangia on highly branched sporangiophore, MSU-401. (H) Mature globose sporangium containing sporangiospores, MSU-401. (I) Terminal chlamydospores with papillate ornamentation and hyphal segment remaining at the distal end, MSU-501. (J) Net of hypha with branching and septation, MSU-501. (K) Net of hypha with branching and chlamydospore, MSU-501. (L) Developing sporangium at tip on sporangiophore, MSU-501.\n\nIn the ITS sequences analysis based on BLASTn (Basic Local Alignment Search Tool for nucleotides), MSU-101, MSU-201, MSU-401 and MSU-501 isolates were fall within the order Mortierellales as depicted in Figures 3 and 4, which matches with morphological identification of isolates as described above. These four fungal isolates (barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) were compared and aligned with earlier submitted closely related species sequences by multiple sequence alignment (FASTA format) with software Clustal_X v.2.1. The phylogenetic tree constructed by neighbour joining mode with 1000 bootstrap values, showed that four oleaginous fungal isolates were 100% similar with earlier M. alpina genomes sequences submitted in GenBank NCBI (closest matching GenBank accession numbers were: EU918703; KX343169; FJ025186; FN689671; FN391358; FJ025158) as shown in Table 2 and Figures 3 and 4. Thus, these isolates were identified as M. alpina species. The ITS sequences of these fungal isolates were deposited in GenBank with accession number of MZ298831:MZ298835.\n\nBootstrap support values are indicated at the nodes.\n\nBootstrap support values are indicated at the nodes.\n\nThe present study added on the Mortierella alpina fungal strains reference collections and describes the diversity of these strains with known strains to date as shown in Figures 1 and 2. These novel Mortierella isolates add on to a large contribution of fungal diversity collections all over the world but still there is a plenty of room for more comprehensive M. alpina collections from Libya and this is the limitation of the present study. Thus, further research work needs to be carried out in future so that the hidden Mortierella fungal diversity and their SCO production potential can be harnessed.\n\nChen and Ho (2008) reported the significance of internal transcribed spacer region (18S-28S ribosomal gene) for the genetic characterization and these strains and found that the 5.8 rDNA regions of M. alpina isolates were conserved except some identified polymorphic sites. Furthermore, the interpretation was made that the variability is present in ITS1 and ITS2 regions, as there was no polymorphic site in the 5.8 rDNA region. Thus, it was evident that the ITS region could be used to confidently discriminate between M. alpina and other closely related species. These researchers also highlighted that NJ (Neighbour-Joining phylogenetic tree) tree analysis provides precise genetic diversity between M. alpina strains to come out with significant interpretation and conclusion.\n\nMany species of Mortierella are potentialistic producers of C18 and C20 PUFAs (polyunsaturated fatty acids) such as γ-linolenic acid and arachidonic acid. M. alpina species is quite famous for the production of single cell oils as describes and reported by multiple scientist’s time by time (Chien et al. 1974; Huang et al. 2013; Tamayo-Velez and Osorio 2018; Osorio and Habte 2014; Ellegaard et al. 2013; Lee et al. 2015; Nguyen and Lee 2016; Hwang et al. 2005; Shin et al. 2005; Tiwari and Razip 2020; Tiwari and Ganesen 2020; Maitig et al. 2028; Khan et al. 2018; Asdren and Faizal 2018; Yu et al. 2019; Alhoot et al. 2019; Tiwari et al. 2018, 2019a,b).\n\nResearch scientists are working to remodel these novel strains so that the SCO production can be enhanced at industrial scale. Shimizu and Sakuradani (2009) reported M. alpina 1S-4 strain by extensive screening, for the large-scale production of variety of PUFAs. This isolate not only had the potential for SCO production but also had several advantages to work as a model for lipogenesis studies. Thus, we can anticipate from earlier published data that the isolates reported from present study can be useful for bioprospecting in terms of single cell oil production. However, the oil production potential of these oleaginous fungal isolates is under investigation and our research group is presently working in this direction to assess the SCO potential of these diverse isolates obtained from Libyan soil.\n\n\nConclusion\n\nIn the present study, four oleaginous fungal isolates barcoded as MSU-101, MSU-201, MSU-401 and MSU-501 were identified and confirmed by morphological and molecular analysis. These fungal isolates had shown highest similarity with Mortierella alpina species and can be potential single cell oil producers, further research work is in progress for assessment and exploitation of these isolates in terms of oil production.\n\n\nData availability\n\nNCBI GenBank: Accession numbers MZ298831 to MZ298835.\n\nhttps://www.ncbi.nlm.nih.gov/nuccore/?term=MZ298831:MZ298835[accn].\n\nZenodo: Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya. https://doi.org/10.5281/zenodo.5239888 (Eltariki, Tiwari, & Alhoot, 2021).\n\nThis project contains the following underlying data:\n\n- Developing sporangia on single sporangiophore, MSU-201 isolate.jpg\n\n- Developing sporangium at tip on sporangiophore, MSU-501.jpg\n\n- Hyaline and ovoid sporangia, MSU-201 isolate.jpg\n\n- Immature sporangia from branched sporangiophore of MSU-101.jpg\n\n- Immature young sporangia on highly branched sporangiophore, MSU-201.jpg\n\n- Immature young sporangia on highly branched sporangiophore, MSU-401.jpg\n\n- Intercalary chlamydospore of MSU-101 isolate.jpg\n\n- Meispore of MSU-101 isolate.jpg\n\n- Mortierell alpina (4 strains) gel image.jpg\n\n- Mortierella alpina novel strain-MSU-201_Front view.jpg\n\n- Mortierella alpina novel strain_MSU-101.jpg\n\n- Mortierella alpina novel strain_MSU-101_Back view.jpg\n\n- Mortierella alpina novel strain_MSU-201_Back view.jpg\n\n- Mortierella alpina novel strain_MSU-401_Back view.jpg\n\n- Mortierella alpina novel strain_MSU-401_Front view.jpgMortierella alpina novel strain_MSU-501_Back view.jpg\n\n- Mortierella alpina novel strain_MSU-501_Front view.jpg\n\n- Net of hypha with branching and chlamydospore, MSU-501.jpg\n\n- Net of hypha with branching and septation, MSU-501.jpg\n\n- Phylogenetic tree MSU-101 and MSU-401.jpg\n\n- Phylogenetic tree_MSU-201 and MSU-501.jpg\n\n- Terminal chlamydospores with papillate ornamentation and hyphal segment remaining at the distal end, MSU-501.jpg\n\n- Terminal chlamydospores.jpg\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nAuthors would like to thank Management and Science University (MSU), Malaysia for the research laboratory facilities. The laboratory research work has been carried out by Miss Fuzia Elfituri Muftah Eltariki from Libya for the fulfilment of her Ph.D. degree under the supervision of Dr. Mohammed Abdelfatah Alhoot and Dr. Kartikeya Tiwari. All authors have given consent for acknowledgement. An earlier version of this article can be found on Research Square (DOI: https://doi.org/10.21203/rs.3.rs-673772/v1).\n\n\nReferences\n\nAlhoot MA, Eltraiki MEF, Ridzuan PM, et al.: The inhibitory effect of the Mentha piperita leaves extracts on the mycotoxin producer Aspergillus niger. Int. J. Med. Tox. Legal Med. 2019; 22(1-2): 179–183.\n\nAriyawansa HA, Hyde KD, Jayasiri SC: Fungal diversity notes 111–252 – taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers. 2015; 75: 27–274. Publisher Full Text\n\nAsdren Z, Faizal MZ: Investigation of potential antibacterial activity of Salvadora persica in combination with Mentha arvensis against Staphylococcus spp.2018; 21(3-4): 288–292.\n\nChien CY, Kuhlman EG, Gams W: Zygospores in two Mortierella species with “stylospores”. Myco. 1974; 66: 114–121.\n\nCoemans E: Quelques hyphomycetes nouveaux. – Ire. – I. Mortierella polycephala et II. Martensella pectinata. Bull l’ Acad Royale Sci, Lett, Beaux-Arts Belgique. Ser. 2.1863; 15: 536–544.\n\nDegawa Y, Gams W: A new species of Mortierella, and an associated sporangiiferous mycoparasite in a new genus. Nothadelphia Stud. Myco. 2004; 50: 576–572.\n\nEllegaard-Jensen L, Aamand J, Kragelund BB: Strains of the soil fungus Mortierella show different degradation potentials for the phenylurea herbicide diuron. Biodegradation. 2013; 24: 765–774. PubMed Abstract | Publisher Full Text\n\nEltariki FEM, Tiwari K, Alhoot MA: Molecular characterization and genetic diversity of four undescribed novel oleaginous Mortierella alpina strains from Libya (Mega X software 16.04.4 (with unity desktop, ANALYZE mode)). Zenodo. 2021. Publisher Full Text\n\nGams W: A key to the species of Mortierella. Persoonia. 1977; 9: 381–391.\n\nHa SJ, Park CS, Ryu YW: Selection of organic nitrogen source and optimization of culture conditions for the production of arachidonic acid from Mortierella alpina. Korean J. Biotech. Bio. 2004; 19: 78–82.\n\nHibbett DS, Binder M, Bischoff JF: A higher-level phylogenetic classification of the fungi. Mycol. Res. 2007; 111: 509–547. PubMed Abstract | Publisher Full Text\n\nHoffmann K, Pawłowska J, Walther G: The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies. Persoonia. 2013; 30: 57–76. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuang C, Chen XF, Xiong L: Single cell oil production from low-cost substrates: the possibility and potential of its industrialization. Biotech. Adv. 2013; 31: 129–139. PubMed Abstract | Publisher Full Text\n\nHwang BH, Kim JW, Park CY, et al.: High-level production of arachidonic acid by fed-batch culture of Mortierella alpina using NH4OH as a nitrogen source and pH control. Biotech. Lett. 2005; 27: 731–735. PubMed Abstract | Publisher Full Text\n\nHyde KD, Hongsanan S, Jeewon R: Fungal diversity notes 367-490: taxonomic and phylogenetic contributions to fungal taxa. Fungal Divers. 2016; 80: 1–270. 10.1007/s13225-016-0373-x\n\nKhan J, Mohammed K, Kaur N, et al.: Synthesis of cinnamic acid amide derivatives and the biological evaluation of a-glucosidase inhibitory activity. Int. J. Med. Tox. Legal Med. 2018; 21(3-4): 216–220. Publisher Full Text\n\nKimura MA: Simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evo. 1980; 16: 111–120. PubMed Abstract | Publisher Full Text\n\nKirk PM: Mortierella elongata. IMI Description Fungi Bact. 1997; 1303: 1–2.\n\nLee HY, Nguyen TT, Mun HY: Confirmation of two undescribed fungal species from Dokdo of Korea based on current classification system using multi loci. Mycobiology. 2015; 43: 392–401. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLinnemann G: Die Mucorineen-Gattung Mortierella Coemans. Pflanzenforschung. 1941; 23: 1–64.\n\nMaitig AMA, Alhoot MAM, Tiwari K: Isolation and screening of extracellular protease enzyme from fungal isolates of soil. J. Pure Appl. Microbio. 2018; 12(4): 2059–2067. Publisher Full Text\n\nNagy NG, Petkovits T, Kovács GM, et al.: Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences. New Phytol. 2011; 191: 789–794. PubMed Abstract | Publisher Full Text\n\nNguyen TTT, Lee HB: Characterization of a zygomycete fungus, Mortierella minutissima from freshwater of Yeongsan river in Korea. Kor. J. Mycol. 2016; 44: 346–349.\n\nOsorio NW, Habte M: Soil phosphate desorption induced by a phosphate-solubilizing fungus. Comm. Soil Sci. Plant Anal. 2014; 45: 451–460. Publisher Full Text\n\nRhie SG, Kang HY, Park YJ: The effects of Mortierella alpina fungi and extracted oil (arachidonic acid rich) on growth and learning ability in dam and pups of rat. J. Korean Soc. Food Sci. Nutri. 2002; 31: 1084–1091. Publisher Full Text\n\nRhie SG, Park YJ: The growth effects of Mortierella alpina contained diets and burn healing effects of Mortierella alpina extracted oil (arachidonic acid rich) in rat. Thesis Collect. Univer. Suwon. 2001; 19: 285–297.\n\nShin HS, Oh IH, Lee JH: Isolation and production of arachidonic and eicosapentaenoic acid by fungi. J. Ind. Tech. 1994; 2: 43–52. PubMed Abstract | Publisher Full Text\n\nShin HT, Lee SW, Park KM, et al.: Characteristics of submerged and solid-state fermentations for production of arachidonic acid by Mortierella alpina. Korean J. Biotech. Bio. 2005; 20: 60–65.\n\nShimizu S, Sakuradani E: Single cell oil production by Mortierella alpina. J. Biotech. 2009; 144: 31–36. PubMed Abstract | Publisher Full Text\n\nSpatafora JW, Chang Y, Benny GL: A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia. 2016; 108: 1028–1046. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTamura K, Stecher G, Peterson D, et al.: MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013; 30: 2725–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTamayo-Velez A, Osorio NW: Soil fertility improvement by litter decomposition and inoculation with the fungus Mortierella sp. in avocado plantations of Colombia. Comm. Soil Sci. Plant Anal. 2018; 49: 139–147.\n\nTiwari K, Razip NAFBM: Antagonistic activity and molecular characterization of endophytic biocontrol agent Trichoderma harzianum fungal strains isolated from medicinal plant Terminalia catappa L. in West Malaysia. Int. J. Med. Tox. Legal Med. 2020; 23(3-4): 48–53. Publisher Full Text\n\nTiwari K, Ganesen M: Novel endophytic Penicillium chrysogenum strains isolated from Plectranthus amboinicus L. of West Malaysia. Res. J. Microbio. 2020; 15(1): 15–21.\n\nTiwari K, Alhoot MA, Eltraiki MEF, et al.: Prevalence and genetic diversity assessment of mycotoxigenic Colletotrichum gleosporioides in wheat grains collected from different regions of Libya. Int. J. Med. Tox. Legal Med. 2019a; 22(1-2): 184–185.\n\nTiwari K, Alhoot MA, Sharma AK: Paclitaxel of fungal origin: challenges and updates. Int. J. Med. Tox. Legal Med. 2019b; 22(1-2): 160–161. Publisher Full Text\n\nTiwari K, Alhoot MA, Eltraiki MEF: Occurrence and prevalence of mycotoxigenic Fusarium solani in onion samples collected from different regions of Libya. Asian J. Biol. Sci. 2018; 11(4): 192–196. Publisher Full Text\n\nWang L, Chen W, Feng Y, et al.: Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One. 2011; 6: e28319. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWagner L, Stielow B, Hoffmann K: A comprehensive molecular phylogeny of the Mortierellales (Mortierellomycotina) based on nuclear ribosomal DNA. Persoonia. 2013; 30: 77–93. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWhite TJ, Bruns T, Lee S, et al.: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, et al., editors. PCR protocols: a guide to methods and applications. San Diego: Academic Press; 1990; 315–22.\n\nYu K-X, Norhisham SN, CH NG: Antimicrobial potential of Padina australis and Sargassum polycystum against respiratory infections causing bacteria. Int. J. Med. Tox. Legal Med. 2019; 22(1-2): 138–141."
}
|
[
{
"id": "93648",
"date": "17 Sep 2021",
"name": "Kavindra Kumar Kesari",
"expertise": [
"Reviewer Expertise Cell and cancer biology",
"plant biotechnology",
"industrial 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\nComments:\nJustification on the research work shown is manuscript is profound and significant since the research manuscript describes valuable information on Mortierella alpina novel strains isolated from Libya.\nStepwise flowsheet and methodology discuss the isolation, identification and molecular characterization of M. alpina strains from Al-Jabal Alakdar (Northeast of Libya).\nMortierella alpina strains are well known and documented for the potential of single cell oil production (SCO) at large scale. So, the conserved internal transcribed spacer regions amplification and assessment of genetic diversity carried out in this research work will give insight on future standard protocols and further work in this field for exploitation and production of arachidonic acid/poly-unsaturated fatty acids production. The novel strains sequences submitted in NCBI GenBank with specific barcode (barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) (accession no. MZ298831: MZ298835) and cultures preserved at Culture Collection Center of University.\nFurther research work in connection with single cell production can be done and set a benchmark for bioprospecting in future. The work was carried out by a PhD candidate and will facilitate the career growth for the candidate for future opportunities and prospects.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "93650",
"date": "02 Nov 2021",
"name": "Digpal Singh Gour",
"expertise": [
"Reviewer Expertise Genetics & Genomics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe research study documented four novel M. alpina strains to produce single cell oil and describes the isolation, identification, and molecular characterization of M. alpina strains from al-Jabal al-Akhḍar (Northeast of Libya) by standard protocols. The conserved internal transcribed spacer regions amplified, and assessment of genetic diversity carried out in this research work.\nThe novel strains sequences submitted in NCBI GenBank with specific barcodes (barcoded as MSU-101, MSU-201, MSU-401, and MSU-501) (accession no. MZ298831: MZ298835) were given.\nHowever, further research work in connection with single cell production can be done and set a benchmark for bioprospecting in the future. I hope in future the work will be carried out in this direction. As far as the present research study is concerned, the novel strains are described, organized, and documented, thus accepted for indexing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "93646",
"date": "02 Nov 2021",
"name": "Abhijeet Singh",
"expertise": [
"Reviewer Expertise Molecular Biology",
"Bionanotechnology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 study addresses and discusses the novel strains isolation, identification and genetic diversity assessment by standard protocols. The conserved internal transcribed spacer regions amplified and probably gives idea about the specific region in internal transcribed spacer for loci in terms of bioprospecting and exploitation of these novel strains for single soil production. The methodology discusses the isolation, identification and molecular characterization of M. alpina strains from Al-Jabal Alakdar (Northeast of Libya). The novel strains sequences submitted in NCBI GenBank with specific barcode (barcoded as MSU-101, MSU-201, MSU-401 and MSU-501) (accession no. MZ298831: MZ298835) and cultures preserved at Culture Collection Center of University. Thus, the research work is accepted and recommended for indexing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-895
|
https://f1000research.com/articles/10-533/v1
|
05 Jul 21
|
{
"type": "Research Article",
"title": "Isolation and characterization of a heavy metal- and antibiotic-tolerant novel bacterial strain from a contaminated culture plate of Chlamydomonas reinhardtii, a green micro-alga.",
"authors": [
"Mautusi Mitra",
"Kevin Manoap-Anh-Khoa Nguyen",
"Taylor Wayland Box",
"Taylor Lynne Berry",
"Megumi Fujita",
"Kevin Manoap-Anh-Khoa Nguyen",
"Taylor Wayland Box",
"Taylor Lynne Berry",
"Megumi Fujita"
],
"abstract": "Background: Chlamydomonas reinhardtii, a green micro-alga, is normally cultured in laboratories in Tris-Acetate Phosphate (TAP), a medium which contains acetate as the sole carbon source. Acetate in TAP can lead to occasional bacterial and fungal contamination. We isolated a yellow-pigmented bacterium from a Chlamydomonas TAP plate. It was named Clip185 based on the Chlamydomonas strain plate it was isolated from. In this article we present our work on the isolation, taxonomic identification and physiological and biochemical characterizations of Clip185. Methods: We measured sensitivities of Clip185 to five antibiotics and performed standard microbiological tests to characterize it. We partially sequenced the 16S rRNA gene of Clip185. We identified the yellow pigment of Clip185 by spectrophotometric analyses. We tested tolerance of Clip185 to six heavy metals by monitoring its growth on Lysogeny Broth (LB) media plates containing 0.5 mM -10 mM concentrations of six different heavy metals. Results: Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. It can ferment glucose, sucrose and mannitol. It is starch hydrolysis-positive. It is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. Clip185 produces a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with a commercial demand. Decaprenoxanthin production is induced in Clip185 under light. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Clip185 is able to tolerate toxic concentrations of six heavy metals. Conclusions: Our results show that Clip185 belongs to the genus Microbacterium. In the future, whole genome sequencing of Clip185 will clarify if Clip185 is a new Microbacterium species or a novel strain of Microbacterium binotii, and will reveal its genes involved in antibiotic-resistance, heavy-metal tolerance and regulation of decaprenoxanthin biosynthesis.",
"keywords": [
"Chlamydomonas",
"Microbacterium binotii",
"heavy metal tolerance",
"Clip185",
"bioremediation",
"antibiotic-resistant",
"Vancomycin-sensitivity",
"Decaprenoxanthin."
],
"content": "Introduction\n\nChlamydomonas reinhardtii is a green unicellular alga in the phylum Chlorophyta. It is an excellent experimental system to plant biologists, medical and bioenergy researchers.1–3 Chlamydomonas is normally cultured in the lab in Tris-Phosphate-Acetate (TAP), a medium which contains acetate as the sole carbon source.4 When cultured in TAP, Chlamydomonas can perform net biosynthesis of glucose from acetate in TAP via the glyoxylate/C2 cycle, without being strictly dependent on photosynthesis for carbon dioxide fixation.5 Many aerobic bacteria can also utilize the glyoxylate cycle to convert acetate to glucose.6,7 These aerobic bacteria are capable of growing in TAP. Hence occasionally, we get bacterial contamination on Chlamydomonas TAP plates.8,9\n\nThe research presented in this article originated from a high school student research project. This research project was centered on eradicating bacterial contamination from Chlamydomonas TAP plates. We observed a yellow-pigmented bacterial contamination on a Chlamydomonas strain TAP plate and isolated the bacterium from the contaminated plate. We named this bacterium Clip185 after the Chlamydomonas Library Project (CLiP) strain it contaminated. The primary goal of the high school student project was to identify a specific antibiotic and its right concentration that will eliminate Clip185 contamination, without affecting Chlamydomonas growth on TAP media plates. This high school microbiology research project was further extended by two undergraduates from the University of West Georgia, to characterize Clip185 on biochemical and physiological levels and determine the genus identity of Clip185.\n\nClip185 is highly sensitive to vancomycin but is resistant to other microbial cytoplasmic membrane- or translation- disrupting antibiotics. In addition to testing antibiotic-sensitivity of Clip185, we performed several growth analyses and basic microbiological tests to characterize Clip185. It grows better in a Lysogeny Broth (LB) medium than in a TAP medium. Clip185 is an aerobic, mesophilic, alpha-hemolytic, starch hydrolysis-positive, gram-positive bacillus. Clip185 can ferment glucose and sucrose but not lactose. It is a slow fermenter of mannitol compared to Staphylococcus aureus, when grown on Mannitol Salt Agar (MSA).\n\nWe partially amplified and sequenced the 16S rRNA gene of Clip185. In 2019, NCBI Basic Local Alignment Search Tool (NCBI-BLAST) analyses of the partial 16S rRNA gene sequence of Clip185 showed 99.10% sequence identity to that of the 16S rRNA gene of Microbacterium binotii strain PK1-12M (Accession #: MN428150.1). In November 2019, we submitted the partial 16S rRNA gene sequence of Clip185 to the NCBI GenBank (Accession #: MN633284.1). In early 2021, BLAST analyses showed that the best match to the partial 16S rRNA gene sequence of Clip185 is that of Microbacterium sp. strain MDP6 (Accession #: MK128451.1) with 99.33% sequence identity.\n\nThe genus Microbacterium belongs to the family Microbacteriaceae in the order of Actinomycetales and suborder Micrococcineae.10 Microbacterium was first described by Orla-Jensen in 1919.11 In 1983, Collins et al.12 rectified the description of the genus Microbacterium. In 1998, Takeuchi & Hatano13 fused the closely related genera Microbacterium and Aureobacterium into the single genus Microbacterium. Members of the genus Microbacterium have been isolated from diverse environmental sources including soil, water, plants insects, clinical specimens, heavy-metal contaminated sites, deep-sea sediments, dairy products etc.10,14 Members of the phylum Actinobacteria produce several secondary metabolites like siderophores, antibiotics, and terpenoid pigments that have diverse biological functions, ranging from light absorption, protection against oxidative stress to conferring membrane stability.15\n\nClip185 is a yellow-pigmented bacterium. Spectrophotometric analyses of the extracted yellow pigment of Clip185 showed that it is a ε-cyclic C50 carotenoid, decaprenoxanthin. C50 carotenoids are predominantly found in gram-positive Actinomycetales members.16–18 In many Actinobacteria, decaprenoxanthin biosynthesis is not light-regulated, but in some Actinobacteria decaprenoxanthin biosynthesis is strictly induced under light.19 Light induces decaprenoxanthin biosynthesis in Clip185 like it does in the actinobacterium Corynebacterium glutamicum,19 but the induction is weaker than that in C. glutamicum.\n\nThere are several reports of Microbacterium sp. thriving in heavy metal-contaminated environments,15,20,21 reducing heavy metals like hexavalent chromium (Cr6+)22–24 and showing the ability to alter the mobility of heavy metals in contaminated soils.25,26 We tested for Clip185 tolerance of heavy metal stress induced by toxic concentrations of six heavy metals namely zinc (Zn), copper (Cu2+), cadmium (Cd), cobalt (Co2+), nickel (Ni2+) and, hexavalent chromium (Cr6+). Clip185 could grow in the presence of 6 mM chromium, 2 mM of nickel, cadmium and zinc and 0.5 mM of copper and cobalt in the LB medium. We will have funding in fall 2021 for whole genome sequencing of Clip185 using the PacBio sequel technology.\n\nWhole genome sequencing data analyses will not only help us to identify genes in Clip185 that are responsible for antibiotic-resistance, metal tolerance/detoxification and C50 carotenoid production, but will also help to clarify whether Clip185 is a new Microbacterium sp. or a new environmental strain of Microbacterium binotii. In this article, we present our research on the isolation of Clip185 and its physiological and biochemical characterizations.\n\n\nMethods\n\nChlamydomonas wild type strain 4A+ (CC-4051 4A+ mt+) was cultured in the lab on TAP agar (Chlamydomonas Resource Center) under dim light (15-20 μmol m-2s-1) at 22°C. TAP medium recipes are described in Mitra et al., 2020.9 4A+ liquid TAP cultures were grown on a shaker under low light (70-80 μmol m-2s-1) for 3 days for aeration as described in Mitra et al, 2020.8,9 Clip185 stock was maintained in the lab under dim light (15-30 μmol m-2s-1) at 22°C on Lysogeny Broth (LB) agar medium (Cold Spring Harbor Protocols). Experiment-specific temperature and light intensities can be found in the result section of this article under specific experiment descriptions. Clip185 liquid cultures were grown in LB on a shaker at 30°C-37°C for aeration. Light from 1-2 cool white fluorescent lights were used in experiments. A LI-250A light meter (LI-COR, Inc., Lincoln, NE) was used to measure light intensities.\n\nWe tested the following antibiotics: penicillin; neomycin, chloramphenicol, polymyxin B and vancomycin. Antibiotics were purchased from Sigma-Aldrich (St. Louis, MO). Two different amounts (50 μg and 100 μg) of each of these five antibiotics were tested using the Kirby-Bauer (KB) disc diffusion antibiotic susceptibility tests as described in the American Society for Microbiology (ASM) protocol with one modification: we used TAP agar medium instead of Mueller-Hinton agar medium as stated in the ASM. KB tests of 4A+ and Clip185 were performed on TAP-agar plates as described in Mitra et al., 2020.9,27,28 A 12-hours old LB liquid culture of Clip185 was used for plating on the antibiotic-containing TAP plates. Antibiotic plates were incubated at 22°C. Clip185 and Chlamydomonas plates were imaged after 7 days of incubation. Diameters of zones of inhibitions were measured in Microsoft PowerPoint by importing free Google ruler available on Chrome. Means and standard deviations were calculated using Microsoft Excel. Microsoft Excels’ t-Test: Paired Two Sample for Means tool in the analysis ToolPak was used for statistical analyses of the data, using three biological replicates per experiment (each with three internal replicates). To test the efficacy of vancomycin as a potent antibiotic in eradicating Clip185 contamination on Chlamydomonas TAP plates, Clip185 and 4A+ strains were jointly streaked on TAP media plates containing 50 μg/mL of vancomycin. Streaked TAP + vancomycin plates were imaged after incubation at 22°C for 2.5 weeks.\n\nGrowth at different temperatures: Clip185 was streaked on LB agar and TAP agar prepared at our laboratory and media plates were incubated at 22°C and 37°C. LB-agar and TAP agar culture plates were imaged after 3 days and 7 days of growth, respectively.\n\nGrowth assays on Tryptic Soy Blood Agar (TSBA): Clip185 and an Acidovorax sp.9 were streaked on TSBA plates, purchased from Carolina Biological (Burlington, NC). Plates were incubated at 37°C and were imaged after 3 days of growth. Hemolysis classifications were assigned according to the information stated in the ASM protocol.\n\nGrowth assays on Mannitol Salt Agar (MSA): MSA plates purchased from Carolina Biological (Burlington, NC). Clip185 and Staphylococcus aureus (a mannitol fermenter which produces acid, used here as positive control) were streaked on MSA plates, and the plates were incubated at 22°C. The Clip185 MSA plate was imaged after 3-6 days of growth. After 3 days of growth, the S. aureus plate was imaged.\n\nGrowth assays on Tris-Phosphate (TP)-phenol red-sugar-agar medium: TP is the TAP medium without acetate (https://doi.org/10.17504/protocols.io.bgzujx6w).9 Clip185 was streaked on TP-phenol red-agar medium (pH of 7.2) containing three different sugars as stated under the result section, and the plates were incubated at 22°C. Culture plates were imaged after 7 days of growth. Results were interpreted as described in Mitra et al., 2020.9\n\nComparative growth assays on Potato Dextrose Agar (PDA) and Mueller-Hinton-Agar (MHA): Clip185 was streaked on PDA and MHA plates and incubated at 30°C for three days. The plates were imaged after three days of growth. The PDA and MHA plates were purchased from Carolina Biological (Burlington, NC).\n\nTesting Light-regulation of decaprenoxanthin production: Clip185, Corynebacterium glutamicum strain ATCC13032 and Kocuria rhizophila were streaked on two LB media plates per strain. For each strain, one plate was kept under dim light (20-25 μmol m-2s-1) and the other was kept in the dark at 22°C for five days. Culture plates were imaged after 5 days of growth.\n\nGrowth assays on LB media containing heavy metals: LB media containing the following concentrations of metal salts were prepared: a) 0.5 mM, 1 mM and 2 mM of cadmium chloride; b) 0.5 mM and 1 mM of cobalt (Co2+) chloride; c) 0.5 mM, 1 mM and 2 mM zinc sulfate heptahydrate; d) 0.5 mM and 1 mM of cupric sulfate pentahydrate; e) 1 mM, 2 mM and 4 mM of nickel (Ni2+) bromide and; f) 2 mM, 4 mM, 6 mM and 10 mM of chromium (Cr6+) standard solution. Cobalt chloride and cadmium chloride salts were purchased from Strem Chemicals (Newburyport, MA). Nickel bromide salt was purchased from Acros organics (Fair Lawn, NJ). Cupric sulfate pentahydrate salt and the chromium (Cr6+) standard solution were purchased from Fisher Scientific (Thermo Fisher Scientific, Waltham, MA). A sterile wooden applicator was lightly tapped over Clip185 growth on a 2-3 days old Clip185 LB-agar plate to collect approximately the same amounts of cells for each experiment. This wooden applicator was used for streaking cells on the respective LB metal plates. The LB metal plates were imaged after a specific period of growth labeled on the figures and also stated in figure legends (Figures 14-19). As a control, Clip185 was streaked on a LB plate and the plate was imaged after 8 days and 28 days of growth. All plates were incubated under 15-20 μmol m-2s-1 light intensity. Three replicates per metal concentration were used in this experiment.\n\nGram staining: Gram staining of Clip185 was performed using commercial Gram stain reagents (VWR, Radnor, PA). Gram-stained Clip185 cells were imaged under an oil immersion lens using a Samsung Galaxy S5 camera and a cell phone adapter for the microscope eyepiece.\n\nCytochrome c oxidase test: Oxidase test was performed as described in Mitra et al., 20208,9 using Difco DrySlide Oxidase Disposable Slide purchased from Carolina Biological (Burlington, NC).\n\nStarch hydrolysis test: Starch hydrolysis test was performed as described in Mitra et al., 20208,9 using commercial Mueller-Hinton-agar (MHA) medium plates (Carolina Biological, Burlington, NC). Clip185 and Bacillus subtilis were streaked on MHA medium plates and incubated for 3 days at 30°C. After 3 days of growth, starch hydrolysis tests were performed. MHA plates were imaged before and after the starch hydrolysis tests.\n\nClip185, C. glutamicum and K. rhizophila strains were grown under a light intensity of 15-20 μmol m-2s-1. Cells of these three strains were treated with 5 mL of 100% methanol for carotenoid extraction. Pigment extraction was carried out in the dark for 6 hours at 22°C. Extracted pigments were processed as described in Mitra et al., 2020.8 Spectrophotometric wavelength (400 nm – 600 nm) scan analyses of extracted pigments were performed using a Beckman Coulter DU 730 Life science UV/Vis spectrophotometer (Brea, CA). Three maximum absorption peaks of decaprenoxanthin were monitored at 413 nm, 437 nm and 467 nm, as described for decaprenoxanthin and its glucosides in the literature.29–31 C. glutamicum and K. rhizophila were used as positive controls in spectrophotometric analyses. Three replicates per strain were used in this experiment.\n\nIsolation of Clip185 genomic DNA and DNA concentration and purity checking of the isolated genomic DNA were performed as described in Mitra et al., 2020.8,9 Forward and reverse 16S rRNA PCR primer sequences can be found in Mitra et al., 20208,9 and in Klindworth et al., 2013.32 PCR was performed as described in Mitra et al., 20208,9 with an extension time of 1 minute.\n\nThe PCR-amplified partial 16S rRNA Clip185 genomic product (product size approximately 445 bp) was purified from the agarose gel and cloned in pCR4-TOPO TA vector as described in Mitra et al., 2020.8,9 One clone containing the Clip185 partial 16S rRNA gene was sequenced at the UC Berkeley DNA Sequencing Facility. Analyses of DNA sequences were performed using the Chromas Lite (Technelysium) and BLAST programs.\n\nA Samsung Galaxy S5 cell phone camera was used for imaging all culture plates. Image cropping and adjustments were made using the Photos app in Windows 10 and Adobe Photoshop version 22.3. Visualization and imaging of ethidium bromide -stained DNA gels were performed using a Bio-Rad Molecular Imager Gel Doc XR+ (Bio-Rad, Hercules, CA).\n\n\nResults\n\nWe isolated a yellow-pigmented bacterium from a contaminated TAP media plate of the Chlamydomonas strain, CLiP strain LMJ.RY0402.18514 (Figure 1A). We purified the bacterium from the contaminated Chlamydomonas culture plate using the streak plate method. We picked twenty-one single colonies from Clip185 streaked-LB plate and transferred them to a fresh LB agar plate using a numbered grid (Underlying data33). Colony # 37 was selected for further studies (Underlying data33). We maintained colony # 37 stock on LB agar at 22°C under 15-25 μmol m-2s-1 light intensity (Figure 1B). We named this bacterium Clip185 after the Chlamydomonas Library Project (CLiP) and the first three numerical digits in the second part of the name of the Chlamydomonas CLiP strain LMJ.RY0402.185141 it contaminated. We have deposited the Clip185 strain to the ARS Culture Collection (NRRL Accession number: B-65609).\n\n(A) Tris-Acetate-Phosphate (TAP)-agar medium plate showing bacterial contamination of a Chlamydomonas strain at room temperature (22°C). (B) LB-agar medium plate of purified Clip185 strain. Culture plate shown in (B) was imaged after 5 days of growth at 22°C under 20-25 μmol m-2s-1 light intensity.\n\nWe monitored relative antibiotic-sensitivities of Clip185 and Chlamydomonas 4A+ wild type strain using KB disc diffusion tests as described in Mitra et al. 2020.8,9 In our experiments we used two different amounts (50 μg and 100 μg) of penicillin, chloramphenicol, neomycin, polymyxin B and vancomycin. The mean diameters of zones of growth inhibitions for each antibiotic amount with respective standard deviations are shown in Table 1. For detailed statistical analyses of the data from three biological replicates (each of which had three internal replicates) please refer to our underlying data.34\n\nZones of growth inhibitions in the presence of five different antibiotics (Penicillin, Chloramphenicol, Neomycin, Polymyxin B and Vancomycin) were studied for Chlamydomonas reinhardtii and the bacterial strain, Clip185. Grey and white rows represent 50 μg and 100 μg of each antibiotics applied on the filter paper discs, respectively. Three biological replicates (each had three internal replicates) were used to calculate means and standard deviations shown in the table. Statistical analyses are available as Underlying data.34\n\nClip185 and Chlamydomonas were both resistant to penicillin and chloramphenicol for both amounts (50 μg and 100 μg) as no zones of growth inhibitions were observed (Table 1; Underlying data34). Chlamydomonas and Clip185 were sensitive and resistant to 50 μg polymyxin B (420.15 IU), respectively (Table 1, Underlying data34). Both Chlamydomonas and Clip185 were sensitive to the 100 μg (840.3 IU) polymyxin B (Table 1, Underlying data34). P- values from the 1-tailed and 2-tailed hypothesis tests for sensitivity to 100 μg dose of polymyxin B were 3% and 7%, respectively. It is known that if the diameter of the zone of growth inhibition is more than 12 mm with the application of 300 IU of polymyxin B in a KB test, then a bacterium is sensitive to polymyxin B.35 We used polymyxin B amounts that were 1.4-fold to 2.8-fold higher than what is used for KB tests, and growth inhibition zones of Chlamydomonas and Clip185 were less than 13 mm (Table 1). Hence, both Chlamydomonas and Clip185 are resistant to polymyxin B (Table 1, Underlying data34).\n\nChlamydomonas was slightly less sensitive to 50 μg (38.75 IU) neomycin than Clip185 (Table 1). P value from the 1-tailed hypothesis test was statistically significant (3%) but the P value from the 2-tailed hypothesis test was not statistically significant for 50 μg neomycin (Underlying data34). Clip185 was more sensitive to 100 μg neomycin (77.5 IU) than Chlamydomonas and, the data was statistically significant (Table 1, Underlying data34). It is known that if the diameter of the growth inhibition zone is more than 16 mm, then a bacterium is sensitive to 30 μg neomycin in a KB test. We used neomycin amounts that were 1.7-fold to 3.3-fold higher than what is used for KB tests (Table 1), and growth inhibition zones of Chlamydomonas and Clip185 were less than 16 mm. Hence Chlamydomonas and Clip185 are resistant to neomycin (Table 1, Underlying data34). Clip185 was highly sensitive to both 50 μg (50.35 IU) and 100 μg (100.7 IU) vancomycin while Chlamydomonas was resistant to vancomycin as it did not show any zones of growth inhibitions (Table 1, Underlying data34). In summary, our KB test results show that vancomycin is the best drug to minimize Clip185 contamination on TAP agar.\n\nNext, we streaked Chlamydomonas and bacterium Clip185 together on TAP agar plates containing 50 μg of vancomycin per mL of the TAP medium and incubated the plates at room temperature for a period of 2.5 weeks (Figure 2). Clip185 did not grow on the TAP plate containing 50 μg/mL of vancomycin but Chlamydomonas did (Figure 2). Hence vancomycin at a concentration of 50 μg/mL in the TAP medium is sufficient to inhibit the growth of Clip185 on Chlamydomonas culture plates without hindering algal growth.\n\nChlamydomonas wild type 4A+ and Clip185 strains were streaked on TAP-agar plate containing 50 μg of Vancomycin/mL of medium. TAP-agar antibiotic plate was incubated at room temperature (22°C) for 2.5 weeks before it was imaged.\n\nGram staining revealed that Clip185 is a gram-positive small bacillus. Cells were small rods, and often two rods were joined to each other (Figure 3).\n\nClip185 cells from a three days-old LB-agar medium culture plate were used for gram-staining. Gram-stained cells were visualized under an oil immersion lens of a bright-field microscope and imaged with a smart phone camera.\n\nClip185 grew well on LB at 22°C as well at 37°C on LB-agar (Figure 4A-B). It grew slowly on TAP-agar at 22°C and 37°C (Figure 4C-D). Hence, Clip185 is a mesophile.\n\n(A) Growth on LB-agar medium plate at room temperature (22°C). (B) Growth on LB-agar medium plate at 37°C. (C) Growth on TAP-agar medium plate at 22°C. (D) Growth on TAP-agar medium plate at 37°C. LB-agar culture plates were imaged after 3 days of growth. TAP-agar culture plates were imaged after 7 days of growth.\n\nClip185 could partially lyse red blood cells when grown on tryptic soy blood agar plates for three days at 30°C, as evident from the greenish discoloration around the Clip185 growth (Figure 5A).\n\n(A) 72 hours-growth of Clip185 on tryptic soy-blood agar plate. (B) 72 hours-growth of a gamma-hemolytic Acidovorax sp. on tryptic soy-blood agar plate. Media plates were incubated at 37°C.\n\nWe used a gamma-hemolytic strain of Acidovorax as a control in this experiment (Figure 5B). There was no trace of hemolysis around the growth of Acidovorax9 on the tryptic soy agar plate (Figure 5B).\n\nWe conducted oxidase test on Clip 185 and a gram-negative bacterium Sphingobium yanoikuyae. Our oxidase test results showed that S. yanoikuyae is oxidase-positive (Figure 6; left) and Clip185 is oxidase-negative (Figure 6; right). Results were interpreted as stated under the method section of this article.8,9 Hence Clip185 does not produce cytochrome c oxidase, an enzyme involved in the electron transport chain in bacterial respiration.\n\nCells of Sphingobium yanoikuyae (on the left) and Clip185 (on the right) streaked on a disposable slide containing a film coated with oxidase reagent (tetramethyl-p-phenylenediamine dihydrochloride). Image of the slide was taken after 10 seconds of the application of the cells on the slide.\n\nWe did not want to use LB medium to test the ability of Clip185 to utilize other sugars as carbon source, because excess amino acids present in the nutrient-rich LB medium are converted to glucose via gluconeogenesis. TP agar medium is the TAP medium minus acetate. Hence TP medium lacks a carbon source.8,9 We supplemented TP medium (pH 7.2) separately with three different sugars (glucose, sucrose and lactose) and the pH indicator, phenol red. (Figure 7). We grew Clip185 on these neutral TP + sugar plates. Figure 7A, C and E represent control TP + 1% glucose, TP + 1% sucrose and TP + 1% lactose plates (without Clip185), respectively. These control plates show the light reddish color of phenol red when the pH is 7.2. Clip185 grew on TP + 1% glucose and TP +1% sucrose plates and fermented the respective sugars (Figure 7B; Figure 7D) but it did not grow on TP + 1% lactose plate (Figure 7F). Fermentation of glucose and sucrose produced acids which decreased the pH in the TP medium. With the decrease in pH, phenol red’s light red color changed to a yellow color (Figure 7B; Figure 7D).\n\n(A) Control TP + 1% glucose agar medium plate with phenol red as a pH indicator. (B) Clip185 on TP +1% glucose agar medium plate with phenol red as a pH indicator. (C) Control TP +1% sucrose agar medium plate with phenol red as a pH indicator. (D) Clip185 growth on TP +1% sucrose agar medium plate with phenol red as a pH indicator. (E) Control TP +1% lactose agar medium plate with phenol red as a pH indicator. (F) Clip185 growth on TP +1% lactose agar medium plate with phenol red as a pH indicator. Culture plates were imaged after 7 days of growth at room temperature.\n\nClip185 grew on MSA (Figure 8A-B) and fermented mannitol in MSA to acid slowly compared to the fast mannitol fermentation displayed by the gram-positive bacterium. Staphylococcus aureus (Figure 8C). Acid production decreased the pH of MSA. With the decrease in pH, phenol red’s light red color changed to a yellow color (Figure 8).\n\n(A) 3 days-growth of Clip185 on MSA plate. (B) 6 days-growth of Clip185 on MSA plate. (C) 3 days-growth of Staphylococcus aureus on MSA plate. Media plates were incubated at 30°C.\n\nStarch has two forms: linear amylose and branched amylopectin. The large sizes of amylose and amylopectin prevent these chemicals from being transported across the bacterial cell wall. Bacteria secrete out the α-amylase and oligo-1,6-glucosidase enzymes to degrade starch. These enzymes degrade extracellular starch into glucose/dextran which can be utilized by bacteria as carbon sources. A starch hydrolysis test is used to identify bacteria that can utilize extracellular starch as a carbon/energy source. Traditionally, potato dextrose agar (PDA) is used for starch hydrolysis tests. Clip185 did not grow well on PDA (Underlying data36). It grew well on Mueller-Hinton Agar (MHA), which is a rich medium used for growing bacteria that have special nutritional requirements (fastidious bacteria) (Underlying data36). Hence, we chose MHA, which contains 0.15 % starch, to test Clip185’s ability to hydrolyze starch.\n\nWe used Bacillus subtilis, which is known to hydrolyze starch, as a positive control in the experiment. We grew both Clip185 and B. subtilis on MHA for 3 days and imaged the plates (Figure 9A; Figure 9C). Gram iodine was then added to the both Clip185 and B. subtilis plates. Iodine reacted with the starch in MHA to produce a light blue color. Both Clip185 (Figure 9B) and B. subtilis (Figure 9D) tested positive in the starch hydrolysis test as there is a visible clear zone surrounding the growth of each of these two strains on the MHA due to the hydrolysis of starch.\n\n(A) 3 days -growth of Clip185 at 30°C on Mueller-Hinton medium which contains 0.15% starch. (B) Clip185 Mueller-Hinton plate shown in (A) was treated with Gram iodine. (C) 3 days-growth of Bacillus subtilis at 30°C on Mueller-Hinton medium which contains 0.15% starch. (D) B. subtilis Mueller-Hinton plate shown in (C) treated with Gram iodine.\n\nThe 16S rRNA gene has nine hypervariable (V1-V9) and nine conserved regions (C1-C9).37–39 We used the Escherichia coli 16S rRNA gene which is 1541 bp long (Figure 10A), as a reference in the 16S rRNA gene schematics in Figure 10. A total of 11 nucleotides (788-798) located within the C4 conserved region are completely conserved in bacteria.40 The 11 bp super-conserved region is represented by the black box within the C4 region in the schematics (Figure 10). The forward and reverse 16S rRNA gene-specific PCR primers are represented by black arrows in the 16S rRNA gene schematics (Figure 10A). A 445 bp amplicon was generated upon PCR amplification of the partial 16S rRNA gene of Clip185 (Underlying data41). This 445 bp amplicon was cloned. A clone harboring the Clip185 amplicon was then sequenced to determine the taxonomic identity of Clip185.\n\n(A) A schematic diagram showing the nine conserved and hypervariable regions in the 16S rRNA gene. The interspersed conserved regions (C1– C9) are shown in dark gray, and the hypervariable regions (V1–V9) are depicted in white. The black box within the C4 region represents 11 nucleotides (788-798 base pairs) that are invariant in bacteria.8,9 Thick black arrows denote 16S rRNA gene-specific forward and reverse PCR primers in the C2 region and in the C4 region, respectively. The gene diagram is based on the 16S rRNA gene sequence of E. coli. See also Underlying data.41 (B) A schematic diagram showing the nucleotide changes in Clip185 in the 16S rRNA region spanning the C2 and C4 regions in comparison to the best NCBI- BLAST hit in 2019 (score of 800; E-value 0 and percent identity of 99.10%): Microbacterium binotii strain PK1-12M 16S ribosomal RNA gene, partial sequence (GenBank Accession #: MN428150.1). (C) A schematic diagram showing the nucleotide changes in Clip185 in the 16S rRNA region spanning the C2 and C4 regions in comparison to the best NCBI- BLAST hit in 2021 (score of 806; E-value 0 and percent identity of 99.33%): Microbacterium sp. strain MDP6 16S ribosomal RNA gene, partial sequence (GenBank Accession #: MK128451.1). Black nucleotides show the native nucleotides in the BLAST hits Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6 that were substituted by the depicted red nucleotides in Clip185 16S rRNA gene sequence. The black bold numbers within the parenthesis beside the nucleotides show the specific nucleotide positions where the nucleotide changes have occurred. Nucleotide positions shown in the figures have been assigned according to that of the 16S rRNA gene sequence of E. coli.\n\nIn 2019, NCBI-nucleotide BLAST analyses detected Microbacterium binotii strain PK1-12M (GenBank Accession #: MN428150.1) as the nearest match to Clip185 based on the partial 16S ribosomal RNA gene sequence, with a score of 800, an E-value of 0 and percent identity of 99.10%. Four nucleotide substitutions were identified in Clip185’s 16S rRNA partial gene sequence relative to that in Microbacterium binotii strain PK1-12M (Figure 10B). In the C4 region, one transition and one transversion were detected (Figure 10B). We found one transition in the C2 region and one transversion in the 11 bp super-conserved sub-region within C4 region (Figure 10B). We deposited this partial 16S rRNA gene sequence of Clip185 in NCBI GenBank with the description: Microbacterium binotii strain PK1-12M variant 16S ribosomal RNA gene, partial sequence (Accession number: MN633284.1). In early 2021, BLAST analyses detected a new match: Microbacterium sp. strain MDP6. (Accession #: MK128451.1) with a score of 806, E-value of 0 and percent identity of 99.33%) (NCBI last accessed 6-18-21, Figure 10C). We detected three nucleotide changes in the 16S rRNA gene of Clip185 with respect to this new hit: one transition in the C2 region, one transversion in the 11 bp super-conserved sub-region within C4 region and one deletion in the C4 region (Figure 10C). Analyses of available genome sequences of Microbacterium sp. on NCBI revealed that whole genome sequences for Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6 are not available (NCBI data last accessed on 6-18-2021).\n\nCarotenoids are synthesized from the precursor isopentenyl pyrophosphate and its isomer dimethylallyl pyrophosphate in the terpenoid biosynthetic pathway16 (Figure 11). Two molecules of geranylgeranyl diphosphate condense to form phytoene (Figure 11). Lycopene (a red C40 carotenoid) is formed by the four-step enzymatic desaturation of phytoene (Figure 11). Lycopene is diprenylated and hydroxylated to form C50 carotenoids16,17 (Figure 11). To date, three different C50 carotenoid biosynthetic pathways are known in the literature: 1) the ε-cyclic C50 carotenoid decaprenoxanthin biosynthetic pathway in Corynebacterium glutamicum;16,42,43 2) the β-cyclic C50 carotenoid C.p.450 biosynthetic pathway in Dietzia sp. CQ444 and; 3) the γ-cyclic C50 carotenoid sarcinaxanthin biosynthetic pathway in Micrococcus luteus NCTC2665.18 Microbacterium belongs to the gram-positive order of Actinomycetales. Many members of Actinomycetales produce the C50 carotenoid, decaprenoxanthin.16\n\nC40 carotenoid lycopene is diprenylated to form an acyclic C50 carotenoid, flavuxanthin. Flavuxanthin undergoes cyclization in three different ways to form three types of natural C50 carotenoids in bacteria. Substrates and intermediate products names are abbreviated and are shown in black. Genes encoding enzymes catalyzing specific reactions/steps in the pathways are shown in blue. Abbreviations: IPP, isopentenyl pyrophosphate; DMPP, dimethylallyl pyrophosphate; GPP, geranyl pyrophosphate; FPP, farensyl pyrophosphate; GGPP, geranylgeranyl pyrophosphate; C.p. 496, 2,2′-Bis-(3-methylbut-2-enyl)-3,4,3′,4′-tetradehydro-1,2,1′,2′-tetrahydro-ψ, ψ-carotene-1, 1-diol; C.p.450, 2,2′-Bis-(4-hydroxy-3- methybut-2-enyl)-β, β-carotene. Superscripted numbers: 1 denotes lbtC in the lbtBC fused gene; 2 denotes lbtA and lbtB in the lbtBC fused gene; 3 denotes Micrococcus luteus gene; 4 denotes Corynebacterium glutamicum genes and 5 denotes Dietzia sp. CQ4 genes.\n\nSince our 16S rRNA partial gene sequencing showed that Clip185 is a Microbacterium sp. we extracted the yellow pigment from Clip185 (Figure 12A; Figure 12C) and performed spectrophotometric analyses to determine whether Clip185 produces decaprenoxanthin (Figure 12). As actinobacteria C. glutamicum and Kocuria rhizophila are known to produce decaprenoxanthin,16,29 we used extracted pigments from these two bacterial strains (Figure 12A; Figure 12C) as positive controls in the spectrophotometric assays (Figure 12).\n\n(A) Falcon tubes containing methanol-extracted pigments of Corynebacterium glutamicum (X) and Clip185 (Y). (B) Absorption spectra of extracted pigments C. glutamicum (X, dark blue spectrum) and Clip185 (Y, pale blue spectrum). (C) Falcon tubes containing methanol-extracted pigments of Kocuria rhizophila (Z) and Clip185 (Y). (D) Absorption spectra of extracted pigments K. rhizophila (Z, dark blue spectrum) and Clip185 (Y, pale blue spectrum). Three major absorption peaks of decaprenoxanthin are labeled.\n\nWe found that the C. glutamicum (X spectrum in Figure 12B) and K. rhizophila (Z spectrum in Figure 12D) pigment absorption spectra exhibited three major absorption peaks that are representative of decaprenoxanthin absorption at 413 nm, 437 nm and 467 nm as described in the literature.29–31 These three absorption peaks from C. glutamicum absorption spectrum X and K. rhizophila absorption spectrum Z very nicely overlaid against the three absorption peaks from the Clip185 absorption spectrum (Y spectrum in Figure 12B and Figure 12D). This result very strongly indicates the presence of decaprenoxanthin in Clip185. We could not perform HPLC and/or LC/MS analyses as we do not have access to such analytical tools at our institution.\n\nIt is known that in non-phototrophic bacteria, biosynthesis of C50 carotenoids can be modulated by growth conditions (e.g. presence/absence of light).15,45,46 We studied the production of decaprenoxanthin in Clip185, C. glutamicum and K. rhizophila under dim light (20-25 μmol m-2s-1). In dark conditions, Clip185 appears cream color with a light yellowish tinge (Figure 13A, left). Decaprenoxanthin production in Clip185 was induced under light (Figure 13A, right). Decaprenoxanthin production is strongly induced under light in C. glutamicum as stated in published literature19 in contrast to that in Clip185 (Figure 13A; Figure 13B). K. rhizophila produces decaprenoxanthin constitutively irrespective of light conditions (Figure 13C).\n\n(A) Decaprenoxanthin production in Clip185 under darkness and light. (B) Decaprenoxanthin production in C. glutamicum under darkness and light. (C) Decaprenoxanthin production in K. rhizophila under darkness and light. Bacterial culture plates were exposed to darkness or light for 5 days at 22°C and then imaged. Light intensity was 20-25 μmol m-2s-1.\n\nSince Microbacterium sp. has been isolated from heavy metal-contaminated environments,15 we decided to test whether Clip185 could tolerate toxic concentrations (ranging from 0.5 mM - 6 mM) of six different heavy metals: cadmium, cobalt (Co2+), zinc, copper (Cu2+), nickel (Ni2+) and chromium [Cr6+] (Figures 14-19). Clip185 can grow well with yellow pigmentation on 0.5 mM of cadmium plate (Figure 14A) but grows slowly on 1 mM cadmium plate and retains pigment production (Figure 14B). Clip185 slowly grows on 2 mM cadmium plate, but over time stops growing and is white in color (Figure 14C; Figure 14D). Growth of Clip185 for 8 days and 28 days on LB plate are shown for comparisons (Figure 14E). Clip185 grew well with yellow pigmentation on 0.5 mM cobalt plate (Figure 15A) but failed to grow on 1 mM cobalt plate (Figure 15B). Clip185 grew well with yellow pigmentation on 0.5 mM and 1 mM zinc plates (Figure 16A-B) but grew very slowly on 2 mM zinc plate (Figure 16C). Clip185 grew well with yellow pigmentation on 0.5 mM copper plate (Figure 17A) but failed to grow on 1 mM copper plate (Figure 17B). Clip185 grew well with yellow pigmentation on 1 mM and 2 mM nickel plates (Figure 18A-B) but failed to grow on 4 mM nickel plate (Figure 18C). Clip185 could grow well with yellow pigmentation on 2 mM and 4 mM chromium plate (Figure 19A-D) but grew extremely slowly with yellow pigmentation on 6 mM chromium plate (Fig 19E-H). Clip185 failed to grow on 10 mM of chromium plate after 90 days of incubation (Underlying data47).\n\n(A) 8 days-growth of Clip185 on LB media containing 0.5 mM Cadmium. (B) 8 days (left) and 28 days (right)-growth of Clip185 on LB media containing 1 mM Cadmium. (C) 8 days-growth of Clip185 on LB media containing 2 mM Cadmium. (D) 45 days-growth of Clip185 on LB media containing 2 mM Cadmium. (E) 8 days (left) and 28 days (right)-growth of Clip185 on LB media (control). Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1.\n\n(A) 8 days-growth of Clip185 on LB media containing 0.5 mM Cobalt. (B) 8 days (left) and 28 days (right)-growth of Clip185 on LB media containing 1 mM Cobalt. Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1.\n\n(A) 8 days-growth of Clip185 on LB media containing 0.5 mM Zinc. (B) 8 days-growth of Clip185 on LB media containing 1 mM Zinc. (C) 8 days (left) and 28 days (right)-growth of Clip185 on LB media containing 2 mM Zinc. Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1. Light intensity was 10-15 μmol m-2s-1.\n\n(A) 8 days-growth of Clip185 on LB media containing 0.5 mM Copper. (B) 8 days (left) and 28 days (right)-growth of Clip185 on LB media containing 1 mM Copper. Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1.\n\n(A) 8 days-growth of Clip185 on LB media containing 1 mM Nickel. (B) 8 days-growth of Clip185 on LB media containing 2 mM Nickel. (C) 8 days (left) and 28 days (right)-growth of Clip185 on LB media containing 4 mM Nickel. Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1.\n\n(A) 8 days-growth of Clip185 on LB media containing 2 mM Cr6+. (B) 28 days-growth of Clip185 on LB media containing 2 mM Cr6+. (C) 8 days-growth of Clip185 on LB media containing 4 mM Cr6+. (D) 28 days-growth of Clip185 on LB media containing 4 mM Cr6+. (E) 8 days-growth of Clip185 on LB media containing 6 mM Cr6+. (F) 28 days-growth of Clip185 on LB media containing 6 mM Cr6+. (G) 67 days-growth of Clip185 on LB media containing 6 mM Cr6+. (H) 90 days-growth of Clip185 on LB media containing 6 mM Cr6+. Number of days of growth are labeled on the figures. Light intensity was 10-15 μmol m-2s-1. See also Underlying data.47\n\n\nDiscussion\n\nOur biochemical and physiological analyses of Clip185 and its partial 16S rRNA gene sequencing have shown that Clip185 belongs to the Microbacterium taxon. Microbacterium belongs to the class Actinobacteria. Actinobacteria are mainly aerobic, gram-positive bacteria with a high G + C content and B-type cross linkages in peptidoglycan.48,49 As of 06-18-21, 122 species of Microbacterium have been identified with a validly published name. Microbacterium species have been isolated from a diverse range of environments and hosts.14,15,48,50–52 We isolated Clip185 from a contaminated TAP medium plate of C. reinhardtii but, it surprisingly did not grow well on TAP agar (not enriched in amino acids/peptides) like it grew on LB agar, which is enriched in peptides, amino acids and vitamins (Figure 1; Figure 4). It also did not grow well on PDA (not enriched in amino acids/peptides) while it grew fine on MHA, which contains beef extract and acid hydrolysate of casein as rich source of amino acids (Underlying data36). These results taken together indicate that Clip185 has a high amino acid/peptide/vitamin requirement for growth and is a fastidious bacterium.\n\nClip185 was resistant to penicillin, chloramphenicol, neomycin, and polymyxin B but was very sensitive to the cell wall-disrupting antibiotic vancomycin (Table 1, Underlying data;34 Figure 2). Thirteen Microbacterium isolates from metal-contaminated soil in Seymour, Indiana (USA) were resistant to chloramphenicol, ampicillin and vancomycin.53 In contrast, M. yannicii PS01, a multi-drug resistant strain isolated from a cystic fibrosis patient was sensitive to chloramphenicol, amoxicillin, vancomycin and colistin (polymyxin E) but resistant to Tobramycin48 (an aminoglycoside antibiotic like neomycin, that binds to the 30S subunit of the prokaryotic ribosome).\n\nBacteremia-causing Microbacterium sp. have been isolated from clinical specimens like catheter, blood etc.54–56 Partial 16S rRNA gene of Clip185 has a 99.1% sequence identity with that of M. binotii PK1-12M strain whose genome has not been sequenced yet (Figure 10B). There was a reported case of bacteremia caused by M. binotii in a sickle cell anemia patient.56 M. binotii strains CIP 101303T and CIP 102116 from the Collection de l’Institut Pasteur were isolated from human blood in 1976 and 1977, respectively.57 As Clip185 is resistant to four major antibiotics, it has the potential to become an opportunistic human pathogen as previously reported for other species of Microbacterium, especially in immune-compromised patients.\n\nSeveral heavy metal-tolerant environmental isolates of Microbacterium exist in the literature.15,20–26 One of the two nearest relatives of Clip185, M. binotii strain PK1-12M, was isolated from primary peat swamp forest soil in the Suratthani Province of Thailand (Accession number: MN428150.1). Peat soils are known to be enriched in heavy metals, especially in raised bogs located near mining and smelting areas.58 Lowland rain forests and salt-water mangrove forests typically surround peat swamp forests near the coast.59 Four Microbacterium bio-emulsifier-producing strains were isolated from oil contaminated mangrove sediments in Guanabara Bay (Rio de Janeiro, Brazil). These strains were able to remove cadmium and zinc from contaminated industrial sites with varying abilities according to the carbon sources used.59 In 2021, BLAST analyses identified Microbacterium sp. strain MDP6 as the nearest relative of Clip185 (Accession number: MK128451.1). Microbacterium sp. strain MDP6 strain is a zinc- and cadmium-tolerant endophytic bacteria isolated in Thailand from Murdannia spectabilis (Kurz) Faden. with plant growth-stimulating properties.60\n\nClip 185 can tolerate 2 mM of cadmium, zinc & nickel, 0.5 mM of cobalt and copper and 6 mM of Cr6+ on LB-agar (Figures 14-19). Clip185 showed a higher cadmium, nickel and zinc tolerance but lower Cr6+ tolerance than the 16 Microbacterium strains isolated from a heavy-metal contaminated site in Indiana.53 Based on Clip185’s heavy-metal tolerance we can speculate that it can thrive in heavy-metal enriched ecological niches in nature. We used LB in our lab to grow Clip185. LB is a nutrient-rich medium that allows growth of most bacteria. Fastidious bacteria have complex nutritional requirements. Literature reviews have shown that researchers usually use Tryptic Soy Agar/Broth (TSA/B) to grow Microbacterium.15,16 TSA/B is a complex nutrient medium that has a higher concentration of amino acids/peptides and carbohydrates compared to that in LB. Hence it is possible that Clip185 has a higher heavy-metal tolerance capability which was not on full display when grown on the LB media used in our experiments. In the future, we would like to assess the heavy-metal tolerance of Clip185 in TSA/B more fully.\n\nExtracellular heavy metal barriers, extracellular metal sequestration, active efflux of metal ions, intracellular metal sequestration, and reduction of metal ions are some of the microbial protective mechanisms employed to combat heavy metal-induced stress.61–63 In the future, we want to spectrophotometrically monitor the growth of Clip185 at 600 nm in TSB containing heavy metals, to determine if Clip185 is able to resist heavy metals.16,53 In the environment, Cr6+, (a soluble, highly toxic form of chromium) is reduced to Cr3+, an insoluble, less toxic form.64 Clip185’s ability to reduce Cr6+ to Cr3+ in TSB can be tested using spectrophotometric assays as described in Henson et al., 2015.16 Results from these experiments will help us to conclusively determine the metal-mobilizing ability of Clip185, and possibly its potential use in bioremediation.\n\nCarotenoids are yellow-red-colored pigments found in all photosynthetic eukaryotes and prokaryotes as well as in non-phototrophic microbes.65 Prokaryotic carotenoids display diverse chemical structures compared to the eukaryotic ones.66 Carotenoids have diverse biological roles (e.g. as anti-oxidants and light harvesting pigments, photo-protection, acting as membrane stabilizers or repressors of translational surveillance and defense pathways in nematodes etc.).29,67,68 Commercially, carotenoids are used as food colorants, animal feed supplements, cosmetics, antioxidants and other health supplements.67,69 Pathways and related enzymes for carotenoid biosynthesis are well characterized (Figure 11).\n\nC40 carotenoids are the predominant class of carotenoids. C30 and C50 carotenoids are rare.70 To date C50 carotenoids have mainly been isolated from non-phototrophic bacteria like the halophilic Archaebacteria, Halobacteria and Halococcus,71,72 gram-positive Actinobacteria18 and one gram-negative bacterium, Pseudomonas.16,73 C50 carotenoids have multiple conjugated double bonds and polar hydroxyl groups, which influences their anti-oxidant and light harvesting properties. These chemical properties make them attractive candidates for their use in photo-protective cosmetics and sun screens.16,18\n\nWhole genome sequencing of Microbacterium sp. strain PAMC28756, isolated from Stereocaulon sp., an Antarctic lichen, revealed the presence of C50 carotenoid biosynthesis gene clusters.74 Recently, C50 carotenoid biosynthesis gene clusters were shown to be the most common secondary metabolite gene clusters in 70 Microbacterium strains isolated from metal contaminated and non-contaminated sites.15 We have shown that Clip185 produces decaprenoxanthin like actinobacteria, C. glutamicum and K. rhizophila (Figure 12). In non-phototrophic bacteria, carotenoid production is mainly classified into three types: 1) light-inducible, 2) constitutive, and 3) cryptic.66,75 A majority of bacteria produce carotenoids constitutively but, bacteria like Myxococcus, Streptomyces, Mycobacterium, Agromyces and Sulfolobus only produce carotenoids under light. Carotenoid production in two Streptomyces species, i.e. Streptomyces setonii and Streptomyces griseus are designated as cryptic, since the growth conditions that trigger carotenoid biosynthesis in these bacteria are unknown at this point.66,75 Carotenoid production is weakly induced in two environmental isolates of Microbacterium, i.e. M. phyllosphaerae and M. foliorum but strongly induced in two isolates of M. natoriense.19\n\nWe have shown that Clip185 synthesizes decaprenoxanthin under light, but the induction is not as strong as that seen in C. glutamicum (Figure 13A-B). In 2019, Sumi et al.19 have shown that light strongly induces decaprenoxanthin production in C. glutamicum, and our findings consolidate this (Figure 13B). K. rhizophila produces decaprenoxanthin irrespective of light conditions (Figure 13C). Both Clip185/Microbacterium and Kocuria belong to the suborder of Micrococcineae under the order Actinomycetales. This shows that the regulation of decaprenoxanthin production in closely related Actinobacteria can differ. CrtR is a transcriptional regulator in the MarR family that represses crtE gene (Figure 11) transcription in the dark in Micrococcales and Corynebacteriales members.19 It would be interesting to check whether the CrtR gene is present and/or altered in Clip185 compared to that in C. glutamicum19 (Figure 13A-B) once we have sequenced the whole genome of Clip185.\n\nSecondary metabolism occurs in bacteria during stationary growth phases, when the energy and carbon pool is diverted away from biomass production towards the production of secondary metabolites like antibiotics, carotenoids etc.76 Pigment production can be modulated by changing the carbon and nitrogen sources and salt concentrations in the growth medium.77 In the future, we would like to test different carbon and nitrogen sources and salt concentrations to see if we can formulate a growth medium that will enhance decaprenoxanthin production in the stationary phase.\n\nCarotenoids help to quench reactive oxygen species (ROS) which are generated under abiotic, stressful conditions. To the best of our knowledge, very little information is available about functional roles of decaprenoxanthin in combating specific types of abiotic stresses. Clip185 growth can be monitored spectrophotometrically in an optimized growth medium under different ROS-generating stressful conditions (e.g. high light, in the presence of ROS like hydrogen peroxide or single oxygen generators like Rose Bengal; UVB light; salt and temperature stress, heavy metal stress etc.). The results from these experiments can shed light on specific stresses that stimulate decaprenoxanthin biosynthesis in bacteria, and might have applications in improving decaprenoxanthin production on a commercial scale.\n\nCurrently the NCBI genomic database has 777 Microbacterium genome assemblies (last accessed on 6-18-2021); out of these 777 assemblies, 288 are from environmental isolates without a validly published species name. Clip185’s nearest relatives are two Microbacterium strains, whose whole genome sequencing data are not available on NCBI at the time of writing. The Microbacterium genus contains species that have highly similar 16S rRNA gene sequences and are difficult to identify at the species level, simply based on 16S rRNA gene sequences.13\n\nBecause of funding limitations at the time of submission of this manuscript, we could not sequence the whole genome of Clip185. We will receive funding in fall 2021 for whole Clip185 genome sequencing. Clip 185 displayed variations in antibiotic sensitivity and heavy metal tolerance when compared to other Microbacterium isolates from metal-contaminated soil and a clinical setting.48,53 These observed variations can stem from the differences among specific ecological niches from where these bacterial strains were isolated. Comparative whole genome sequence analyses of different environmental Microbacterium isolates with that of Clip185 will show us the importance of an ecological niche in shaping genetic diversity in a species, in addition to clarifying its taxonomic identity.\n\n\nData availability\n\nNRRL ARS Culture Collection: Clip185/Microbacterium binotii strain PK1-12M variant; Accession number: B-65609.\n\nNCBI GenBank: Microbacterium binotii strain PK1-12M variant; 16S ribosomal RNA gene, partial sequence, Accession number MN633284.1: https://www.ncbi.nlm.nih.gov/nuccore/MN633284.1.\n\nFigshare: Antibiotic sensitivity data of the bacterial strain Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) and Chlamydomonas reinhardtii strain 4A+ from disc diffusion antibiotic susceptibility tests, https://doi.org/10.6084/m9.figshare.14668914.34\n\nThis project contains the following underlying data:\n\n• Supplemental Data S1 (XLSX). Contains means and standard deviations of zones of growth inhibitions of Clip185 and Chlamydomonas on antibiotic containing TAP plates.\n\n• Supplemental Data S2 (XLSX). Statistical analyses of the zones of growth inhibitions of the bacterial strain Clip185 and Chlamydomonas induced by five antibiotics.\n\nFigshare: Image of a LB plate with single colonies of Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1), https://doi.org/10.6084/m9.figshare.14669214.33\n\nThis project contains single colonies of Clip185 Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) on a LB plate.\n\nFigshare: Images of Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) growth on Potato Dextrose Agar (PDA) and Mueller-Hinton Agar (MHA), https://doi.org/10.6084/m9.figshare.14669397.36\n\nThis project contains an image that shows the growth of Clip185 on Potato Dextrose Agar (PDA) and Mueller-Hinton Agar (MHA).\n\nFigshare: Image of the DNA agarose gel showing the electrophoretic analysis of PCR products obtained using the 16S rRNA gene-specific primers on Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) genomic DNA, https://doi.org/10.6084/m9.figshare.14669400.41\n\nThis project contains one DNA agarose gel image that shows DNA agarose gel electrophoresis analysis of PCR products obtained using the 16S rRNA gene-specific primers on Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) genomic DNA.\n\nFigshare: Image of growth of Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) on a LB plate containing 10 mM hexavalent Chromium (Cr6+), https://doi.org/10.6084/m9.figshare.14669421.47\n\nThis project contains one image of a 10 mM hexavalent Chromium (Cr6+) containing LB media plate on which Clip185/Microbacterium binotii strain PK1-12M variant (Accession number: MN633284.1) was streaked and incubated for 90 days for growth analysis.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThe authors would like to thank the following scientists: Dr. Krishna K. Niyogi (Professor, Department of Plant and Microbial Biology, UC Berkeley, CA, USA) for providing us with the Chlamydomonas wild type strain 4A+; Professor Volker F. Wendisch, (Chair of Genetics of Prokaryotes (Bio 6), Faculty of Biology & CeBiTec, Bielefeld University, Germany) for providing us the C. glutamicum ATCC 13032 strain; Dr. Gary Ruvkun’s laboratory (Professor of Genetics, Harvard Medical School Department of Molecular Biology, Massachusetts General Hospital, MA, USA) for providing us the wild type K. rhizophila strain. We would like to give special thanks to Mr. Seth Hamby (Undergraduate student, Department of Mathematics, Sciences and Technology [MSAT], University of West Georgia [UWG], GA, USA) for preparing media for culturing bacteria in this project and Mrs. Erin Duckett (Lecturer, MSAT, UWG, GA, USA) for providing us with experimental reagents.\n\n\nReferences\n\nMerchant SS, Prochnik SE, Vallon O, et al.: The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12; 318(5848): 245–250. PubMed Abstract | Publisher Full Text | Free Full Text\n\nScranton MA, Ostrand JT, Fields FJ, et al.: Chlamydomonas as a model for biofuels and bio-products production. Plant J. 2015 May 1; 82(3): 523–531. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRadakovits R, Jinkerson RE, Darzins A, et al.: Genetic engineering of algae for enhanced biofuel production. Vol. 9, Eukaryotic Cell. Am Society Microbiol (ASM) . 2010: 486–501. 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Publisher Full Text\n\nSharma P, Diene SM, Thibeaut S, et al.: Phenotypic and genotypic properties of Microbacterium yannicii, a recently described multidrug resistant bacterium isolated from a lung transplanted patient with cystic fibrosis in France. BMC Microbiol. 2013; 13(1): 97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchleifer KH, Kandler O: Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. American Society for Microbiology (ASM); 1972: 407–477. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBehrendt U, Ulrich A, Schumann P: Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb. nov. Int J Syst Evol Microbiol. 2001; 51(4): 1267–1276. PubMed Abstract | Publisher Full Text\n\nPark MJ, Kim MK, Bin KH, et al.: Microbacterium ginsengisoli sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol. 2008 Feb; 58(2): 429–433. PubMed Abstract | Publisher Full Text\n\nHadjadj L, Rathored J, Keita MB, et al.: Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov. Stand Genomic Sci. 2016 Dec 14; 11(1): 32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLearman DR, Ahmad Z, Brookshier A, et al.: Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics. PeerJ. 2019 Jan 14; 2019(1): e6258. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLau SKP, Woo PCY, Woo GKS, et al.: Catheter-related Microbacterium bacteremia identified by 16S rRNA gene sequencing. J Clin Microbiol. 2002; 40(7): 2681–2685. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaffineur K, Avesani V, Cornu G, et al.: Bacteremia due to a novel Microbacterium species in a patient with leukemia and description of Microbacterium paraoxydans sp. nov. J Clin Microbiol. 2003 May 1; 41(5): 2242–2246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBuss SN, Starlin R, Iwen PC: Bacteremia caused by microbacterium binotii in a patient with sickle cell anemia. J Clin Microbiol. 2014 Jan; 52(1): 379–381. PubMed Abstract | Publisher Full Text | Free Full Text\n\nClermont D, Diard S, Bouchier C, et al.: Microbacterium binotii sp. nov., isolated from human blood. Int J Syst Evol Microbiol. 2009; 59(5): 1016–1022. PubMed Abstract | Publisher Full Text\n\nBorgulat J, Mętrak M, Staszewski T, et al.: Heavy metals accumulation in soil and plants of polish peat bogs. Polish J Environ Stud. 2018 Jan 26; 27(2): 537–544. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAniszewski E, Peixoto RS, Mota FF, et al.: Bioemulsifier production byMicrobacterium SP. strains isolated from mangrove and their application to remove cadmiun and zinc from hazardous industrial residue. Braz J Microbiol. 2010 Jan; 41(1): 235–245. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRattanapolsan L, Nakbanpote W, Sangdee A: Zinc- and cadmium-tolerant endophytic bacteria from Murdannia spectabilis (Kurz) Faden. studied for plant growth-promoting properties, in vitro inoculation, and antagonism. Arch Microbiol. 2020 Apr 1; 203(3). PubMed Abstract | Publisher Full Text\n\nIgiri BE, Okoduwa SIR, Idoko GO, et al.: Toxicity and and Bioremediation of Heavy Metals Contaminated Ecosystem from Tannery Wastewater: A Review. J Toxicol. Hindawi Limited; 2018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChoudhury R, Srivastava S: Zinc resistance mechanisms in bacteria. Curr Sci. 2001; 81(7): 768–775.\n\nBruins MR, Kapil S, Oehme FW: Microbial resistance to metals in the environment. Ecotoxicol Environ Saf. Academic Press; 2000; 45: p. 198–207. PubMed Abstract | Publisher Full Text\n\nBartlett RJ: Chromium cycling in soils and water: Links, gaps, and methods. Environ Health Perspect. 1991: 17–24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArmstrong GA: Eubacteria show their true colors: Genetics of carotenoid pigment biosynthesis from microbes to plants. Vol. 176. J Bacteriol. American Society for Microbiology; 1994: 4795–4802. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTakano H, Asker D, Beppu T, et al.: Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol. 2006 Feb 10; 33(2): 88–93. PubMed Abstract | Publisher Full Text\n\nLee PC, Schmidt-Dannert C: Metabolic engineering towards biotechnological production of carotenoids in microorganisms. Appl Microbiol Biotechnol. Springer Verlag; 2002; 60: p. 1–11. PubMed Abstract | Publisher Full Text\n\nSandoval H, Aguilar A, Paniagua C, et al.: Isolation and physical characterization of plasmid pCCl from Corynebacterium callunae and construction of hybrid derivatives. Appl Microbiol Biotechnol. 1984 Jun; 19(6): 409–413.\n\nYe VM, Bhatia SK: Pathway engineering strategies for production of beneficial carotenoids in microbial hosts. Biotechnol Letters. Springer; 2012; 34: p. 1405–14. PubMed Abstract | Publisher Full Text\n\nTobias AV, Arnold FH: Biosynthesis of novel carotenoid families based on unnatural carbon backbones: A model for diversification of natural product pathways. Biochim Biophys Acta - Mol Cell Biol Lipids. 2006 Feb 1; 1761(2): 235–246. PubMed Abstract | Publisher Full Text\n\nKelly M, Jensen SL: Bacterial carotenoids. XXVI. C50-carotenoids. 2. Bacterioruberin. Acta Chem Scand. 1967; 21(9): 2578–2580. PubMed Abstract | Publisher Full Text\n\nPfander H: C45- and C50-carotenoids. Pure Appl Chem. 1994 Jan 1; 66(10–11): 2369–2374.\n\nMiki W, Otaki N, Yokoyama A, et al.: Okadaxanthin, a novel C50-carotenoid from a bacterium, Pseudomonas sp. KK10206C associated with marine sponge, Halichondria okadai. Experientia. 1994 Jul; 50(7): 684–686.\n\nHan SR, Kim KH, Ahn DH, et al.: Complete genome sequence of carotenoid-producing Microbacterium sp. strain PAMC28756 isolated from an Antarctic lichen. J Biotechnol. 2016 May 20; 226: 18–19. PubMed Abstract | Publisher Full Text\n\nTakano H: The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria. Biosci Biotechnol Biochem. 2016 Jul 2; 80(7): 1264–1273. PubMed Abstract | Publisher Full Text\n\nRuiz B, Chávez A, Forero A, et al.: Production of microbial secondary metabolites: Regulation by the carbon source. Vol. 36, Critical Reviews in Microbiology. Crit Rev Microbiol . 2010: 146–167. PubMed Abstract | Publisher Full Text\n\nOjha S, Kapoor S, Mishra S: Carotenoid Production by a Novel Isolate of Microbacterium paraoxydans. Indian J Microbiol. 2018 Mar 1; 58(1): 118–122. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "89080",
"date": "12 Aug 2021",
"name": "David Dewez",
"expertise": [
"Reviewer Expertise Toxicology and chemistry of aquatic microorganisms."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 research work, the authors isolated and characterized a novel bacterial strain, named Clip185, which belongs to the genus Microbacterium. They showed that Clip185 is an aerobic, gram-positive rod, oxidase-negative, mesophilic, alpha-hemolytic bacterium. In particular, they demonstrated that Clip185 is antibiotic-resistant and heavy metal tolerant. Overall, this paper is well written and clearly explained. The methodology is also described in detail.\nThe results are of high quality and well discussed. However, there are some mistakes that need to be corrected:\nBy reading the Table 1 caption, I understand that the grey rows represent 50 μg and the white rows 100 μg of each antibiotic applied, but I believe it is the opposite.\n\nIn Figure 6 caption, please add the abbreviation (TMPD) after ‘tetramethyl-p-phenylenediamine dihydrochloride’.\n\nThere is a mistake in the images showing the results of Figures 15, 16, and 17. They do not correspond to their respective captions. For example, Figure 15 shows the results of zinc which is supposed to be the ones of cobalt. It is very important to correct that.\n\nIn the Discussion section, at line 3: ‘As of 06-18-21’, what do you mean? I think you mean ‘As indicated in the NCBI genomic database last accessed on 6-18-2021’. Please correct.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7084",
"date": "07 Sep 2021",
"name": "Mautusi Mitra",
"role": "Author Response",
"response": "Please see our point-by-point responses to your queries given below. Thanks for investing your time and energy to review our manuscript and providing us valuable inputs to improve the manuscript quality. Hope you will be willing to review our version 2 of the article that has addressed your comments. 1. Reviewer's query/comment: By reading the Table 1 caption, I understand that the grey rows represent 50 μg and the white rows represent 100 μg of each antibiotic applied, but I believe it is the opposite. Our answer: Table 1 captions are correct in version 1 of the article. The grey rows represent 50 μg and the white rows 100 μg of each antibiotic applied. The numerical values in each row denote the diameters of zones of antibiotic-induced growth inhibitions. The diameter of the zone of growth inhibition is directly proportional to the sensitivity of the bacterium to the applied antibiotic. Hence, the larger the diameter of the zone of growth inhibition is, the more sensitive is the bacterium to the applied antibiotic and vice versa. But we did find contradictory wordings and phrases in the text that describes Table 1 which might have confused the reviewer. We have revised the text description of Table 1. We hope this clarifies the concern of the reviewer. 2. Reviewer's query/comment: In Figure 6 caption, please add the abbreviation (TMPD) after ‘tetramethyl-p-phenylenediamine dihydrochloride’. Our answer: In Figure 6 caption, we have added the abbreviation (TMPD) after ‘tetramethyl-p-phenylenediamine dihydrochloride’ in version 2 of the article as per the suggestion of the reviewer. 3. Reviewer's query/comment: There is a mistake in the images showing the results of Figures 15, 16, and 17. They do not correspond to their respective captions. For example, Figure 15 shows the results of zinc which is supposed to be the ones of cobalt. It is very important to correct that. Our answer: We have uploaded correct Figures 15, 16, and 17 which match the respective figure legends in version 2. We did submit the correct figures/legends when we submitted version 1 of the article but during the publication process, for some reason the figures and legends got switched. 4. Reviewer's query/comment: In the Discussion section, at line 3: ‘As of 06-18-21’, what do you mean? I think you mean ‘As indicated in the NCBI genomic database last accessed on 6-18-2021’. Please correct. Our answer: The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes. As of 8-26-21, 124 species of Microbacterium have been identified with a validly published name in LPSN. We have clarified the sentence in line #3 under the Discussion section as per the reviewer’s suggestion by incorporating the above-stated information."
}
]
},
{
"id": "89082",
"date": "12 Aug 2021",
"name": "Ruby A. Ynalvez",
"expertise": [
"Reviewer Expertise Cell biology and biochemistry"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title of the article under review is appropriate for the content of the article. In addition, the abstract represents a suitable and complete summary of this interesting work. Most current literature was cited in the article. The authors were able to clearly present their work on the isolation, taxonomic identification, and physiological and biochemical characterizations of Clip185. Using several microbiological tests, the authors were able to characterize Clip 185. Their disc diffusion assays showed that Clip 185 is very sensitive to vancomycin but resistant to penicillin and other bacterial cell membrane- and protein synthesis-disrupting antibiotics. In addition, the results of their experiment suggests the potential use of vancomycin in preventing not only Microbacterium species but also other bacteria without being detrimental to C. reinhardtii.\nResults also showed that Clip185 is likely to produce a C50 carotenoid, decaprenoxanthin, which is a powerful anti-oxidant with commercial demand. A confirmation of decaprenoxanthin via analytical tools, i.e. HPLC, is recommended for future studies. Clip185 is able to tolerate toxic concentrations of six heavy metals. This finding is relevant in future bioremediation studies. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of Clip185 revealed a 99% sequence identity to that of Microbacterium binotii strain PK1-12M and Microbacterium sp. strain MDP6. Interestingly, Clip185 could be a potentially new strain of Microbacterium binotii or a new Microbacterium species. Overall, this is an interesting article. The findings of their research will open up new research ideas related to bioremediation, antioxidants, gene isolation and regulation, and biotechnology. Thus, the publication of this article will warrant the attention and interest of scientists from diverse fields. I only have several comments that the authors need to consider:\nIn Keywords:\nItalicize \"Chlamydomonas\", \"Microbacterium binotii\".\n\nIn Introduction:\nTris-Phosphate-Acetate (TAP) change to Tris- Acetate- Phosphate (TAP).\n\nIt was mentioned that Clip 185 grows better in a Lysogeny Broth (LB) medium than in a TAP medium and although it was mentioned later in the article, I think it will be to the benefit of the readers to right away mention why the bacterium grows better in LB.\n\nClip185 could grow in the presence of 6mM chromium, 2mM of nickel, cadmium and zinc, and 0.5 mM of copper and cobalt in the LB medium. As a reader, I was wondering what will be the bacteria’s minimum tolerable concentration of each of these heavy metals? It will be helpful to have these tolerable concentrations as reported in the literature. It does not have to be Microbacterium sp., but if there were reports for Microbacterium sp. then the better.\nIn Methods:\nAntibiotic plates were incubated at 22°C. Clip185 and Chlamydomonas plates were imaged after 7 days of incubation. On the other hand, streaked TAP + vancomycin plates were imaged after incubation at 22°C for 2.5 weeks. What is the reason there is a difference in incubation, 7 days versus 2.5 weeks between the other antibiotics and that of vancomycin?\n\nIn Clip 185 growth analysis: The same thing, it will be clearer to all readers if the authors will add why LB-agar and TAP agar culture plates were imaged after 3 days and 7 days of growth, respectively.\n\nThe authors specified why S. aureus was used in MSA. Thus, also specify why Acidovorax sp was used on TSBA.\n\nPlease indicate why Corynebacterium glutamicum strain ATCC13032 and Kocuria rhizophila ATCC?? were used along with Clip 185 testing light-regulation of decaprenoxanthin production? Although it was mentioned later in the article why, I think it’s better to clarify this already in the Methods section, again, just like how it was clear why S. aureus was used in MSA.\n\nIt was mentioned that there were three replicates per metal concentration in the growth assays on LB media containing heavy metals experiment. On the other hand, how many trials were there per replicate? Same thing, three replicates per strain were used in the decaprenoxanthin extractions and spectrophotometric analyses experiment. On the other hand, how many trials were there per replicate?\n\nThere was no mention of how many replicates and trials were performed in the other experiments. I recommend mentioning the number of replicates and trials within replicates for the other experiments.\nIn Results:\nGrey and white rows represent 50 µg and 100 µg of each antibiotic applied on the filter paper discs – please double-check Table 1.\n\nAuthors stated: “We used polymyxin B amounts that were 1.4- fold to 2.8-fold higher than what is used for KB tests, and growth inhibition zones of Chlamydomonas and Clip185 were less than 13 mm (Table 1).” Why not use less than 12 mm instead of less than 13 mm to be consistent with a previous statement that used less than 12 mm as a reference?\n\nIn Figure 9, it could be helpful to add: Both Clip185 (B) and (D) were tested positive in the starch hydrolysis test as shown by a visible clear zone indicated by the arrows surrounding the growth (or if not an arrow perhaps encircle that area, so that the clear zone will be more easily seen by the readers).\n\nI recommend a revision to: This result strongly suggests the presence of decaprenoxanthin in Clip185. HPLC and/or LC/MS analyses could confirm the presence of decaprenoxanthin in Clip185. However, we do not have access to such analytical tools at our institution.\n\nOriginal statements were: This result very strongly indicates the presence of decaprenoxanthin in Clip185. We do not have access to such analytical tools at our institution.\n\nPlease double-check the figures and the corresponding figure titles for Figures 15, 16, and 17. For example, Figure 15 has plates labelled Zinc but the title is Figure 15. Growth of Clip185 on LB media containing Cobalt.\n\nThank you for the opportunity to review this 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?\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": "7085",
"date": "07 Sep 2021",
"name": "Mautusi Mitra",
"role": "Author Response",
"response": "Please see our point-by-point responses to your queries given below. Thanks for investing your time and energy to review our manuscript and providing us valuable inputs to improve the manuscript quality. Hope you will be willing to review our version 2 of the article that has addressed your comments. 1. Reviewer’s query/comments for Keywords: Italicize \"Chlamydomonas\", \"Microbacterium binotii\". Our answer: We had the above-stated two words in italics when we submitted our article in version 1. The italicization was not retained after publication as the italics function is not yet implemented into this section of the F1000Research article management system. Hence we are unable to implement this change. 2. Reviewer’s query/comments for Introduction section: a. Reviewer’s query/comments: Tris-Phosphate-Acetate (TAP) change to Tris- Acetate- Phosphate (TAP). Our answer: We have made the change. b. Reviewer’s query/comments: Clip185 could grow in the presence of 6 mM chromium, 2 mM of nickel, cadmium and zinc, and 0.5 mM of copper and cobalt in the LB medium. As a reader, I was wondering what will be the bacteria’s minimum tolerable concentration of each of these heavy metals? It will be helpful to have these tolerable concentrations as reported in the literature. It does not have to be Microbacterium sp., but if there were reports for Microbacterium sp. then the better. Our answer: We agree that this is a very good suggestion. We could not find any literature record of minimum concentrations of different heavy metals tolerated by Microbacterium sp. or by any species of bacteria. There is a report of heavy metal tolerance of 16 Microbacterium sp. strains isolated from metal-contaminated soil in Indiana, USA. We have compared the heavy metal tolerance of Clip185 with these 16 Microbacterium sp. isolates and have added the information with citations under Introduction and also in paragraph 5 under the Discussion section. 3. Reviewer’s query/comments for the Methods section: a. Reviewer’s query/comments: Antibiotic plates were incubated at 22°C. Clip185 and Chlamydomonas plates were imaged after 7 days of incubation. On the other hand, streaked TAP + vancomycin plates were imaged after incubation at 22°C for 2.5 weeks. What is the reason there is a difference in incubation, 7 days versus 2.5 weeks between the other antibiotics and that of vancomycin? Our answer: We have added the explanation for monitoring Clip185 growth for 3 days on LB plates vs. monitoring Clip185 growth for 7 days on TAP plates under the Methods section sub-section: Testing antibiotic sensitivity of Clip185. We have also revised the Results section sub-section: Clip185 antibiotic susceptibility tests accordingly. We wanted to see if the selected amount of vancomycin was bactericidal or bacteriostatic. In other words, we wanted to see if we will see re-growth of Clip185 on the antibiotic-containing plate if we have a longer incubation of 2.5 weeks compared to 7-days incubation. b. Reviewer’s query/comments: In Clip 185 growth analysis: The same thing, it will be clearer to all readers if the authors will add why LB-agar and TAP agar culture plates were imaged after 3 days and 7 days of growth, respectively. Our answer: We have added the explanation in the Methods section sub-section: Clip185 growth analyses and also have revised the result section sub-section: Clip185 growth analyses on TAP- and LB-agar medium plates at different temperatures. c. Reviewer’s query/comments: The authors specified why S. aureus was used in MSA. Thus, also specify why Acidovorax sp. was used on TSBA. Our answer: We have added the explanation under the Methods section sub-section: Growth assays on Tryptic Soy Blood Agar (TSBA) and also have revised the Results section sub-section: Testing for Clip185’s ability to lyse red blood cells. d. Reviewer’s query/comments: Please indicate why Corynebacterium glutamicum strain ATCC13032 and Kocuria rhizophila ATCC?? were used along with Clip 185 testing light-regulation of decaprenoxanthin production? Although it was mentioned later in the article why, I think it’s better to clarify this already in the Methods section, again, just like how it was clear why S. aureus was used in MSA. Our answer: We have added the explanation under the Methods section sub-section: Decaprenoxanthin extractions and spectrophotometric analyses. We also added the K. rhizophila ATCC strain number (ATCC 9341) in version 2. e. Reviewer’s query/comments: It was mentioned that there were three replicates per metal concentration in the growth assays on LB media containing heavy metals experiment. On the other hand, how many trials were there per replicate? Same thing, three replicates per strain were used in the decaprenoxanthin extractions and spectrophotometric analyses experiment. On the other hand, how many trials were there per replicate? Our answer: We had three biological replicates. Each biological replicate had three internal replicates. This information has been added under the Methods section sub-sections: Growth assays on LB media containing heavy metals and Decaprenoxanthin extractions and spectrophotometric analyses. f. Reviewer’s query/comments: There was no mention of how many replicates and trials were performed in physiological and biochemical experiments. I recommend mentioning the number of replicates and trials within replicates for the other experiments. Our answer: We have added the number of biological replicates and technical replicates for all experiments under the Methods section. 4. Reviewer’s query/comments for the Result section: a. Reviewer’s query/comments: Grey and white rows represent 50 µg and 100 µg of each antibiotic applied on the filter paper discs – please double-check Table 1. Our answer: We have double-checked Table 1. The Table 1 legend is correct. Grey and white rows represent 50 µg and 100 µg of each antibiotic applied on the filter paper discs, respectively. Table 1 captions are correct in version 1 of the article. The numerical values in each row denote the diameters of zones of antibiotic-induced growth inhibitions. The diameter of the zone of growth inhibition is directly proportional to the sensitivity of the bacterium to the applied antibiotic. Hence, the larger the diameter of the zone of growth inhibition is, the more sensitive is the bacterium to the applied antibiotic and vice versa. But we did find contradictory wordings and phrases in the text that describes Table 1 which might have confused the reviewer. We have revised the text description of Table 1. We hope this clarifies the concern of the reviewer. b. Reviewer’s query/comments: Authors stated: “We used polymyxin B amounts that were 1.4- fold to 2.8-fold higher than what is used for KB tests, and growth inhibition zones of Chlamydomonas and Clip185 were less than 13 mm (Table 1).” Why not use less than 12 mm instead of less than 13 mm to be consistent with a previous statement that used less than 12 mm as a reference? Our answer: We have rectified the typographic error and have changed the growth inhibition zone diameter from 13 mm to 12 mm. Thanks for catching that mistake. c. Reviewer’s query/comments: In Figure 9, it could be helpful to add: Both Clip185 (B) and (D) were tested positive in the starch hydrolysis test as shown by a visible clear zone indicated by the arrows surrounding the growth (or if not an arrow perhaps encircle that area, so that the clear zone will be more easily seen by the readers). Our answer: We have added black arrows in Figure 9B and Figure 9D to highlight the clear starch-hydrolyzed zone in these two figures. We have revised the Figure 9 legend and the respective result section accordingly. d. Reviewer’s query/comments: I recommend a revision to: This result strongly suggests the presence of decaprenoxanthin in Clip185. HPLC and/or LC/MS analyses could confirm the presence of decaprenoxanthin in Clip185. However, we do not have access to such analytical tools at our institution. Original statements were: This result very strongly indicates the presence of decaprenoxanthin in Clip185. We do not have access to such analytical tools at our institution. Our answer: We have accepted the reviewer’s suggestion and have revised the sentences under the Results section sub-section: Spectrophotometric analyses of pigments synthesized by Clip185. e. Reviewer’s query/comments: Please double-check the figures and the corresponding figure titles for Figures 15, 16, and 17. For example, Figure 15 has plates labelled Zinc but the title is Figure 15. Growth of Clip185 on LB media containing Cobalt. Our answer: We have uploaded correct Figures 15, 16, and 17 which match the respective figure legends in version 2. We did submit the correct figures/legends when we submitted version 1 of the article but during the publication process, for some reason the figures and legends got switched."
}
]
}
] | 1
|
https://f1000research.com/articles/10-533
|
https://f1000research.com/articles/10-471/v1
|
15 Jun 21
|
{
"type": "Research Article",
"title": "Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals",
"authors": [
"Ivan Buljan",
"David G Pina",
"Ana Marušić",
"Ivan Buljan",
"David G Pina"
],
"abstract": "Background: We assessed the ethics review of proposals selected for funding under the Marie Skłodowska-Curie Actions (MSCA) and the European Research Council (ERC) in Horizon 2020, EU’s framework programme for research and innovation, 2014-2020. Methods: We analysed anonymized datasets for 3,054 MSCA individual fellowships (IF), 417 MSCA Innovative Training Networks (ITN), and 1,465 ERC main-listed proposals with ethics conditional clearance, over four years (2016 to 2019). The datasets included the information on ethics issues identified by applicants in their proposal and ethics issues and requirements identified by ethics experts during the ethics review. Results: 42% of proposals received ethical clearance. For proposals with conditional ethics clearance (n=3546), most of the identified ethics issues by both applicants and ethics experts were in the ethics categories related to humans; protection of personal data; environment, health and safety; and non-EU countries. Ethics experts identified twice as many ethics issues compared to applicants across funding schemes, years, and from high- and low-research performing countries. ERC grants had the highest number of ethics requirements per proposal (median (Md)=8, interquartile range (IQR=4-14), compared to ITN (Md=6, IQR=3-13) and IF grants (Md=3, IQR=2-6). The majority of requirements had to be fulfilled after grant agreement: 99.4% for IF, 99.5% for ITN, and 26.0% for ERC. For 9% of the proposals, the requirements included the appointment of an independent ethics advisor and 1% of the proposals had to appoint an ethics advisory board. Conclusions: Many applicants for highly competitive H2020 funding schemes lack awareness of ethics issues raised by their proposed research. There is a need for better training of researchers at all career stages about ethics issues in research, more support to researchers from research organizations to follow the funding agencies requirements, as well as further development and harmonization of the ethics appraisal process during grant assessment.",
"keywords": [
"research ethics",
"ethics review",
"grant assessment",
"Horizon 2020"
],
"content": "Introduction\n\nEthics is a universal aspect of the research process, from planning and conduct of research, social and cultural relations in research, to reporting of research findings and use of research results. In recent years, ethics has received significant attention from not only researchers, but also policy makers, funders, and lay population due to the rising awareness of the importance of ethics issues in research and consequences of unethical behaviour in research (ALLEA, 2017; Mejlgaard et al., 2020). The existence of ethics standards in research leads to the greater cultural, social, and national equality in research by providing standardized approach to issues in different contexts (Nordling, 2018), and compliance with ethics standards is expected from all who perform research. It is also an important part of education and training in research (Resnik, 2020).\n\nResearchers should be aware of ethics issues that arise from their research plan and take necessary steps to address these issues. However, evidence shows that researchers generally do not perform well in identifying ethics issues in their own research (Taljaard et al., 2011). We have even less evidence about how researchers identify and address ethics issues in grant proposals, mostly due to the lack of available data on this aspect of research grant evaluation, despite abundance of information and instructions by funding agencies (European Commission, 2013). The evaluation of researcher’s ability to identify and address ethics issues in research proposals follows the same principles as scientific evaluation of grant proposals, so that the current gold standard in granting agencies is evaluation by ethics experts in a process of ethics review, which comes usually just after scientific evaluation of grant proposals (European Commission, 2019a). It is expected that, if grant applicants are fully capable to detect ethics issues in research proposals, their assessments should not differ from that of ethics experts.\n\nThe aim of this study was to describe the ethics review process in two of the flagship funding programmes of Horizon 2020 (H2020) – the EU’s research and innovation framework programme from 2014 to 2020: the Marie Skłodowska-Curie Actions (MSCA) and the European Research Council (ERC). More specifically, we analysed the Individual Fellowships (IF) and Innovative Training Networks (ITN) from MSCA, and ERC grants (namely the Starting, Consolidator and Advanced grants). We compared ethics issues identified by the applicants in grant proposals with those identified by ethics experts during the ethics review, as well as ethics requirements resulting from this process.\n\n\nMethods and analytical framework\n\nThe MSCA and ERC programmes are two flagships of H2020. Their initial earmarked budget amounted to 6.2 and 13.1 billion Euro, respectively, representing around 25% of the initial H2020 overall budget (European Commission, 2013).\n\nThe MSCA programme is composed of a set of funding schemes (actions), mostly dedicated to research training and career development of mobile researchers, especially those at an earlier career stage (Pina et al., 2015). Among those actions, the IF covers transnational postdoctoral research training, and ITN specifically targets doctoral training of early-stage researchers. These two actions represent around 95% of the total number of MSCA proposals submitted and funded.\n\nThe ERC grants are funding principal investigators and their teams on frontier research. The programme has remained quite stable since its inception in 2007. Taken together, the MSCA IF, ITN, and the ERC grants represent more than 42% of the overall eligible proposals submitted to the whole H2020 programme, and with success rates in the range of around 8–15%, they are among the most competitive funding scheme of the framework programme.\n\nBoth MSCA and ERC programmes cover all fields of research, in a so-called bottom-up approach. This means that applicants are free to apply for any type of research, with no ex-ante priority given to specific topics. This contrasts with most of the rest of the H2020 programmes. However, for evaluation purposes, MSCA applicants are asked to submit proposals in one of eight scientific panels: Chemistry (CHE), Social Sciences and Humanities (SOC), Economic Sciences (ECO), Information Science and Engineering (ENG), Environment and Geosciences (ENV), Life Sciences (LIF), Mathematics (MAT), and Physics (PHY). In the ERC, proposals are submitted to scientific panels belonging to one of the three following research domains: Life Sciences (LS), Physical Sciences and Engineering (PH), and Social Sciences and Humanities (SH). To facilitate the comparison of the two programmes, we grouped the ECO and SOC panels of MSCA as a proxy for the SH domain of ERC, and the CHE, ENG, ENV, MAT, PHY panels of MSCA as a proxy for the PH domain of ERC. Only the LIF panel in MSCA was considered as an equivalent of the LS domain of ERC.\n\nThe ethics review procedure applies systematically for all proposals considered for funding (i.e. proposals ranked in the main list for funding) (Figure 1). It usually follows the scientific evaluation, where expert reviewers assess and score proposals based on a set of three criteria for the MSCA (Excellence, Impact, and Implementation) and the sole criterion of Excellence for ERC. All submitted proposals contain an ethics self-assessment checklist filled in by the applicants, where they list, in their views and opinion, the ethics issues raised by their proposed research (European Commission, 2019a). The applicants must explain in the proposal how they will address and manage these ethics issues over the course of their projects, if funded.\n\nPS – pre-screening, S – screening. Pre-screening in European Research Council (ERC) evaluation process is performed by internal ERC staff.\n\nProposals that do not raise immediate ethics issues are generally pre-screened by ERC dedicated internal staff, to assess if a full screening is necessary. In MSCA, main-listed proposals are in most of the cases sent automatically for screening. The following step in the ethics review process, the ethics screening, is performed by two or more external independent experts and, in some cases, it is followed by an ethics assessment when a more in-depth analysis is needed for serious or complex ethics issues raised by the proposed research. Grant proposals involving research with human embryonic stem cells or human embryos automatically go for ethics assessment (European Commission, 2019a). Ethics experts are involved in both the screening and the assessment phase. For ERC proposals, ethics assessments are managed internally, whereas MSCA ethics assessments are conducted by the Ethics Sector within the Directorate-General for Research and Innovation (DG RTD).\n\nThe final output of the ethics review is the Ethics Summary Report (EthSR), drafted by ethics experts, which include an ethics opinion on the proposal. This opinion can have the following outcome: i) No ethics issues, when the ethics review confirms that the proposal does not raise any ethics issue; ii) Ethics clearance, when ethics issues are adequately addressed in the proposals, and there is no need for change upon signature of the grant agreement; and iii) Conditional ethics clearance, when the clearance is subject to conditions, usually in the form of “ethics requirements” listed in the EthSR. Ethics requirements must be implemented either before the grant signature, by updating the ethics section of the project description, or at a specific time after the grant signature in the form of ethics deliverables. When an ethics assessment is needed for proposals raising serious or complex ethics issues, the applicants are usually requested to submit additional information for an in-depth ethics analysis before the ethics experts formulate their opinion. Proposals conditionally cleared can therefore be the result of an ethics screening or an ethics assessment. In very rare cases, a project proposal can be rejected on ethics grounds (European Commission, 2019a)\n\nWe analysed the data for main-listed proposals from MSCA IF, MSCA ITN calls in 2016-2019, and for ERC calls in 2017-2019, the year for which the data were available in the electronic Submission and Evaluation of Proposals (SEP) tool of the European Commission. SEP integrated the full ethics evaluation process in 2016 for MSCA and in 2017 for ERC. When this study was initiated in 2020, the ethics evaluation process was still not fully completed for IF and ERC, so we considered only the data up to the 2019 calls. As our datasets were based on the structured information available in the EthSR from SEP, they are partially incomplete. They did not include MSCA proposals for which an ethics assessment was performed by the Ethics Sector from DG RTD. Those proposals include the cases with human embryonic stem cells or human embryos. The proposals that did not raise any ethics issues or were cleared by the ethics experts were not analysed further, as they correspond to the cases where the applicants either addressed correctly the ethics issues in their proposals or the proposed research did not raise any ethics issues. We focused on the main-listed proposals that were conditionally cleared, as they correspond to the cases where differences existed between what was declared by the applicants and what was later flagged by ethics experts.\n\nThe data from SEP were split into two datasets, the first containing the information about the ethics issues identified by applicants and ethics experts, and the second one containing the information about ethics requirements listed by ethics experts. For both datasets, we collected data about the proposal call year, scientific panel/domain, the host country (of the coordinating institution), and ethics issues/requirements categories. We also had the information related to ethics checks. The list of ethics issues as categorized by the European Commission is available in the Extended data (Buljan et al., 2021). The ethics issues are divided into 11 distinct categories, as listed in the Ethics Self-Assessment Checklist: Human embryos/foetuses; Humans; Human cells/tissues; Personal data; Animals; Third countries; Environment, Health & safety; Dual use; Exclusive focus on civil applications; Misuse; and Other ethics issues (European Commission, 2019a).\n\nFor ethics requirements dataset, there was no Exclusive focus on civil applications category, and the category General was merged with the Other category.\n\nWe worked on anonymized datasets, without insight about the actual content of the proposal, or the names of the applicants or ethics experts, so that issues of personal data protection were not applicable.\n\nEthics issues and requirements are presented as frequencies and percentages, by type of action (for MSCA) or grant (ERC), call year, and scientific domain. Ethics issues identified by the applicants and ethics experts are presented separately. The number of ethics issues/requirements per proposal is presented as median, with interquartile range (IQR). We calculated odds ratios for the probability that ethics issues in a specific category is identified by ethics experts vs. that it is identified by applicants.\n\nWe performed linear regression analysis, where the criterion was the number of ethics issues in a proposal identified by ethics experts, and with the type of action, year, host country, and number issues in a specific category in a proposal identified by applicants as potential predictors. Host countries ware categorized into research low- and high-performing categories, based on a previously reported composite indicator (Pina et al., 2019). Research high-performing countries were Austria, Belgium, Denmark, Finland, France, Germany, Israel, the Netherlands, Norway, Sweden, Switzerland, and the United Kingdom, and low-performing countries were Bulgaria, Croatia, Cyprus, Czech Republic, Estonia, Greece, Spain, Hungary, Ireland, Iceland, Italy, Lithuania, Luxemburg, Latvia, Malta, Poland, Portugal, Romania, Serbia, Slovenia, Slovakia, and Turkey.\n\nTo determine the characteristics of main-listed proposals subject to ethics review, we collected the information about call year, type of action, number of requirements per proposal and research domain in logistic regression. For this analysis, we recoded ethics category groups by omitting Human embryos/foetus category due to small sample size and collapsing Dual use; Misuse; Other, Exclusive use on civil applications (linear regression only) and General (logistic regression only) categories into Other category.\n\nThe results are presented as odds ratios with 95% confidence intervals (CI) and Nagelkerke R squared. All analyses were performed using the R programming software v.4.0.3 (R Core Team, 2020).\n\n\nResults\n\nThe total number of main listed proposals in the period from 2016-2019 for MSCA and 2017-2019 for ERC, was 485 proposals from ITN, 5365 proposals from IF, and 2632 proposals from ERC (Table S1 in Extended data (Buljan et al., 2021)). Of these, we identified 4936 proposals (58%) that received conditional ethics clearance during the ethics review (excluding those from MSCA that went for an ethics assessment by DG RTD). This means that the remaining 3546 (42%) proposals either had no ethics issues or received ethical clearance (Figure 1, Table S1 in Extended data (Buljan et al., 2021)). Proposals from individual granting schemes more often received ethics clearance (44.3% for ERC proposals and 43.1% for IF proposals) than proposals from research consortia (14.1% for ITN proposals).\n\nApplicants identified 707 ethics issues in 417 proposals from ITN (85.9% out of all main-listed proposals), 4469 issues in 3054 proposals from IF (56.9%), and 2826 issues in 1465 proposals from ERC (55.7%) (Figure 2, Table S1 in Extended data (Buljan et al., 2021)). Ethics experts identified more than two times more issues than applicants: 1676 for ITN, 9695 for IF, and 6912 for ERC proposals. That trend was stable across different types of grants and call years (Figure 2).\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission.\n\nThe median (Md) number of ethics issues identified by an applicant per proposal was 1 (IQR=0-3) for ITN, 1 (IQR=0-2) for IF, and 2 (IQR=1-3) for ERC, whereas ethics experts identified a median of 4 ethics issues (IQR=2-5) for ITN, 3 (IQR=2-4) for IF, and 4 (3-6) for ERC. This was true for all call years (Figure 3). The most frequently identified ethics issues categories overall were Humans; Protection of personal data; Animals; and Non-EU countries (Table S1 in Extended data (Buljan et al., 2021)). Applicants had higher odds to identify ethics issues related to Humans, Human cells/tissues, Protection of personal data, and Animals categories, whereas ethics experts were more likely to identify ethics issues in categories Non-EU countries and Environment, health and safety (Table S1 in Extended data (Buljan et al., 2021)).\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission.\n\nWith regard to the research domain, applicants from Life Sciences identified the most issues, with 3719 ethics issues (n=3719), followed by Social Sciences and Humanities (n=2916) and Physical Sciences and Engineering (n=1367). On the other side, ethics experts identified two times more ethics issues for proposals in Life Sciences (n=7652) and Social Sciences and Humanities (n=6055), and three times more ethics issues in Physical Sciences and Engineering (n=4576) (Table S2 in Extended data (Buljan et al., 2021)). The same was found for the median number of ethics issues per proposal (Figure 4).\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission. Soc/Hum – Social Sciences and Humanities, Phys/Eng – Physical Sciences and Engineering, Life sci – Life Sciences.\n\nFor Social Sciences and Humanities, the most prevalent categories were Humans, Protection of personal data and Non-EU countries, whereas in Life Sciences and Physical Sciences and Engineering, Animals, Human cells/tissues, and Environment, health and safety categories were more often identified by both the applicants and ethics experts (Figure 5). When observing the total number of ethics issues by category, the above six categories comprised most of the identified ethics issues, regardless of the type of grant (Figure 6). The greatest discrepancy in absolute numbers between project applicants and ethics experts was for the Non-EU countries and Environment, health and safety categories (Figure 6). Proposals from the Physical Sciences and Engineering were characterized by the highest number of issues related to Dual (military) use, identified by both the applicants and the experts (Figure 6).\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission. Soc/Hum – Social Sciences and Humanities, Phys/Eng – Physical Sciences and Engineering, Life sci – Life Sciences.\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission.\n\nRegression analysis, where we assessed which proposal characteristics predicted higher number of identified ethics issues per ethics category by ethics experts, showed that it was more likely that the proposal will have significantly more ethics issues in the same category, identified by ethics experts when it was an ERC proposal, coming either from Life Sciences or Social Sciences and Humanities, or a newer proposal, as well as if it had issues related to the Protection of personal data, Non-EU countries, and Environment, health and safety categories, and had multiple issues identified by applicants in the same ethics category (Table S3 in Extended data (Buljan et al., 2021)). On the other hand, lower number of ethics issues in a same category identified by ethics experts were related to the proposals from MSCA funding schemes (both ITN and IF), from Physical Sciences and Engineering, from an earlier call, and had issues related to the Human cells/tissues, Animals or Other categories, as well as fewer ethics issues by ethics category identified by applicants (Table S3 in Extended data (Buljan et al., 2021)). However, the best predictor for the number of ethics issues identified by ethics experts was the number of ethics issues by ethics category identified by applicants, and it explained 19% of the variance of the criteria when independently entered in linear regression. Proposals which had multiple identified ethics issues per ethics category were more likely to have more ethics issues in a specific category identified by ethics experts.\n\nThe number of ethics requirements was greater than the number of ethics issues identified by ethics experts (3625 for ITN, 14249 for IF and 13846 for ERC) (Figure 2). ERC had the highest median number of ethics requirements per proposal (Md=8, IQR=4-14), compared to ITN (Md=6, IQR=3-13) and IF (Md=3, IQR=2-6) (Figure 7). The greatest proportion of ethics requirements was in the Humans, Human Cells/Tissues, Non-EU countries, and Environment, health and safety categories (Figure 8; Table S4 in Extended data (Buljan et al., 2021)). Proposals from Life Sciences and Social Sciences and Humanities domains had the greatest number of requirements (n=12544 and n=12377, respectively). There were 6799 requirements for proposals in Physical Sciences and Engineering (Table S5 in Extended data (Buljan et al., 2021)). All three types of grants were similar in the number of ethics requirements per proposal across domains (Figure 9). Although proposals from Life Sciences and Social Sciences and Humanities had a similar total number of requirements, most of the ethics requirements for Social Sciences and Humanities were in the Humans and Protection of personal data categories. Requirements for proposals in Life Sciences were linked to all ethics categories (Figure 10).\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission.\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission.\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission. Soc/Hum – Social Sciences and Humanities, Phys/Eng – Physical Sciences and Engineering, Life sci – Life Sciences.\n\nITN – Innovative Training Networks, IF – Individual Fellowships, ERC – European Research Council grants. The data are from years available in the SEP tool of the European Commission. Soc/Hum – Social Sciences and Humanities, Phys/Eng – Physical Sciences and Engineering, Life sci – Life Sciences.\n\nThe majority of requirements’ deliverables were scheduled to be fulfilled after the grant agreement signature: 14162 (99.4%) for IF; 3606 (99.5%) for ITN, and 3600 (26.0%) for ERC. The median deliverable’s month of implementation, when a requirement had to be fulfilled, was month 3 for IF (IQR=1-5, range=1-36), month 12 for ITN (IQR=12-12, range=1-48), and month 12 (IQR=12-12, range=0-55) for ERC.\n\nEthics checks were required for 43 ITN proposals (10.2%), 141 IF proposals (4.6%), and 185 ERC proposals (12.6%). The predictors of whether a proposal will involve an ethics check were a higher number of ethics requirements, being an MSCA ITN proposal, coming from Social Sciences and Humanities, and being a proposal from an older call year (Table S6 in Extended data (Buljan et al., 2021)). It was also more likely that a proposal will go for an ethics check if it had multiple ethics requirements in the collapsed Other category, and less likely if the multiple requirements were for Animals or Environment, health and safety categories (Table S6 in Extended data (Buljan et al., 2021)).\n\nEthics experts can require the appointment of an independent ethics advisor or an ethics advisory board, for proposals with complex or serious ethics issues, or when they consider that the applicants did not demonstrate sufficient proficiency in identifying or managing ethics issues. 6.2% of all conditionally cleared proposals had such a requirement (5.3% for ethics advisor and 0.9% for ethics advisory boards). ERC proposals had more such requirements: 14.9% proposals needed ethics advisor vs 1.2% of MSCA proposals, and 2.5% needed ethics advisory boards vs 0.3% for MSCA proposals. For MSCA proposals, there was no clear difference, except for the predominance of proposals from Social Sciences and Humanities among proposals needing an ethics advisor (8 out of 11 proposals) and Life Science proposals among ITN (12 out of 32 proposals). Half (51.1%) of the proposals that required some kind of ethics monitoring, either by ethics advisors or boards, during the project lifetime also required an ethics check.\n\n\nDiscussion\n\nTo the best of our knowledge, this is the first study that explored in detail the characteristics of the ethics review in highly competitive H2020 proposals across research disciplines and funding schemes. We showed that about half (42%) of the proposals did not require an ethics review, either because the proposed research did not raise ethics issues or the applicants adequately addressed ethics issues. However, for those that received conditional ethics clearance, both the individual researchers (in IF and ERC granting schemes) and research consortia (ITN grants) were not good in identifying ethics issues generated by the proposed research because ethics experts identified two times more ethics issues. The applicants were better at identifying “classical” ethics issues – those related to research involving humans or human cells and tissues, protection of personal data, and animals, but not as good in identifying ethical challenges related to the research involving collaboration with other countries, and environmental, health and safety issues. The reason for this may be the fact that the latter ethics categories are more legal in nature, requiring different types of legal documentation and procedures (European Commission, 2019b), and may not be perceived as a “true” ethics issue. The same was true for ethics categories that were generally rarely identified: Dual-use and Exclusive focus on civilian applications (research that could be used for military applications) and Misuse (research for unethical purposes such as terrorism). Ethics experts, who are considered as the “golden standard” for ethics review, identified twice as more ethics issues, in general and per proposal. For some proposals, they required formal ethical support and monitoring in the form of individual ethics advisors or ethics advisory board or as ethics checks at some points during the life time of the project.\n\nWe observed important differences in identified ethics issues between different research domains and grant types. The proposals with fewer ethics issues in the same category identified by ethics experts were those where applicants identified fewer issues in the same category, in MSCA compared to ERC grant calls, those from Physical sciences and Engineering domain, proposals from older years and those with ethics issues in categories Human cells/tissues, Animals or Other (including Dual use, Misuse, General and Other ethics issues). There was general congruence between the applicants and ethics experts in identification of ethics issues categories, except that experts identified more issues. The finding that ERC proposals had more ethics issues than MSCA ITN and IF may be related to the ERC selection priority for breakthrough research, which brings higher risk and uncertainty (European Research Council, 2019). Proposals from Life Sciences and Social Sciences and Humanities had more ethics issues and resulting ethics requirements than those from Physical Sciences and Engineering because they more often include research with human and animal participants. Finally, very small but significant influence of the year of proposal was found for both the number of issues and ethics requirements, with higher numbers in later years. The study time period (2016–2019) was the period of significant change for one of the major ethics issues: in 2016, the General Data Protection Regulation (GDPR) was enacted in the EU, with the implementation starting from mid-2018 (European Commission, 2016). This means that the researchers in later grant years could become more aware of these new requirements and paid more attention to ethical issues in general. However, the Personal data protection category did not emerge as a predictor in any of the regression analyses in our study. It is also possible that the efforts that the European Commission and research performing or research granting institutions have invested in the promotion responsible conduct of research (Ščepanović et al., 2021; Mejlgaard et al., 2020) had an effect over the years. However, the median number of ethics issues per proposal remained stable over the study period, implying that applicants did not improve their performance in identifying ethics issues over time. Longer follow-up studies and controlled study designs, such as interrupted time series (Pina et al., 2021), are needed to test the effect of time on ethics appraisal of grant proposals.\n\nThe need for more proactive approach to ethics training and assistance to researchers is clearly visible in the number of proposals where the ethics experts required appointment of an Ethics Advisor to help in the management of the future project ethics issues, or the proposals where the establishment of a larger Ethics Advisory Board was deemed necessary to coordinate the management of complex and/or serious ethics issues. Such projects very rarely included ethics monitoring already in the proposal, meaning that the applicants and their institutions were not aware of the complexities or seriousness of ethics issues in their research.\n\nThe complexity of ethics issues raised by proposed research differed between different grant calls. While individual fellowship (IF) proposals required an ethics check during the ethics review process in about 5% of the cases, ITN proposals, which are submitted by a consortium of research institutions, and ERC grants, which are individual proposals but involving high-risk research, required ethics checks two times more often. Taking ethics check requirement as a proxy for complex and specific ethics issues, regression analysis identified that such proposals had more ethics requirements and were coming from the Social Sciences and Humanities Domain, had more ethics requirements in the Non-EU and Dual use, Misuse, General and Other categories and from older calls. This complexity is also reflected in the number of proposals that had to fulfil ethics requirements during the project lifetime (around 99% for IF and ITN and 26% for ERC). ERC proposals also had almost ten times more requirements for an ethics advisor than MSCA grants. The reasons for these differences are not clear – they may be related to the specificities of the calls or proposed research, or the organization of the ethics appraisal process. Our study showed clear differences between the ethics review procedure between ERC and MSCA, but we currently do not have any evidence on relevant outcomes that would indicate possible differences in their effectiveness.\n\nOur study had some limitations that need to be acknowledged. We did not have information about the actual content of the proposals so that the ethics issues could be assessed independently. We considered ethics experts review procedure as the golden standard in ethics assessment, just as scientific expert review is used as a measure of the scientific quality of the proposal (Pina et al., 2021). The sample in our study included only the highest ranked proposals considered for funding, as only these proposals undergo ethics review. We do not know whether the applicants whose proposals did not get funded had better, worse or similar skills in identifying ethics issues as those of funding proposals. We also did not evaluate the proposals that received ethics clearance, so we did not determine whether the reason for ethical clearance of half of the main-listed projects was because the applicants adequately addressed ethics issues or if it was because the project did not raise ethics issues. The results of our study could be considered as an indication of best ethics practices among participants in EU grant proposals, as they select the best proposals in highly competitive calls. Finally, we did not explore in detail the qualitative (textual) content of the ethics review, which could identify in specific ethics issues raised by the proposed research and those addressed in ethics requirements.\n\nIt is difficult to put the results from our study in a more general context as there are no studies of ethics as an important aspect of grant evaluation (Buljan et al., 2020). We know that authors of research papers are generally poor in reporting ethics issues (Taljaard et al., 2011). There are many studies assessing different aspects of publications ethics, including examples such as consent for publishing identifiable medical images (Roguljić et al., 2020) or authorship (Marušić et al., 2011), because the data for such studies are publicly available, in contrast to the information on grant evaluation.\n\nResearch performing and research funding organizations are the places where the problem of the competence of researchers to identify and address ethics issues must be addressed. This problem is a part of a greater problem of shaping structures and processes for research ethics and research integrity to promote responsible conduct of research (Mejlgaard et al., 2020). Different approaches to these issues have been described, ranging from education and training in research ethics (Dubois et al., 2008) and research integrity (Marušić et al., 2016). For example, some organizations (LARI, 2021) provide ethics and integrity support to early-stage researchers in the form of integrity coaches or advisors, which help researchers navigate through ethics and integrity requirements during their research. There are also efforts at the policy level (ALLEA, 2017), as well as at the level of organizational culture and climate for responsible research (Viđak et al., 2021), but we do not have quality evidence of whether these efforts actually work.\n\nIt is also important to keep in mind the differences between research disciplines, which have been already recognized in the context of ethics codes (Aagaard-Hansen & Johansen, 2008). In our study, research in different disciplines did not result in the difference in the number of identified ethics issues, but in the different pattern of the distribution among ethics categories. Research proposals from Physical Sciences and Engineering had mostly ethics issues related to collaboration with non-EU countries and those related to environment, health and safety. They also had the largest prevalence of ethics issues in Dual use category, compared to other domains. While the proposals from Life Sciences did not have a clear predominance among major ethics issues – those related to research involving humans and animals, non-EU countries and health and environment, dominating ethics issues in the proposals from Social Sciences and Humanities were related to the involvement of human participants and personal data protection. Researchers from Social Sciences and Humanities were not good at identifying these issues, as the difference in ethics issues identified by applicants and the issues and requirements put forward by ethics experts was greatest for proposals in this research domain. This has been recognized by the European scientific community and specific research ethics guidance has been developed for social sciences (European Commission, 2018).\n\nFinally, the heterogeneity of research ethics and research integrity structures and processes in Europe (European Commission, 2019b), as well as differences in research integrity codes across Europe (Desmond & Dierickx, 2021), do not help researchers in understanding what is expected from them in regard to research ethics, especially when they work in collaborations that cross country boundaries. As we did not find differences between countries that are high performers in research and those that are not, the problems in identifying ethics issues in their research proposals seem to be common to all research communities across Europe.\n\n\nConclusion\n\nOur study demonstrated that researchers are not always adequately competent in recognizing and addressing ethics issues in research that they propose to grant agencies, and that this problem persisted over the last four years of EU research funding framework. Although there are intensive efforts to promote training and restructuring of research ethics and research integrity framework at all levels of research in Europe (Mejlgaard et al., 2020), more concrete actions that are actually resulting in a positive change are needed. We also need to study the process of ethics evaluation of grant proposals and research project execution in order to identify critical points for change and/or improvement, as well as facilitators and barriers to successful management of ethics issues in research. Although such studies may me methodologically complex and demanding, and involve both quantitative and qualitative approaches, they are needed so that we can better understand the problem and formulate solutions. Only when we have evidence for effective actions, we will be able to provide support to researchers to deal with ethical issues in their research and prepare for emerging ethical challenges, such as the use of gene-editing (European Group on Ethics in Science and New Technology, 2021) and artificial intelligence (European Parliament, 2019) in research.\n\n\nData availability\n\nOSF: Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals. https://doi.org/10.17605/OSF.IO/T765V (Buljan et al., 2021).\n\nThis project contains the following underlying data:\n\n- Data file 1. Datasets.xlsx\n\nOSF: Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals. https://doi.org/10.17605/OSF.IO/T765V (Buljan et al., 2021).\n\nThis project contains the following extended data:\n\nList of ethics issues as categorized by the European Commission\n\nTable S1. Number of ethical issues identified by applicants and ethics experts for MSCA ITN and IF and the ERC, per call year\n\nTable S2. Number of ethical issues identified by applicants and ethics experts, by scientific domain, for MSCA ITN and IF and the ERC\n\nTable S3. Linear regression for predicting number of ethics issues per category in a proposal identified by ethics experts\n\nTable S4. Number of ethics requirements identified by applicants and ethics experts in MSCAITN and IF and the ERC, per call year\n\nTable S5. Number of ethics requirements, by scientific domain, for the ERC\n\nTable S6. Logistic regression for prediction of whether a proposal will go to ethics check (0-No,1-Yes)\n\nOSF: STROBE checklist for ‘Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals’. https://doi.org/10.17605/OSF.IO/T765V (Buljan et al., 2021).\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\nAll views expressed in this description are strictly those of the authors and may in no circumstances be regarded as an official position of the European Research Executive Agency or the European Commission.",
"appendix": "Acknowledgment\n\nWe thank Antonija Mijatović, PhD, University of Split School of Medicine, for her help in extracting data.\n\nThis study was presented in part at the PEERE Conference, Valencia, Spain, 29 September-1 October 2020.\n\n\nReferences\n\nAagaard-Hansen J, Johansen MV: Research ethics across disciplines. Anthropology Today. 2008; 24(3): 15–19. Publisher Full Text\n\nEuropean Federation of Academies of Sciences and Humanities (ALLEA): The European Code of Conduct for Research Integrity. 2017; Accessed 17 August 2020. Reference Source\n\nBuljan I, Pina D, Marušić A: Meta Research: Ethics assessment of H2020 Marie Skłodowska-Curie individual fellowships. PEERE Conference, Valencia, Spain, 29 September–1 October 2020. Reference Source\n\nBuljan I, Marusic A, Pina D: Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals: Supplementary files. 2021; Retrieved from osf.io/cyp4w.\n\nDesmond H, Dierickx K: Research integrity codes of conduct in Europe: Understanding the divergences. Bioethics. 2021; 35(5): 414–428. PubMed Abstract | Publisher Full Text\n\nDuBois JM, Dueker JM, Anderson EE, et al.: The development and assessment of an NIH-funded research ethics training program. Acad Med. 2008; 83(6): 596–603. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEuropean Commission: Regulation (EU) No 1291/2013 of the European Parliament and of the Council of 11 December 2013 establishing Horizon 2020 - the Framework Programme for Research and Innovation (2014-2020) and repealing Decision No 1982/2006/EC Text with EEA relevance. 2013; viewed 15 April 2021. Reference Source\n\nEuropean Commission: Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation). 2016; viewed 12 March 2021. Reference Source\n\nEuropean Commission: Ethics in Social Science and Humanities. 2018; viewed 12 March 2021. Reference Source\n\nEuropean Commission: Horizon 2020 Guidance: How to complete your ethics self-assessment. 2019a; viewed 20 October 2020. Reference Source\n\nEuropean Commission: Mutual Learning Exercise (MLE) on Research Integrity: Final Report. 2019b; viewed 12 March 2021. Reference Source\n\nEuropean Group on Ethics in Science and New Technology: Ethics of Genome Editing. 2021; viewed 15 April 2021. Reference Source\n\nEuropean Parliament: EU guidelines on ethics in artificial intelligence: Context and implementation. 2019; viewed on 12 March 2021. Reference Source\n\nEuropean Research Council: Information for Applicants to the Starting and Consolidator Grant 2020 Calls. 2019; viewed 12 March 2021. Reference Source\n\nLuxembourg Agency for Research Integrity (LARI). viewed 15 April 2021. Reference Source\n\nMarušić A, Bošnjak L, Jerončić A: A systematic review of research on the meaning, ethics and practices of authorship across scholarly disciplines. PLoS One. 2011; 6(9): e23477. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarusic A, Wager E, Utrobicic A, et al.: Interventions to prevent misconduct and promote integrity in research and publication. Cochrane Database Syst Rev. 2016; 4(4): MR00038. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMejlgaard N, Bouter LM, Gaskell G, et al.: Research integrity: nine ways to move from talk to walk. Nature. 2020; 586(7829): 358–360. PubMed Abstract | Publisher Full Text\n\nNordling L: Europe's biggest research fund cracks down on 'ethics dumping'. Nature. 2018; 559(7712): 17–18. PubMed Abstract | Publisher Full Text\n\nPina DG, Barać L, Buljan I, et al.: Effects of seniority, gender and geography on the bibliometric output and collaboration networks of European Research Council (ERC) grant recipients. PLoS One. 2019; 14(2): e0212286. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPina DG, Buljan I, Hren D, et al.: A retrospective analysis of the peer review of more than 75,000 Marie Curie proposals between 2007 and 2018. eLife. 2021; 10: e59338. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPina DG, Hren D, Marušić A: Peer Review Evaluation Process of Marie Curie Actions under EU's Seventh Framework Programme for Research. PLoS One. 2015; 10(6): e0130753. PubMed Abstract | Publisher Full Text | Free Full Text\n\nR Core Team: R: A language and environment for statistical computing. 2021; viewed 20 Spril 2021. Reference Source\n\nResnik DB: What Is Ethics in Research & Why Is It Important?2020; viewed 18 January 2021. Reference Source\n\nRoguljić M, Buljan I, Veček N, et al.: Deidentification of facial photographs: a survey of editorial policies and practices. J Med Ethics. 2020; medethics-2019-105823. PubMed Abstract | Publisher Full Text\n\nŠčepanović R, Labib K, Buljan I, et al.: Practices for Research Integrity Promotion in Research Performing Organisations and Research Funding Organisations: A Scoping Review. Sci Eng Ethics. 2021; 27(1): 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaljaard M, McRae AD, Weijer C, et al.: Inadequate reporting of research ethics review and informed consent in cluster randomised trials: review of random sample of published trials. BMJ. 2011; 342: d2496. PubMed Abstract | Publisher Full Text | Free Full Text\n\nViđak M, Barać L, Tokalić R, et al.: Interventions for organizational climate and culture in academia: A scoping review. Sci Eng Ethics. 2021; 27(2): 24. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "87517",
"date": "26 Jul 2021",
"name": "Vasiliki Mollaki",
"expertise": [
"Reviewer Expertise Genetics",
"Ethics",
"Bioethics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript aims to assess the ethics review of proposals selected for funding under specific H2020-funded programmes between 2016-2019. It is found that ethics experts identified twice as many ethics issues compared to applicants across funding schemes, years, and from high- and low-research performing countries, indicating the need to train researchers in identifying and addressing ethics issues raised by their research.\nThe manuscript is well structured and the methodology is clearly presented.\nMinor comments:\nSection The MSCA and ERC programme: \"Among those actions\" should be \"Among these actions\".\n\nSection Ethics review procedure: \"which include an ethics opinion on the proposal\" should be \"which includes an ethics opinion on the proposal\".\n\nSection Data sources and description of ethics issues categories: \"Those proposals include the\" should be \"These proposals include the\".\n\n\"The ethics issues are divided into 11 distinct categories\" should be \"The ethics issues are divided into 12 distinct categories\".\n\nSection Data analysis: \"and number issues in a specific category\" should be \"and number of issues in a specific category\".\n\nSection Results: \"had no ethics issues or received ethical clearance\" should be \"had no ethics issues or received ethics clearance\".\n\nSection Ethics issues identified by applicants and ethics experts in conditionally cleared main-listed proposals: \"That trend was stable across\" should be \"This trend was stable across\".\n\nFigure 5 and 10: Label \"Human embryos/fetus\" should be \"Human embryos/fetuses\".\n\nFigure 5 and 6: Label \"exclusive use on civil applications\" should be \"exclusive focus on civil applications\".\n\nSection Discussion: \"with human and animal participants\" do you mean \"with human participants and animals\"?\n\nSection Conclusion: \"Although such studies may me methodologically\" should be \"Although such studies may be methodologically\".\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7089",
"date": "06 Sep 2021",
"name": "Ana Marušić",
"role": "Author Response",
"response": "Thank you for the comments - we made all suggested changes in the revised manuscript"
}
]
},
{
"id": "90648",
"date": "10 Aug 2021",
"name": "Juraj Koppel",
"expertise": [
"Reviewer Expertise developmental physiology",
"bioethics",
"research integrity",
"science management"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting article summarizing important data concerning ethics review processes in MSCA and ERC grants. The manuscript is well presented, the design is fully appropriate and adequate details are given. The discussion section is well elaborated, conclusions are clear and fully adequate. Indeed, the reviewer acknowledges that this is a unique study exploring in details the ethics review in H2020 grant proposals across research disciplines and funding schemes.\nFew minor comments and suggestions:\n“All submitted proposals contain an ethics self-assessment checklist filled in by the applicants, where they list, in their views and opinion, the ethics issues raised by their proposed research (European Commission, 2019a). The applicants must explain in the proposal how they will address and manage these ethics issues over the course of their projects, if funded.“ In fact, applicants have to submit an (ideally explanatory) Ethics Annex only in the case if they declare any ethics issue in the checklist.\n\n“All analyses were performed using the R programming software v.4.0.3 (R Core Team, 2020).“ Perhaps a better description is \"the R software environment for statistical computing and graphics“.\n\n“proposals from older years“ could be rephrased as \"proposals from earlier periods/years\".\n\nIn the context of number of ethics issues frequently seen in grant proposals the statement “The need for more proactive approach to ethics training and assistance to researchers“ is really crucial and has to be underlined. For illustration – applicants e.g. in ENG or PHY focused on the development of new instruments or software are in general fully unaware that any testing involving humans raises ethics 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?\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": "7090",
"date": "06 Sep 2021",
"name": "Ana Marušić",
"role": "Author Response",
"response": "Thank you for the comments, we made all suggested changes in the revised manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/10-471
|
https://f1000research.com/articles/10-892/v1
|
06 Sep 21
|
{
"type": "Research Article",
"title": "Bridging skill gaps and creating future ready accounting and finance graduates: an exploratory study",
"authors": [
"Saravanan Muthaiyah",
"Karen Phang",
"Sanjaya Sembakutti",
"Karen Phang",
"Sanjaya Sembakutti"
],
"abstract": "Background: Changing trends in the use of technology have become an impelling force to be reckoned with for the accounting and finance profession. The curriculum offered in higher learning institutions must be quickly revamped so that students who complete a bachelor’s degree are digitally competent upon graduation. With US$55.3 billion invested in FinTech in 2019 alone and more than 72% of accounting jobs being automated, graduates must be trained on digital skills to be future proof. Accounting and finance graduates must be made competent in skills that are related to digital content such as blockchain technology, information assets and autonomous peer to peer systems, to name a few. Methods: We used a three-phase approach: 1) careful mapping of digital topics taught within the course structure offered at these institutions; 2) review of current best practices and digital learning tools for digital inclusion which was ascertained from literature; and 3) 80 experts in a think tank group were interviewed on antecedents, awareness and problems in relation to digital inclusion within the curriculum to validate our research objective. Results: Eleven key tools for inclusion in the curriculum were discussed with experts and then mapped to current curriculum offered at institutions. We discovered that less than 5% of these were being taught. In total, 78% of experts agreed that digital content is inevitable, 90% agreed that digital inclusion based on tools that were discussed will yield great benefits for students, and lastly 75% agreed that giving digital exposure to students must be standard practice. Conclusions: The response from experts confirms that digital inclusion is imperative, but instructors themselves lacked the know-how of emerging technologies. Only the curriculum of institutions with approved bachelor’s programs were included in this research. In our future work we hope to include all institutions and professional bodies as well.",
"keywords": [
"Digital transformation",
"Pedagogy",
"FinTech",
"Teaching and Learning."
],
"content": "Introduction\n\nFintech is a fusion of emerging technologies and finance to provide greater insights to the practice of accounting and finance. However, academic content in the curriculums offered in degree programs do not include these digital topics due to multiple factors, and this has caused education programs to have suffered severe criticism over recent years.\n\nMoffitt listed 30 emerging technologies that will have an enormous impact on jobs and artificial intelligence (AI) was the top of that list.1 Blockchain has been listed as the 4th most prominent emerging technology that will impact jobs.2 Blockchain platforms resolve the core trust issue by maintaining a shared distributed ledger.3,4 Smart contracts within a blockchain can enable the transfer of titles, physical goods and assets simultaneously. Given that a sharing economy will be embedded in every financial system by 2020, financial systems will operate like any other sharing economy.\n\nThis gives rise to cloud computing which would perhaps have the second highest impact on accounting jobs.5 Artificial intelligence (AI) has also found its way into predictive models.6 Audit tasks will also benefit from AI, as the use of artificial neural networks (ANN) for audit tasks thus increases the ability to track and uncover control flaws that humans can’t.4,7 There is a high demand for digital skills, however due to the lack of digital skill sets companies aren’t able to hire a skilled tech-savvy financial workforce.8 Employers have demonstrated their disappointment as the digital gap widens among finance graduates.9 In a study conducted on 200 accounting and finance firms, where 105 graduate students from different universities were evaluated for their digital know-how, results indicated that these graduate students largely lacked in analytical and other digital skills. Hiring personnel equipped with skills in finance-related software, data analytics, and modelling programs is becoming difficult because of the outdated curriculum, which focuses more on traditional and obsolete concepts.4,10\n\nToday’s accounting curriculum is focused on descriptive accounting (see Figure 1).3 Prescriptive accounting is rather limited, with the exception of managerial and cost accounting only (see Figure 2). For example, assets are still recorded and maintained at cost which is not aligned to fair value accounting principles.\n\nAt the operational level most activities can be fully automated. Activities at this level, such as journal entries, are mostly descriptive. The tactical layer requires some level of automation but will mostly be prescriptive (see Figure 3).\n\nBased on the earlier discussion, we proceeded to attempt to understand how much of these essential digital topics (see Table 1) were embedded in the accounting curriculum, as these tools have been endorsed by the literature. Upon mapping to the existing curriculum of major accredited institutions we found very little or no evidence of these digital tools being embedded into the taught curriculum. Out of 11 teaching technologies or tools we could only partially map one item. Table 1 summarizes our findings.\n\nThe objective of this section was to ascertain technological content gaps with reference to tools discussed earlier within the accounting curriculum offered by higher learning institutions. Additional research questions that this paper aimed to address were as follows:\n\n• What is the level of awareness of classroom teaching technologies among accounting educators?\n\n• What are the antecedents for technology inclusion into existing Institutions of Higher Learning (IHL) curriculums?\n\n• What are the problems associated with technology implementation?\n\n\nMethods\n\nThis was an exploratory study with the main focus of understanding how much technological context was covered in the existing accounting curriculum. Throughout the study, Table 2 (detailed description of digital tools) was used as a reference for experts to evaluate and benchmark best practices. A total of 80 individuals, comprising of experts, academicians, program counselors, curriculum experts, program coordinators, subject experts, industry advisory panel members and practitioners were interviewed (with their consent) for feedback. Detailed curriculum and program structures were also reviewed for comparison. The authors Saravanan Muthaiyah and Sanjaya Chamara Sembakutti conducted the interviews; only participants who were willing took part were interviewed, the rest left the hall. The interview took about 10 minutes for each person. We prompted the respondents to talk about the level of digital awareness among instructors and express freely on what were challenges that they faced in updating existing curriculum. We took about 5 days to collect the information needed. Notes were taken during the sessions.\n\nEthical approval was obtained from the research management center at the university. Researchers had to first submit the title of the project, what the author planned to do for the interviews and details of study objectives. The officer at the research management center after reviewing the documents will then issue a letter of clearance for the data collection to be carried out. The approval letter was then obtained, and the reference number of this letter is EA1212021. Consent was obtained verbally prior to the interview and only respondents who were agreeable to be interviewed were approached. The reason for this was this was done in conjunction to a digital transformation workshop in which academics were allowed to express themselves freely about issues and challenges with regards to the teaching curriculum. The review board approved this as it was on voluntary basis.\n\n\nResults\n\nTable 3 below shows how much instructors were aware of tools that could be used to teaching emerging arrears. For this section we interviewed 52 people inclusive of subject matter experts and instructors. We selected those who had at least 5 years of teaching experience. In total, 58 % of educators were not aware about most of the technologies discussed earlier.11 Among those who said they were aware, 23% had only superficial knowledge. For instance, some instructors did not know that Bloomberg Lab provided datasets that could be used for big data and predictive analytics.\n\nInterviewees were requested to rank order factors for the implementation of emerging teaching technologies in the accounting curriculum (see Table 4). Specific reasons that were listed included: 1) training on specific technologies; 2) cost for software licensing; 3) technological resources available (computer labs and hardware); 4) compliance on ministry and accounting body standards; 5) program sustainability; and 6) others.\n\nThe most significant factor was assigned six points, followed by the second most significant value with five points and so on. The results show the overall ranking of the reasons that contributed to the antecedents of classroom technology implementation. Data shows that training on specific technologies was the most significant contributor.\n\nTable 5 highlights the overall ranking of further issues faced by IHL with regards to the inclusion of classroom technologies into the curriculum. The most important factor was assigned four points, followed by three points for the second most important factor and so on.\n\nTable 6 summarizes key hypotheses that were formulated to facilitate this study. In this hypothesis, the objective is to find out whether the implementation of digital content is desirable, the impact of regulatory requirements and will it improve job possibilities significantly.\n\nThe questions that were developed to support the hypothesis are:\n\nHypothesis 1 - digital content is significant for the accounting curriculum\n\n• Do you think digital content inclusion is necessary?\n\n• Will digital content inclusion yield benefits to accounting graduates?\n\n• Digital content inclusion should be standard practice.\n\nOverall, 78% of the experts agree that digital content is necessary, 90% of the respondents agree that digital content will yield benefits to accounting graduates, and lastly, 75% of the respondents agree that this should be standard practice. In this context, the hypothesis that digital content is significant for improved accounting curriculum can be accepted.\n\nHypothesis 2 – regulatory requirements and program standards have a significant relationship with the inclusion of technological content\n\nOut of 80 experts interviewed, 89% agree that regulatory requirements have a significant relationship with the inclusion of technology content. Therefore, this hypothesis can be accepted as well.\n\nHypothesis 3 –Technological competency is highly desirable among potential employers\n\nOut of 80 respondents, 92.5% agree that competency requirement among potential employers has a significant relationship with the inclusion of technology content in the curriculum. Therefore, this hypothesis can be accepted as well.\n\n\nConclusions\n\nResults highlight that there is a significant mismatch of what is needed with what is being taught at universities today. Our hypothesis on technology competency, program standards and digital content required supports this as well. Insights derived from the mapping of existing syllabi enabled us to understand the lack of digital inclusion described earlier in the teaching pedagogy. In summary the findings helped us to provide suggestions as to how universities can improve existing curriculum offered to students. This included eleven essential areas of know-how can be fairly distributed across subjects from year one to year four for a four-year degree program. We are confident that changes made to the program structure and curriculum will definitely produce future ready graduates.\n\n\nData availability\n\nFigshare: FinTech What Should be Taught Really? https://doi.org/10.6084/m9.figshare.14871168.v1.11\n\nThis project contains the following underlying data:\n\n• DataSet FINTECH.xlsx (Dataset includes responses that were documented during the Interview of panel experts, academicians, program counselors, curriculum experts, program coordinators, subject experts, industry advisory panel and practitioners. A total of 15 institutions have been listed and categorically labelled as antecedents, challenges and hypothesis.)\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\nArner DW, Barberis JN, Buckley RP: The Evolution of Fintech: A New Post-Crisis Paradigm? SSRN Electronic J. 2015. Publisher Full Text\n\nSamaduzzaman M: Blockchain: Future of Accounting Education. Asian J Finance Accounting. 2020; 12(2): 14–27. Publisher Full Text\n\nMuthaiyah S: Blockchain for Audit Provenance and Trust: Push Factors, Value Creation and Challenges. Int J Auditing Accounting Studies. Academic Open Access Publishing; 2020; Vol 1(1), pg 13–25.\n\nYoon S: A study on the transformation of accounting based on new technologies: Evidence from Korea. Sustainability. 2020; 12(20): 8669.\n\nTuncay E: Effective use of cloud computing in educational institutions. Proscenia Social and Behavioral Sciences. 2010; 2: 938–942. Publisher Full Text\n\nLam M: Neural network techniques for financial performance prediction: integrating fundamental and technical analysis. Decision Support Systems. 2004; 37(4): 567–581. Publisher Full Text\n\nCalderon TG, Cheh JJ: A roadmap for future neural research in auditing and risk assessment. Int J Accounting Information Systems. 2002; 3: 203–236. Publisher Full Text\n\nHakim RRC: Are accounting graduates prepared for their careers? A comparison of employees’ and employers’ perceptions. Global Review of Accounting and Finance. 2016; 7(2): 1–17. Publisher Full Text\n\nAryanti C, Adhariani D: Students’ perceptions and expectation gap on the skills and knowledge of accounting graduates. J Asian Finance Economics Business. 2020; 7(9): 649–657. Publisher Full Text\n\nAnastasiou EF: Accountancy Graduates’ Employability: Narrowing the Gap between Employers’ Expectations and Students’ Perceptions-The Role of HE.University of Derby (United Kingdom); 2021.\n\nMuthaiyah S, Phang K, Sembakutti S: FinTech What Should be Taught Really?. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "93576",
"date": "23 Dec 2021",
"name": "Indrawati Sambas",
"expertise": [
"Reviewer Expertise Customer adoption in services based on 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\nI think this paper is good and is an imperative addition to the literature. I found that the work was clearly and accurately presented, and it cites the current literature. The study design was appropriate and the work is technically accepted. The work should elaborate more on the explanation of Figure 1 and 2, to make it clearer. The writers have to expand on how the hypotheses are accepted or rejected. What is the threshold? Please cite business research books such as Sekaran (2016). It is better if the verbatim interview can be accessed, to make the explanation of the findings clearer.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "98790",
"date": "11 Jan 2022",
"name": "Samuel Jebaraj Benjamin",
"expertise": [
"Reviewer Expertise Accounting",
"finance"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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; This is an interesting study and timely. Fintech and/or digital skills are highly important for accounting and finance graduates, but is still lacking in their undergraduate syllabus. This study has the potential to contribute to our understanding of this issue. The following are the main issues that the paper needs to address in order to ensure its rigour and contribution are noteworthy.\n\nYou do not define the scope of digital transformation or fintech. Technological areas such as AI, blockchain, cloud computing, ANN, etc. are thrown into the mix without clear coherence with the key focus of the paper. It is hard to follow through chronologically the flow of arguments and paragraph 1 of the Literature Review seems to have been written haphazardly. I suggest to more clearly outline the arguments and motivations of the paper with the proper citations and focus.\n\n“Today’s accounting curriculum is focused on descriptive accounting (see Figure 1). Prescriptive accounting is rather limited, with the exception of managerial and cost accounting only (see Figure 2). For example, assets are still recorded and maintained at cost which is not aligned to fair value accounting principles” ;\nThe relevancy of the statement above is unclear. You are talking about an accounting treatment issue and this has got nothing to do with the fintech or digitalization that your study is concerned with.\n\nI do not see the relevancy of Figure 1 and 2 towards the aims of this study.\n\nIt is unclear why many of the items mentioned in Table 1 were identified, as no prior discussion about it is made in the preceding sections. Only concepts, such the ones I mentioned in Point 1 above, are discussed, but, in Table 1, most of the areas are entirely new in the paper and not previously defined nor addressed. Table 2 should appear before Table 1. However, it is still unclear if how the ‘technologies’ mentioned in Tables 1 and 2 fit under the grand idea of ‘fintech’ or some of the sub-areas that you mentioned in paragraph 1 of the Literature Review.\n\nHypotheses testing approach and how the conclusions are arrived (i.e., valid or not valid) for each hypotheses have to explained.\n\nIs the scope of your study confined to only the undergraduate syllabus in accounting and finance or include postgraduate? You need to clearly indicate this.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-892
|
https://f1000research.com/articles/10-453/v1
|
08 Jun 21
|
{
"type": "Systematic Review",
"title": "Vasoactive agents in acute mesenteric ischaemia in critical care. A systematic review",
"authors": [
"Christopher A Brennan",
"Peter Osei-Bonsu",
"Rachael Eimear McClenaghan",
"Ahmed Nassar",
"Patrice Forget",
"Callum Kaye",
"George Ramsay",
"Peter Osei-Bonsu",
"Rachael Eimear McClenaghan",
"Ahmed Nassar",
"Patrice Forget",
"Callum Kaye",
"George Ramsay"
],
"abstract": "Background: Acute mesenteric ischaemia (AMI) is a surgical emergency which has an associated high mortality. The mainstay of active treatment includes early surgical intervention, with resection of non-viable bowel, and revascularisation of the ischaemic bowel where possible. Due to the physiological insult of AMI however, perioperative care often involves critical care and the use of vasoactive agents to optimise end organ perfusion. A number of these vasoactive agents are currently available with varied mechanism of action and effects on splanchnic blood flow. However, specific guidance on which is the optimal vasoactive drug to use in these settings is limited. This systematic review aimed to evaluate the current evidence comparing vasoactive drugs in AMI. Methods: A systematic search of Ovid Medline, Ovid Embase, Cochrane CENTRAL and the Cochrane Database of Systematic Review was performed on the 5th of November 2020 to identify randomised clinical trials comparing different vasoactive agents in AMI on outcomes including mortality. The search was performed through the Royal College of Surgeons of England (RCSEng) search support library. Results were analysed using the Rayyan platform, and independently screened by four investigators. Results: 614 distinct papers were identified. After screening, there were no randomised clinical trials meeting the inclusion criteria. Conclusions: This review identifies a gap in literature, and therefore recommends an investigation into current practice and clinician preference in relation to vasoactive agents in AMI. Multicentre randomised controlled trials comparing these medications on clinical outcomes will therefore be required to address this question.",
"keywords": [
"Acute Mesenteric Ischaemia",
"AMI",
"Critical Care",
"General Surgery",
"vasoactives",
"vasopressors",
"infarction",
"ischaemic",
"perioperative care",
"splanchnic blood flow",
"noradrenaline",
"levosimendan",
"dobutamine",
"dopexamine",
"dopamine",
"milronone",
"systematic review",
"DELPHI",
"OVID",
"MEDLINE",
"EMBASE",
"COCHRANE",
"CDSR",
"Aberdeen",
"Grampian",
"Human"
],
"content": "Introduction\n\nAcute mesenteric ischaemia (AMI) is a time- critical surgical emergency,1 where early diagnosis and management can prevent bowel infarction, multiorgan failure and death.2–4 It is defined as a sudden inadequacy of arterial supply or venous drainage to the bowel, leading to ischemia and cellular damage, with or without necrosis.5,6 AMI has an estimated incidence of ~1:1000 hospital admissions.1,4,7–9\n\nA number of pathophysiological mechanisms can lead to mesenteric ischaemia.4 “Occlusive” mesenteric ischaemia is due to arterial or venous thrombosis or embolism. “Non-occlusive” is due to acute circulatory failure, usually in the critically unwell patient.10,11 Non-occlusive mesenteric ischaemia (NOMI) can also occur in the setting of critical illness secondary to the use of vasoactive drugs because of splanchnic vasoconstriction.5 Each of these processes cause a gut-derived systemic inflammatory response syndrome (SIRS) or mesenteric ischaemic necrosis, leading to severe metabolic derangement and culminating in multiple organ dysfunction requiring critical care intervention.12,13\n\nEarly imaging with computerised tomography (with arterial and portal venous phase)6 is important for diagnosis and instigating a timely management plan. The optimal management of AMI depends on the underlying pathophysiology and whether the affected bowel is ischaemic or infarcted. Treatment of AMI focuses on reperfusion and/or resection of non-viable bowel.14 As in any critically unwell patient, adequate resuscitation of haemodynamic parameters is important to optimise end-organ perfusion and prevent the development of multiorgan failure.\n\nGiven the extent of sepsis response, AMI management usually requires critical care support. Vasoactive drugs are often required in this setting to optimise haemodynamic status, with the aim of improving supply to the end organs as well as optimising the perfusion of blood to the adjacent intestine segments to the area of ischaemia.15 However, the choice of vasoactive agents is unclear for patients with AMI. This is a result of the various mechanism of action of these medications and differing levels of associated splanchnic vasoconstriction. Some agents, such as noradrenaline and adrenaline, can be effective in improving systemic vascular resistance and thus, maintain the perfusion pressure to the brain and heart. However, they can also be associated with profound splanchnic vasoconstriction which could exacerbate bowel ischaemia by precipitating NOMI.1,16 Other drugs are perceived to have less of an effect on splanchnic vasculature and could theoretically improve perfusion to the primary area of pathology but may impact on perfusion pressure for other organs.\n\nThe mortality rate is variable but often high, especially when detected late or accompanied by metabolic derangement.4,7 This variability in mortality may be secondary to differences in local practice5,17,18 and between clinicians. It may also reflect the lack of evidence-based guidelines available for these conditions.19–23 Vasoactive agents vary in their mechanisms of action, and balance of vasoconstriction, inotropy, and splanchnic vascular dilatation. It is not known whether one may be more beneficial than others in the setting of AMI. This primary aim of this systematic review is to evaluate the current evidence comparing mortality outcomes for vasoactive drugs in AMI. Our PROSPERO summary is illustrated in Figure 1.\n\n\nMethods\n\nThis review has been prepared in line with the Preferred Reporting Items for Systematic reviews and Meta-analyses (PRISMA) statement. The protocol for this systematic review was developed and registered to PROSPERO prior to the analysis of search results (CRD42020212291, 11/11/2020).\n\nThis systematic review aims to identify randomised clinical trials (RCTs) comparing mortality rates associated with different vasoactive agents in AMI. The target population were any patients with AMI admitted into a critical care environment. Vasoactive drugs included were noradrenaline, adrenaline, dopexamine, dobutamine, dopamine, levosimendan, vasopressin, ephedrine or phenylephrine. Comparators were either no vasoactive drug or any other vasoactive drug. The primary outcome was mortality. Secondary outcomes were survival, length of preserved bowel, time to anastomosis, length of critical care admission, and overall length of hospital stay. All published works were searched regardless of date of publication or language.\n\nSearched sources were Ovid Medline, EMBASE, Cochrane CENTRAL and the Cochrane Database of Systematic Review.\n\nThe literature search was conducted by the library department of the Royal College of Surgeons of England. The Patient, Intervention, Control and Outcome (PICO) framework was used and is outlined in Figure 1. Electronic databases of Ovid Medline, EMBASE, Cochrane Central Register of Controlled Trials (CENTRAL) and Cochrane Database of Systematic Reviews (CDSR) were searched for relevant studies. The search was completed on the 5th of November 2020 and included all relevant studies since 1946 including non-English studies and case reports. Search strategies included certain drugs, such as noradrenaline, adrenaline, dopexamine, dobutamine, dopamine, levosimendan, vasopressin, ephedrine or phenylephrine were specified. However, freedom of the searchers to add more terms if required was allowed. A combination of keywords and controlled vocabulary was adapted for each database. Search strategies are outlined in Figures 2, 3 and 4.\n\nSelection process\n\nStudies were screened for relevant phrases of inclusion, where papers were identified as randomised control trials, performed on non-animal subjects, on the subject relating to the usage of vasoactive drugs in AMI. Papers were screened by four reviewers (CB, PO, EM, PF) independently. The process was facilitated using the Rayyan Platform, allowing for independent and anonymous review and analysis of searched literature. Any discrepancies underwent further review until a consensus was reached.\n\nData was collected from the reports identified by the literature search using the Rayyan platform. This platform facilitated independent and anonymous collection of data.https://www.rayyan.ai/\n\nData items\n\nThe Data items we sought were the following: the country of study, the study design, the intervention type (vasoactive medication), pathology and surgery (if any) subtype, the study size, the follow-up-time, the remaining length of small bowel, time to anastomosis, length of critical care stay, length of in hospital stay.\n\nThe reviewers were to assess selected studies using the Grading of Recommendations Assessment, Development and Evaluation (short GRADE) system. GRADE assesses study limitations/risk of bias, inconsistency, indirectness, impreciseness and publication bias. These criteria would have been applied on a study-by-study basis and an outcome level by two reviewers and where there was inconsistency, a third reviewer would assess and provide an outcome. We planned to perform a meta-analysis if the reported results permitted.\n\nIn the case of a negative search without any eligible randomised controlled trials, the plan was to discuss the existing evidence regarding the problem (AMI) and how the intervention might work (use of vasoactive drugs).\n\nThe methods were to be reviewed externally to identify possible sources of potential bias.\n\nStrength was to be assessed using GRADE tools.\n\n\nResults\n\nThis systematic review aimed to identify randomised control trials comparing mortality rates in relation to the use of different vasoactive drugs in AMI. Ovid Medline, EMBASE, Cochrane CENTRAL and the Cochrane Database of Systematic Review were systematically searched as outlined in Figures 1-4.\n\nThe initial search identified a total of 700 articles. After screening for duplicates, 614 articles remained and were reviewed for eligibility. There were no eligible studies identified addressing the specific study question. Reasons for exclusion included: non-randomised controlled trials and studies, non-human trials, and studies which bore no semblance to the question of interest. In view of this, no quantitative analysis was performed. The PRISMA flowchart is outlined in Figure 5.\n\n\nDiscussion\n\nThere is significant variation in the management of AMI, and this may reflect regional variations in mortality associated with this condition. The recent ACPGBI guidance24 on Emergency General Surgery highlighted the relative paucity of research in this field. However, a synthesis of specific aspects of AMI management, such as the choice of vasoactive medications and its influence on mortality was beyond its remit.\n\nThis systemic review aimed to ask that question and assessed the previous publications available. It is of interest that this work failed to identify any studies comparing the use of these drugs in AMI against outcomes.\n\nIn patients who present with symptoms, clinical findings or imaging suggestive of mesenteric arterial ischaemia, resuscitative measures including the avoidance of systemic hypoxia and intravenous fluids are crucial first steps to optimising blood pressure and end organ perfusion.6 Broad spectrum intravenous antibiotics should also be administered promptly due to the potential for bacterial complications in view of the breach of the mucosal barrier.6 Of the small cohort of patients deemed suitable, urgent revascularisation should be pursued to re-perfuse the ischaemic gut through liaison with the interventional radiologists and vascular surgeons. Most patients who are admitted to critical care units will require vasoactive drugs to optimise their blood pressure and cardiovascular status. However, the ideal drug which gives an appropriate increase in systemic arterial pressure without causing a decrease in or compromise of splanchnic perfusion remains to be elicited and the literature on this question is absent.\n\nNoradrenaline and adrenaline\n\nIn the context of AMI, splanchnic blood flow would seem a salient factor. Pharmacologically, noradrenaline is an endogenous catecholamine which primary has a direct alpha-1 effect, although there is a small degree of β-1 adrenergic agonism. It increases systemic vascular resistance (SVR), increasing afterload;- and causes venoconstriction increasing preload. It is weakly a positive inotrope through its β-1 effect. Some studies suggest that noradrenaline reduces hepato-splanchnic blood flow in septic and non-septic patients.25,26 Similarly, adrenaline, a sympathomimetic, was found to have a reductive effect on splanchnic blood flow.27\n\nDopamine and dopexamine\n\nDopamine is a catecholamine, a precursor to noradrenaline, and mediates inotropy via dopamine receptors and vasoconstriction via the alpha-adrenergic pathway. It shows a dose dependent change in action; causing splanchnic dilatation at low doses while increasing SVR at higher doses. Meier-Hellmann et al.28 reported an increase in hepato-splanchnic blood flow in septic patients given dopamine although Neviere and colleagues29 reported a decrease in gut mucosal perfusion. Maynard et al.30 suggested that dopexamine, a dopamine analogue which has vasodilatory effects, may improve gut microcirculation in septic shock; although subsequent investigators did not confirm these beneficial effects.\n\nDobutamine\n\nDobutamine, a synthetic catecholamine is a β1-selective adrenoceptor agonist which is utilised clinically as a positive inotrope in the treatment of acute heart failure and cardiogenic shock. Creteur and colleagues31 determined that a dobutamine infusion did improve both splanchnic oxygenation in septic animals and in septic patients. However, Bomberg et al.32 suggest that in pigs, dobutamine may improve arteriovenous shunting, but conversely may reduce jejunal mucosal perfusion.\n\nVasopressin\n\nOne observational cohort study found that vasopressin, a potent non-catecholamine vasoconstrictor which acts on vasopressin receptors, improved small bowel perfusion and mortality in patients with non-occlusive mesenteric ischaemia (NOMI) who had undergone cardiopulmonary bypass for elective cardiac surgery.13 However, no further assessment of outcome in AMI appears to have been assessed.\n\nLevosimendan and milrinone\n\nLevosimendan is an inotrope which improves contractility by sensitizing cardiac muscle to calcium. It also produces vasodilation by opening ATP-sensitive K+ channels in vascular smooth muscle, although this is not yet demonstrated in the splanchnic circulation.\n\nAn experimental study on hypoxic, stressed new-born piglets showed milrinone, a phosphodiesterase inhibitor which produces an inotropic effect and vascular dilation, improves mesenteric perfusion.33\n\nThere is thus some basic scientific experimental data available on the effects of some vasoactive agents on the splanchnic circulation. However, there are a number of limitations to this, and none have been extrapolated into clinical trials investigating vasoactive medication in AMI, against other agents. In relation to our study question, most of the experimental data focuses on patients in a shocked state as a result of sepsis, or in elective settings such as planned cardiac surgery, rather than in AMI. None of the studies report any clear data in relation to mortality or morbidity, length of hospital or critical care stay associated with any vasoactive agents.\n\nThere may be a role for dobutamine, levosimendan, milrinone, dopamine or vasopressin or other vasoactive agents in improving splanchnic perfusion in mesenteric ischaemia, but further, more extensive, patient-based study is required to elucidate these theories and their clinical significance in relation to patient survival and morbidity.\n\nLimitations\n\nThis study did not identify any qualifying randomised controlled trials in relation to the study question and therefore did not produce a quantitative analysis.\n\n\nConclusions\n\nThis systematic review has identified a gap in literature and research relating to the choice of vasoactive agent in AMI. There are therefore actions we would recommend to aid identifying best practice for this condition. The results of this study would suggest that it is important to investigate current practice and clinician preference. The first step to this would therefore be a Delphi Study which is currently underway and can be found via this link: https://is.gd/vasoactive_agents_AMI. Following the survey is an optionable Delphi process.\n\nRCTs where comparison of outcomes with different vasoactive agents is analysed could ultimately improve the care of the critically ill patient with mesenteric ischaemia and remains absent from any work relating to AMI.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReporting guidelines\n\nHarvard Dataverse. PRISMA checklist and Review Data for: Vasoactive agents in acute mesenteric ischaemia in critical care. A systematic review. DOI: https://doi.org/10.7910/DVN/2GN0BS.34\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\nWith thanks to Helen Fulbright, PhD, MA, PGDip LIS, BA (Hons), MCLIP, Information Specialist, Royal College of Surgeons of England Library and Archives Team, for conducting the literature searches.\n\n\nReferences\n\nTilsed JVT, Casamassima A, Kurihara H, et al.: ESTES guidelines: acute mesenteric ischaemia [Internet]. Eur J Trauma Emerg Surg. 2016 [cited 2020 Sep 24]; 42: 253–270. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHeys SD, Brittenden J, Crofts TJ: Acute mesenteric ischaemia: the continuing difficulty in early diagnosis. Postgrad Med J. 1993 Jan; 69(807): 48–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeone M, Bechis C, Baumstarck K, et al.: Outcome of acute mesenteric ischemia in the intensive care unit: a retrospective, multicenter study of 780 cases. Intensive Care Med. 2015; 41(4): 667–676. PubMed Abstract | Publisher Full Text\n\nCudnik MT, Darbha S, Jones J, et al.: The Diagnosis of Acute Mesenteric Ischemia: A Systematic Review and Meta-analysis. Acad Emerg Med. 2013; 20(11): 1087–1100. PubMed Abstract | Publisher Full Text\n\nOldenburg WA, Lau LL, Rodenberg TJ, et al.: Acute Mesenteric Ischemia: A Clinical Review. Arch Intern Med. 2004 May 24; 164(10): 1054–1062. PubMed Abstract | Publisher Full Text\n\nBala M, Kashuk J, Moore EE, et al.: Acute mesenteric ischemia: guidelines of the World Society of Emergency Surgery. World J Emerg Surg. 2017; 12: 38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHeys SD, Brittenden J, Crofts TJ: Acute mesenteric ischaemia: the continuing difficulty in early diagnosis. Postgrad Med J. 1993. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStoney RJ, Cunningham CG: Acute mesenteric ischemia. Surgery. 1993. PubMed Abstract\n\nAcosta S: Epidemiology of mesenteric vascular disease: Clinical implications. Semin Vasc Surg. 2010. PubMed Abstract | Publisher Full Text\n\nDaviaud F, Grimaldi D, Dechartres A, et al.: Timing and causes of death in septic shock. Ann Intensive Care. 2015; 5: 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuillaume A, Pili-Floury S, Chocron S, et al.: Acute Mesenteric Ischemia Among Postcardiac Surgery Patients Presenting with Multiple Organ Failure. SHOCK. March 2017; 47(3): 296–302. PubMed Abstract | Publisher Full Text\n\nSertaridou E, Papaioannou V, Kolios G, et al.: Gut failure in critical care: old school versus new school. Ann Gastroenterol. 2015. PubMed Abstract | Free Full Text\n\nDeitch EA: Gut-origin sepsis: evolution of a concept. Surgeon. 2012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang RW, Chang JB, Longo WE: Update in management of mesenteric ischemia [Internet]. World J Gastroenterol. WJG Press; 2006 [cited 2020 Sep 24]; 12. : p. 3243–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuther B, Mamopoulos A, Lehmann C, et al.: The Ongoing Challenge of Acute Mesenteric Ischemia. Visc Med. 2018 Jul 1 [cited 2020 Oct 1]; 34(3): 217–223. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBomberg H, Groesdonk H, Raffel M, et al.: Vasopressin as Therapy During Nonocclusive Mesenteric Ischemia. Ann Thorac Surg. 2016; 102(3): 813–819. PubMed Abstract | Publisher Full Text\n\nCrawford RS, et al.: A Statewide Analysis of the Incidence and Outcomes of Acute Mesenteric Ischemia in Maryland from 2009 to 2013. Front Surg. 2016. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLemma AN, et al.: Choice of First Emergency Room Affects the Fate of Patients With Acute Mesenteric Ischaemia: The Importance of Referral Patterns and Triage. Eur J Vasc Endovasc Surg. 2019. PubMed Abstract | Publisher Full Text\n\nKrejci V, Hiltebrand L, Sigurdsson G: Effects of epinephrine, norepinephrine, and phenylephrine on microcirculatory blood flow in the gastrointestinal tract in sepsis. Crit Care Med. 2006; 34(5): 1456–1463. PubMed Abstract | Publisher Full Text\n\nMalay M, Ashton J, Dahl K, et al.: Heterogeneity of the vasoconstrictor effect of vasopressin in septic shock. Crit Care Med. 2004; 32(6): 1327–1331. PubMed Abstract | Publisher Full Text\n\nRussell J, Walley K, Singer J, et al.: Vasopressin versus norepinephrine infusion in patients with septic shock. N Engl J Med. 2008; 358(9): 877–887. PubMed Abstract | Publisher Full Text\n\nAuchet T, Regnier M, Girerd N, et al.: Outcome of patients with septic shock and high-dose vasopressor therapy. Ann Intensive Care. 2017; 7(1): 43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsfar P, Meziani F, Hamel J, et al.: High versus low blood-pressure target in patients with septic shock. N Engl J Med. 2014; 370(17): 1583–1593. PubMed Abstract | Publisher Full Text\n\nACPGBI Emergency General Surgery – A Consensus Statement [Internet]. [cited 2021 Apr 11].. http\n\nReinelt H, Radermacher P, Kiefer P, et al.: Impact of exogenous beta-adrenergic receptor stimulation on hepatosplanchnic oxygen kinetics and metabolic activity in septic shock. Crit Care Med. 1999 Feb; 27(2): 325–31. PubMed Abstract | Publisher Full Text\n\nDuranteau J, Sitbon P, Teboul JL, et al.: Effects of epinephrine, norepinephrine, or the combination of norepinephrine and dobutamine on gastric mucosa in septic shock. Crit Care Med. 1999 May; 27(5): 893–900. PubMed Abstract | Publisher Full Text\n\nBangash MN, Kong ML, Pearse RM: Use of inotropes and vasopressor agents in critically ill patients. Br J Pharmacol. 2012 Apr; 165(7): 2015–33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMeier-Hellmann A, Bredle D, Specht M, et al.: The effects of low-dose dopamine on splanchnic blood flow and oxygen uptake in patients with septic shock. Intensive Care Med. 1997; 23: 31–37. PubMed Abstract | Publisher Full Text\n\nNevière R, Mathieu D, Chagnon JL, et al.: The contrasting effects of dobutamine and dopamine on gastric mucosal perfusion in septic patients. Am J Respir Crit Care Med. 1996 Dec; 154(6 Pt 1): 1684–1688. PubMed Abstract | Publisher Full Text\n\nMaynard ND, Bihari DJ, Dalton RN, et al.: Increasing splanchnic blood flow in the critically III. Chest.1995 Dec; 108(6): 1648–54. PubMed Abstract | Publisher Full Text\n\nCreteur J, De Backer D, Vincent J: A dobutamine test can disclose hepatosplanchnic hypoperfusion in septic patients. Am J Respir Crit Care Med. 1999; 160(3): 839–845. PubMed Abstract | Publisher Full Text\n\nBomberg H, Bierbach B, Flache S, et al.: Dobutamine versus Vasopressin After Mesenteric Ischemia. J Surg Res. 2019 Mar 1; 235: 410–423. PubMed Abstract | Publisher Full Text\n\nManouchehri N, Bigam D, Churchill T, et al.: Milrinone is preferred to levosimendan for mesenteric perfusion in hypoxia-reoxygenated newborn piglets treated with dopamine. Pediatr Res. 2012; 71: 241–246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrennan CA, Osei-Bonsu P, McClenaghan RE, et al.: Review Data for: Vasoactive agents in acute mesenteric ischaemia in critical care. A systematic review Harvard Dataverse. 2021; V1. Publisher Full Text"
}
|
[
{
"id": "87014",
"date": "14 Jun 2021",
"name": "Nick Heywood",
"expertise": [
"Reviewer Expertise My areas of expertise include general surgery with specific interest in collaborative research",
"colorectal sruegry and in particular pelvic floor disorders and cancer"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI would like to thank the authors for the opportunity to review this paper “Review of Vasoactive agents in acute mesenteric ischaemia in critical care. A systematic review.\" This is indeed an area where there is paucity of research and this paper certainly demonstrates that. I do however have the following points which should be addressed before acceptance for indexing in Pub Med.\nThe authors state that their aim in the introduction is: “This primary aim of this systematic review is to evaluate the current evidence comparing mortality outcomes for vasoactive drugs in AMI”, however in the results section they state that “This systematic review aimed to identify randomised control trials comparing mortality rates in relation to the use of different vasoactive drugs in AMI.” The authors state in the abstract results section that there is no randomised controlled trial, and this is the only result. The authors included non-randomised trials including case reports in their search, yet there is no comment on the results, nor any narrative as to the types of study out of the 614 returned in the search. There should be a descriptive in the result section as to the numbers of each types of study, i.e. number of case reports (including number of patients in these case reports), number of observational studies etc.\n\nThe Methods section is very detailed and could be easily replicated. I commend the authors for their thorough search of the all the relevant articles.\n\nWith regards to the findings, they do indeed make this study difficult to write in a manuscript and the authors need to be clear about searching for rCTs vs case inclusion of case reports. For example, if the authors were not interested in case reports, why were they not excluded early in the study. It may be that they wanted to ensure no studies were missed, but this should be discussed in the paper.\n\nThe findings, or lack thereof, makes the discussion limited. Upon reading the discussion, it felt like reading a review article rather than the discussion section of a systematic review. I understand that the authors need to write the discussion, but much of this does not seem relevant to the discussion section of this type of article. It feels more at place in an introduction or a separate article regarding the choices of treatments for this disease process.\n\nThe authors should focus on discussing the types of papers that were found in the review, what types of studies they found and their limitations. The should also discuss why some of the 29 non-relevant RCTs were indeed non-relevant. Although the authors touch upon this in the introduction, they may wish to focus the discussion on the difficulties associated with undertaking this type of study and why there may be lack of data. A degree of speculation is needed here, but would be more relevant than the pharmacology of vasoactive drugs, for which should not really be included in the discussion section.\nOverall, I agree that this message is very important and certainly supports future work, that I am glad to see is being developed, however, this paper needs more work before acceptance for indexing in PubMed\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "7075",
"date": "06 Sep 2021",
"name": "Christopher Brennan",
"role": "Author Response",
"response": "The authors state that their aim in the introduction is: “This primary aim of this systematic review is to evaluate the current evidence comparing mortality outcomes for vasoactive drugs in AMI”, however in the results section they state that “This systematic review aimed to identify randomised control trials comparing mortality rates in relation to the use of different vasoactive drugs in AMI.” The authors state in the abstract results section that there is no randomised controlled trial, and this is the only result. The authors included non-randomised trials including case reports in their search, yet there is no comment on the results, nor any narrative as to the types of study out of the 614 returned in the search. There should be a descriptive in the result section as to the numbers of each types of study, i.e. number of case reports (including number of patients in these case reports), number of observational studies etc. Our primary interest in undertaking this work was to assess whether there was capacity for a randomised clinical trial to be developed comparing different vasoactive agents in this field. Thus, for this systematic review only RCT’s were considered for inclusion. Response: The search protocol identified many non-RCT’s, which were excluded at an early stage and not further analysed. The further RCT’s were excluded for being entirely unrelated, or trials not performed in humans. We have edited the results section to clarify this. We have also added a descriptor in the results section highlighting the breakdown of results, and reasons for exclusion. The Methods section is very detailed and could be easily replicated. I commend the authors for their thorough search of the all the relevant articles. Response: We thank the reviewer for their commendation. With regards to the findings, they do indeed make this study difficult to write in a manuscript and the authors need to be clear about searching for rCTs vs case inclusion of case reports. For example, if the authors were not interested in case reports, why were they not excluded early in the study. It may be that they wanted to ensure no studies were missed, but this should be discussed in the paper. Case reports were identified in the initial search protocol and thus acknowledged. However as we were specifically interested in RCT’s, these were excluded. Response: As the reviewer suggests, we did not want to miss any studies and this is why we did not remove case reports initially. This fact has been further highlighted in the methods section. The findings, or lack thereof, makes the discussion limited. Upon reading the discussion, it felt like reading a review article rather than the discussion section of a systematic review. I understand that the authors need to write the discussion, but much of this does not seem relevant to the discussion section of this type of article. It feels more at place in an introduction or a separate article regarding the choices of treatments for this disease process. Response: Given the results of our systematic review we felt that discussion around the broader topic would be of benefit to provide context to the relevance of our review. Due to the review only specifically looking for RCT’s, further analysis of the case reports identified was not performed. This is an area of research that, with our search strategy freely available, could be performed in the future. We have added this statement to the conclusion section. The authors should focus on discussing the types of papers that were found in the review, what types of studies they found and their limitations. The should also discuss why some of the 29 non-relevant RCTs were indeed non-relevant. Although the authors touch upon this in the introduction, they may wish to focus the discussion on the difficulties associated with undertaking this type of study and why there may be lack of data. A degree of speculation is needed here, but would be more relevant than the pharmacology of vasoactive drugs, for which should not really be included in the discussion section. Response: Of the 29 human non-relevant RCT’s, none were on the subject of mesenteric ischaemia, or vasoactive support. We have specifically clarified this point in the discussion section."
}
]
},
{
"id": "87013",
"date": "21 Jun 2021",
"name": "Norman Galbraith",
"expertise": [
"Reviewer Expertise General surgery",
"colorectal surgery",
"Inflammatory response",
"macrophage/monocyte function"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a systematic review of which vasoactive therapeutics are best in patients with acute mesenteric ischaemia. This is a clinically important and under-researched condition with a poor evidence base. I applaud the authors for raising pursuing this topic and this article is an important step to highlight the lack of evidence, despite being so common, in a systematic way. The article is well written and understandable. Methodologically, it follows the PRISMA steps of a systematic review.\nSome suggestions I have are:\nIt wasn’t entirely clear to me whether this study was to determine which agents were optimum in part of the treatment of acute mesenteric ischaemia (i.e. occlusive), or which agent was a potential cause of acute mesenteric ischaemia in the already critically unwell patient with another primary diagnosis e.g. sepsis. I would suggest clarifying this when stating the aim/hypothesis at the end of the introduction, or in the methods section (and potentially in the “Research question” section of Figure 1 by including the phrase “the treatment of” or “prevention of”).\n\nAs a clinically important, common but well known to be under-researched area, it is maybe not surprising there are no RCT’s in this subject. Did the authors consider widening their search to include non-randomised prospective studies, or observational/retrospective studies where we might expect some evidence to lie? If not, due to the likely biased nature of some of these weaker type of studies, I would suggest the authors state/justify why they have not included this body of evidence in their study. Alternatively, if the authors have searched this or have some data of observational studies, adding this as a table or supplementary table would strengthen the paper.\n\nHaving the exact search strategy included is appreciated and makes the study more reproducible, however, I would suggest putting all of these tables to the supplementary section.\n\nTo further the strength of the methodology, demonstrating that the “grey literature” has been searched to check for additional evidence/publication bias would be helpful. Some articles now use the OpenGrey platform to do this.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "7076",
"date": "06 Sep 2021",
"name": "Christopher Brennan",
"role": "Author Response",
"response": "It wasn’t entirely clear to me whether this study was to determine which agents were optimum in part of the treatment of acute mesenteric ischaemia (i.e. occlusive), or which agent was a potential cause of acute mesenteric ischaemia in the already critically unwell patient with another primary diagnosis e.g. sepsis. I would suggest clarifying this when stating the aim/hypothesis at the end of the introduction, or in the methods section (and potentially in the “Research question” section of Figure 1 by including the phrase “the treatment of” or “prevention of”). Response: Our review intends to look at vasoactive choice in treatment of mesenteric ischaemia, as opposed to risk of causing ischaemia. Although ischaemia as side effect of vasoactive agents was not considered here, it is of interest to consider both for the pathophysiology and for the evaluation of the most promising agent for a future RCT. We have clarified this in the aims section of the introduction. As a clinically important, common but well known to be under-researched area, it is maybe not surprising there are no RCT’s in this subject. Did the authors consider widening their search to include non-randomised prospective studies, or observational/retrospective studies where we might expect some evidence to lie? If not, due to the likely biased nature of some of these weaker type of studies, I would suggest the authors state/justify why they have not included this body of evidence in their study. Alternatively, if the authors have searched this or have some data of observational studies, adding this as a table or supplementary table would strengthen the paper. Response: Many thanks for your comment. For the purpose of this review, only RCT’s were considered. A further review in the future with our search protocol, analysing case reports, would likely be of merit. Our review highlights the lack of RCT’s on the subject matter, which can be used to prompt further analysis of data. We have added a statement to the conclusion. Having the exact search strategy included is appreciated and makes the study more reproducible, however, I would suggest putting all of these tables to the supplementary section. Response: Many thanks. The structure of this systematic review is as per the publishers guidelines. To further the strength of the methodology, demonstrating that the “grey literature” has been searched to check for additional evidence/publication bias would be helpful. Some articles now use the OpenGrey platform to do this. Response: Many thanks for your comment. However, we have not performed a grey literature search as we wish to assess if there is any direct comparison published, in the form of RCT between different vaso-active agents in this setting."
}
]
},
{
"id": "87010",
"date": "29 Jun 2021",
"name": "Xavier Wittebole",
"expertise": [
"Reviewer Expertise Critical Care Medicine",
"Sepsis"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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\nThe authors performed a systematic review to assess the role of vasopressors in acute mesenteric ischemia (AMI). From 614 papers, they could not find any randomized controlled trial and conclude “Multicenter randomized controlled trials comparing these medications on clinical outcomes will therefore be required to address this question.” They further discuss the effects of some of these vasoactive agents.\n\nSPECIFIC COMMENTS:\nThe authors distinguish 2 different mechanisms that may explain AMI and propose vasopressors would be responsible for non-occlusive MI (NOMI). However, in NOMI, it is difficult to assess the exact role of vasopressors versus the cause for which the vasopressors are used. For instance, the microcirculatory changes observed in sepsis may also explain some ischemic lesions without any effect of vasopressors per se. This could be briefly discussed.\n\nThe authors should also better clarify the fact they searched for the best vasopressor therapy in AMI versus the medication that would be responsible for the development of AMI.\n\nA recent meta-analysis (Belletti et al. 20201) assessed the effects of continuous epinephrine infusion on survival in critical care patients. In this MA, a secondary endpoint evaluated the development of bowel ischemia. This study might be a source of other papers that could be assessed for this present study.\n\nIt might be of interest the authors check some large trials on vasopressors (vasopressin and the Vasst study; selepressin and the SepsisAct study; angiotensin II and the Athos-3 study; etc). By evaluating the side effects in those trials (mesenteric ischemia), the authors could already provide a beginning of answer to the question raised. While out of the scope of this study, this might however be of interest.\n\nWhen discussing the various vasoactive drugs, I would propose the authors classify them as “mostly vasopressors” (nor-adrenalin, etc) and “mostly inotropes” dobutamine, etc) and “mixed action” (epinephrine, etc).\n\nSome vasopressors are not discussed. (terlipressin, selepressin, angiotensin II).\n\nMINOR COMMENTS:\nI personally found the abstract’s background too long.\n\nFigures 2, 3 and 4 could be provided in a supplementary appendix.\n\nThe authors could also remind the reader that CT scan has a low sensitivity to diagnose trans-mural ischemia (see for instance Verdot et al. (20212)).\n\nIn the Eligibility Criteria paragraph, the authors propose various secondary outcomes including “length of critical care admission”. I would propose to write “ICU length of stay”.\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": []
}
] | 1
|
https://f1000research.com/articles/10-453
|
https://f1000research.com/articles/10-543/v1
|
07 Jul 21
|
{
"type": "Systematic Review",
"title": "Type 2 Diabetes Mellitus in Nepal from 2000 to 2020: A systematic review and meta-analysis",
"authors": [
"Dhan Bahadur Shrestha",
"Pravash Budhathoki",
"Yub Raj Sedhai",
"Achyut Marahatta",
"Samit Lamichhane",
"Sarbin Nepal",
"Anurag Adhikari",
"Ayusha Poudel",
"Samata Nepal",
"Alok Atreya",
"Dhan Bahadur Shrestha",
"Pravash Budhathoki",
"Yub Raj Sedhai",
"Achyut Marahatta",
"Samit Lamichhane",
"Sarbin Nepal",
"Anurag Adhikari",
"Ayusha Poudel",
"Samata Nepal"
],
"abstract": "Aims: To evaluate the prevalence and risk factors of type 2 diabetes mellitus (T2DM) from 2000-2020 in various parts of Nepal. Methods: PubMed, Embase, Scopus, and Google Scholar were searched using the appropriate keywords. All Nepalese studies mentioning the prevalence of T2DM and/or details such as risk factors were included. Studies were screened using Covidence. Two reviewers independently selected studies based on the inclusion criteria. Meta-analysis was conducted using Comprehensive Meta-Analysis Software v.3. Results: Total 15 studies met the inclusion criteria. The prevalence of T2DM, pre-diabetes, and impaired glucose tolerance in Nepal in the last two decades was 10% (CI, 7.1%- 13.9%), 19.4% (CI, 11.2%- 31.3%), and 11.0% (CI, 4.3%- 25.4%) respectively. The prevalence of T2DM in the year 2010-15 was 7.75% (CI, 3.67-15.61), and it increased to 11.24% between 2015-2020 (CI, 7.89-15.77). There were 2.19 times higher odds of having T2DM if the body mass index was ≥24.9 kg/m2. Analysis showed normal waist circumference, normal blood pressure, and no history of T2DM in a family has 64.1%, 62.1%, and 67.3% lower odds of having T2DM, respectively. Conclusion: The prevalence of T2DM, pre-diabetes, and impaired glucose tolerance in Nepal was estimated to be 10%, 19.4%, and 11% respectively.",
"keywords": [
"Blood Pressure",
"Body Mass Index",
"Diabetes Mellitus Type 2",
"Nepal"
],
"content": "Introduction\n\nIn 2019, the International Diabetes Federation (IDF) estimated that 463 million adults worldwide had diabetes1. The statistics showed that these individuals were in the age range of 20 to 79, have diabetes, and 79.4% were from low- and middle-income countries1. Additionally, IDF estimates that the global prevalence of diabetes will be 578.4 million by 2030, with this rising to 700.2 million by 2045 among adults aged between 20 to 79 years1 In the region of Southeast Asia, the prevalence of diabetes was 8.8% in 2019, and this is projected to increase to 9.7% by 20302. Type 2 diabetes mellitus (T2DM) still remains a major cause of worldwide morbidity and mortality, which leads to complications such as neuropathy, nephropathy, stroke, and coronary artery disease3. In 2017, over 10, 000 individuals died due to T2DM or diabetes-related complications in Nepal, which is the 11th most common cause of disability in terms of disability-adjusted life years (DALYs) (1226 DALYs per 10,000 population)4. In 2020, the prevalence of T2DM in Nepal was 8.5% (95% CI 6.9–10.4%), which was higher than that of 8.4% (95% CI 6.2–10.5%) in 20145,6. Similarly, in 2020 the prevalence of pre-diabetes was 9.2% (95% CI 6.6 – 12.6%) compared to 2014, which was 10.3% (95% CI 6.1–14.4%)5,6. In the advent of growing non-communicable diseases, a Multi-Sectoral Action Plan has been adopted by the government of Nepal to prevent and control non-communicable diseases including T2DM7. However, there have not been many studies that evaluate the risk factors of T2DM in Nepal, which can be helpful for the prevention and control of this disease. We conducted this review to evaluate the prevalence and risk factors of pre-diabetes and T2DM in Nepal over the past 20 years, by pooling the studies done in various parts of the country.\n\n\nMethods\n\nThe systematic review is registered in PROSPERO (CRD42020215247). It is documented as per the guidelines of the Meta-Analysis of Observational Studies in Epidemiology (MOOSE)8,9.\n\nElectronic databases such as PubMed, PubMed Central, Google Scholar, Scopus, and Embase were used to search relevant articles (Extended data file 110). Published articles from 2000 to 2020 were searched with the use of the appropriate keywords such as “diabetes mellitus”, “high blood sugar”, “type 2 diabetes”, “prevalence”, “risk factor” and “Nepal” along with relevant Boolean operators.\n\nAll published studies that took place in Nepal from 2000–2020 were included in this review. These studies comprised of cross-sectional studies, case series that reported on more than 50 patients, cohort study, randomized control trial (RCTs) that were based on prevalence of T2DM and/or its related issues such as risk factors, outcome, and outcome predictors.\n\nEditorials, commentaries, viewpoint articles without adequate data on T2DM and its related issues were excluded. Furthermore, studies that took place before 1999, outside of Nepal, as well as those that were on Type 1 and gestational diabetes were excluded.\n\nThe studies were selected with the use of Covidence11. The title and abstract were screened based on the inclusion criteria independently by two authors (SL, SN). Discrepancies were resolved by consensus obtained from the third author (AM). Further full-text review (SN, AM) was done independently, and discrepancies (SL) were resolved.\n\nThree authors (SL, AM, and SN) were independently involved in the data extraction and adding that to a standardized form in Excel. The accuracy and completion of each other's work was verified by all the reviewers. The characteristics extracted for each selected study included, first author, year, study design, sample size, study location, prevalence rate, and risk factors of T2DM such as Body Mass Index (BMI), exercise (moderate to high level of exercise (≥ 30 minutes/days) is taken as adequate), waist circumference (≥85 cm in females, and ≥90 cm in males were defined as high), family history, fruit and vegetable serving per day, alcohol, smoking/tobacco, literacy, and increased blood pressure (BP) (≥140/90 mmHg is taken as hypertensive) (Please see Underlying data12).\n\nComprehensive Meta-Analysis Software (CMA) v.3 was used to analyze the extracted data.\n\nT2DM was defined as a fasting blood glucose (FBG) of ≥ 126 mg/dl (7.0 mmol/l) or a 2-h oral glucose tolerance test (OGTT) blood glucose level of ≥ 200 mg/dl (11.1 mmol/l). Prediabetes was defined as FBG level between 100 (5.6 mmol/l) and 125 mg/dL (< 7 mmol/l) or a 2-h OGTT blood glucose level between 140 (7.8 mmol/l) and 199 mg/dl (11 mmol/l). Impaired glucose tolerance (IGT) was defined as two-hour glucose levels of 140 to 199 mg per dL (7.8 to 11.0 mmol) on the 75-g oral glucose tolerance test13.\n\nBias assessment of the included studies was done by the Joanna Briggs Institute (JBI) tool (Table 1)14.\n\nThe heterogeneity in the included studies was assessed based on the Cochrane Handbook for Systematic reviews by the I2 statistics (I2>50%)15. Thus, a random-effects model with the inverse variance heterogeneity model was performed. If I²>50% significant heterogeneity random effect model was preferred. If I²<50% then fixed effect model was preferred.\n\nThe sensitivity analysis was performed by excluding studies that did not show any significant difference in the prevalence of T2DM.\n\n\nResult\n\nA total of 4651 studies were analyzed after thorough database search, of which 736 were identified as duplicates and removed. Title and abstracts of 3915 studies were screened and 3822 studies were excluded. The full-text eligibility of 92 studies was assessed and 77 studies were excluded for definite reasons. A total of 15 studies were included in the qualitative and quantitative analysis. The following information is depicted in the PRISMA flow diagram (Figure 1).\n\nA qualitative summary of the individual study is presented in (Table 2).\n\nBPKIHS, B.P. Koirala Institute of Health Sciences; F, female; IGT, Impaired Glucose Test; M, Male.\n\nA total of 15 studies were included in the quantitative analysis.\n\nThe random effects meta-analysis assessment of 15 studies indicated T2DM prevalence at 10% (95% CI, 7.1%- 13.9%) (Figure 2). Sensitivity analysis was performed with the exclusion of individual studies which resulted in no significant differences in the prevalence of T2DM (Extended data file 2, Figure 110)\n\nThe assessment of T2DM prevalence between 2010–2015 with the use of random-effects meta-analysis was 7.75% (Proportion, 0.0775; 95% CI, 0.0367-0.1561; studies: 4; I2:99.62), while this value increased to 11.24%, between 2015–2020 (Proportion, 0.1124; 95% CI, 0.0789-0.1577; I2: 96.74) (Figure 3).\n\nIn relation to the study setting, the re-analysis of the data with the use of the random-effects model showed that 10.4% among surveyed adult population based on community-based studies had T2DM (Proportion, 0.1040; 95% CI, 0.0668-0.1596) (Extended data file 2, Figure 2), while 9.23% among hospital/Directly observed, treatment short-course (DOTS) center-based studies have this disease (Proportion, 0.0923; 95% CI, 0.0509-0.1617) (Extended data file 2, Figure 310).\n\nPre-diabetes was present in 19.4% (Proportion, 0.194; 95% CI, 11.2%- 31.3%) (Extended data file 2, Figure 4) and IGT in 11.0% (Proportion, 0.110; 95% CI, 4.3%- 25.4%) (Extended data file 2, Figure 510).\n\nExercise. Random-effects model that incorporated data from six studies on exercise showed that the difference in T2DM status between adequate and inadequate exercise groups were not statically significant (OR, 0.75, 95% CI, 0.49-1.16; I2, 67.85%) (Figure 4).\n\nBMI. Fixed-effect meta-analysis of five studies that reported on the BMI indicated that with a BMI ≥24.9 kg/m2 the odds of having T2DM is 2.19 times higher than with BMI <24.9 kg/m2 (OR, 2.197; 95% CI, 1.799-2.683) (Figure 5).\n\nWaist circumference. Individuals with healthy waist circumference had 64.1% lower odds of having T2DM compared with those with high waist circumference (OR, 0.361; 95% CI, 0.284-0.460; I2, 0%) (Extended data file 2, Figure 410).\n\nSmoking status. The random-effects meta-analysis of four T2DM studies based on smoking status indicated that the differences in T2DM status among smokers and non-smoker were not significant (OR, 0.752; 95% CI, 0.366-1.546; I2; 87.2%) (Figure 6).\n\nAlcohol consumption. T2DM status in relation with alcohol consumption was assessed by four studies with the use of random-effects model. The results showed that T2DM status among alcoholic and non-alcoholic groups were not statistically significant (OR, 0.750; 95% CI, 0.439-1.281 I2; 37.72%) (Figure 7).\n\nBP. Fixed-effect meta-analysis of three studies that have reported on T2DM status in relation with BP has indicated that the odds of individuals with normal BP having T2DM is 62.1% lower than those with high BP (OR, 0.379; 95% CI, 0.290-0.495) (Figure 8).\n\nLiteracy. The assessment of four studies that reported on T2DM based on literacy status did not show any significant differences in T2DM between literate and illiterate groups (OR, 1.165; 95% CI, 0.664-2.045; I2, 93.61%) (Figure 9).\n\nFamily history. The random-effects meta-analysis of three studies indicated that the odds of T2DM in individuals without a family history of T2DM were 67.3% lower in comparison to those with a family history (OR, 0.327; 95% CI, 0.202-0.529; I2, 56.62%) (Figure 10).\n\nFruits and vegetables intake. The data assessment of the two studies that had reported on T2DM status in relation to fruits and vegetable intake did not reach a significant difference (OR, 0.933; 95% CI, 0.441-1.976; I2, 78.72%). (Extended data file 2, Figure 710).\n\nPublication bias. Publication bias among the included studies were tested with the use of Egger’s test and was presented in a Funnel plot. The prevalence of T2DM in the Funnel plot showed an asymmetric distribution of studies, which suggested publication bias (Extended data file 2, Figure 810).\n\n\nDiscussion\n\nThe prevalence of T2DM, pre-diabetes, and IGT in Nepal was found to be 10%, 19.4%, and 11% respectively. Our results show that in Nepal obesity is the highest risk factor for T2DM, while individuals with normal waist circumference and lack of family history of T2DM had lower risk of T2DM.\n\nThe estimated prevalence of T2DM was higher than that reported in WHO STEP wise approach to Surveillance (STEPS) survey in 2013 (3.6%), and previous meta-analyses (8.4% and 8.5%)5,6,31. Similarly, the estimated prevalence of pre-diabetes in our study was almost double than what has been reported in other studies5,6. One explanation for this finding can be the rapid urbanization, and migration from rural to urban areas which has promoted a sedentary lifestyle among individuals, along with consumption of unhealthy foods32. As per our study, high BMI was the main cause of T2DM in Nepal. In South Asia, lifestyle factors such as poor diet, and increased sedentary behaviors with limited physical activities have contributed to the rise of overweight and obesity among children and adolescents33. Rapid development of the economic situation in developing countries like Nepal has resulted in a change of diet rich in cereal and vegetables to one with animal products and processed food with high fat and sugar content34. In a study by Hills et al. the prevalence of overweight in Nepal was estimated to be 16.7%, with a higher prevalence in women (19.6%) compared to men (13.6%)34. Obesity is closely linked with premature onset of T2DM and cardiovascular disease35. A similar increasing trend of T2DM led by obesity is seen in Africa as well36. It is important to target T2DM risk factors in order to take control of this disease in Nepal. Our finds highlight the importance of exercise and a healthy diet to prevent the increased morbidity among individuals with T2DM in this country. Shrestha et al. found that the T2DM awareness to be low, with nearly half of the population unaware of the fact that they had this disease6. Increasing public awareness about non-communicable diseases like T2DM and hypertension, and the need to implement a healthy lifestyle is of paramount importance given that our results indicated that individuals with normal blood pressure had less chance of developing T2DM compared to those with hypertension. Increased intake of oily foods, reusing cooking oils which can cause increased conversion of unsaturated fats to trans fats, and low consumption of fruits and vegetables have been found throughout South Asia37,38. These unhealthy dietary habits lead to increased risks of non-communicable diseases like T2DM and hypertension. Thus, interventions are needed to better manage the overweight and obesity epidemic. This can be achieved through various measures such as opening public parks in the cities for exercise, educating the population about what a healthy lifestyle entails such as decreasing the intake of oily foods, increasing the intake of fruits and vegetable, as well as improving the quality of food. Our study has several strengths. Firstly, we performed comprehensive literature search to pool the results of fifteen studies over the last twenty years to evaluate the prevalence of T2DM in Nepal. In addition, no prior meta-analysis has evaluated the risk factors for T2DM, specifically IGT in Nepal, prior to our study. We also analyzed data based on a time frame, where significant increase in T2DM prevalence was observed in Nepal when comparing 2010–2015 with 2015–2020. Our study had some limitations. There was heterogeneity in the studies due to variation in the T2DM diagnostic criteria, different demographics of the population, etc. Most of the included studies were based on specific areas such as province 1 and 3, and not enough studies have been done on a national scale. Finally, risk factors for T2DM were not reported in all the studies that were included.\n\n\nConclusion\n\nThe prevalence of T2DM, pre-diabetes and IGT in Nepal was estimated to be 10%, 19.4% and 11% respectively. Obesity is the major risk factor of T2DM in Nepal and people with normal waist circumference, normal blood pressure and lack of family history of T2DM had lower odds of developing this disease.\n\n\nData availability statement\n\nFigshare: Diabetes Mellitus in Nepal from 2000 to 2020: A systematic review and meta-analysis\n\nhttps://doi.org/10.6084/m9.figshare.14706648.v112\n\nThe project contains the following underlying data:\n\nDataset: Quantitative data, glycemic control, socio-economic status, BMI, exercise, T2DM prevalence, waist circumference, family history, fruit and vegetable serving per day, alcohol consumption, smoking, education, and BP)\n\nFigshare: Diabetes Mellitus in Nepal from 2000 to 2020: A systematic review and meta-analysis\n\nhttps://doi.org/10.6084/m9.figshare.14854065.v110\n\nThe project contains the following underlying data:\n\nData file 1: Electronic search details\n\nData file 2: Additional analysis\n\nData file 3: PRISMA 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\n\nAuthors' contributions\n\nDBS, PB, and YRS contributed to the concept and design, analysis, and interpretation of data. DBS, PB, AM, SL, SN, AA, and AP contributed to the literature search, data extraction, review, and initial manuscript drafting. YRS, SN, and AA interpretation of data, revising the manuscript for important intellectual content, and approval of the final manuscript.\n\nAll authors were involved in drafting and revising the manuscript and approved the final version.",
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PubMed Abstract | Publisher Full Text\n\nMehta KD, Karki P, Lamsal M, et al.: Hyperglycemia, glucose intolerance, hypertension and socioeconomic position in eastern Nepal. Southeast Asian J Trop Med Public Health. 2011; 42(1): 197–207. PubMed Abstract\n\nShrestha UK, Singh DL, Bhattarai MD: The prevalence of hypertension and diabetes defined by fasting and 2-h plasma glucose criteria in urban Nepal. Diabet Med. 2006; 23(10): 1130–5. PubMed Abstract | Publisher Full Text\n\nDhimal M, Karki KB, Sharma SK, et al.: Prevalence of Selected Chronic Non-Communicable Diseases in Nepal. J Nepal Health Res Counc. 2019; 17(3): 394–401. PubMed Abstract | Publisher Full Text\n\nKushwaha A, Kadel AR: Prevalence of type 2 diabetes mellitus among people attending medical camp in a community hospital. JNMA J Nepal Med Assoc. 2020; 58(225): 314–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAryal KK, Mehata S, Neupane S, et al.: The burden and determinants of non communicable diseases risk factors in Nepal: Findings from a nationwide STEPS survey. PLoS One. 2015; 10(8): e0134834. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdhikari B, Mishra SR: Culture and epidemiology of diabetes in South Asia. J Glob Health. 2019; 9(2): 020301. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMisra A, Khurana L: Obesity and the metabolic syndrome in developing countries. J Clin Endocrinol Metab. 2008; 93(11 Suppl 1): S9–30. PubMed Abstract | Publisher Full Text\n\nHills AP, Arena R, Khunti K, et al.: Epidemiology and determinants of type 2 diabetes in south Asia. Lancet Diabetes Endocrinol. Lancet Publishing Group; 2018; 6(12): 966–78. PubMed Abstract | Publisher Full Text\n\nGupta N, Goel K, Shah P, et al.: Childhood obesity in developing countries: Epidemiology, determinants, and prevention. Endocr Rev. 2012; 33(1): 48–70. PubMed Abstract | Publisher Full Text\n\nNCD Risk Factor Collaboration (NCD-RisC): Trends in adult body-mass index in 200 countries from 1975 to 2014: a pooled analysis of 1698 population-based measurement studies with 19·2 million participants. Lancet. 2016; 387(10026): 1377–96. PubMed Abstract | Publisher Full Text\n\nBhardwaj S, Passi SJ, Misra A, et al.: Effect of heating/reheating of fats/oils, as used by Asian Indians, on trans fatty acid formation. Food Chem. 2016; 212: 663–70. PubMed Abstract | Publisher Full Text\n\nKanungsukkasem U, Ng N, Van Minh H, et al.: Fruit and vegetable consumption in rural adults population in indepth hdss sites in asia. Glob Health Action. 2009; 2(1): 35–43. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "89249",
"date": "29 Jul 2021",
"name": "Sijan Basnet",
"expertise": [
"Reviewer Expertise Internal Medicine"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very well-written manuscript with robust statistical analysis.\n\nPlease mention the limitations of your study if any.\n\nMost of the studies cited are from the 2010s. There is one from 2000 with 1840 subjects from an outpatient clinic in a city that may not be representative of the country’s demographics and one from 2006 with 1012 subjects from seven wards that are being used to study the trend. Does this skew your results in any way? Also, the authors justify the increasing prevalence of rapid urbanization but the above studies were done in cities.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "7095",
"date": "06 Sep 2021",
"name": "Alok Atreya",
"role": "Author Response",
"response": "Thank you for the comment. Due to the relatively few studies from 2000-2010. We did an analysis based on a published study between 2010-2015, and 2015-2020 as “The assessment of T2DM prevalence between 2010–2015 with the use of random-effects meta-analysis was 7.75% (Proportion, 0.0775; 95% CI, 0.0367-0.1561; studies: 4; I 2:99.62), while this value increased to 11.24%, between 2015–2020 (Proportion, 0.1124; 95% CI, 0.0789-0.1577; I 2: 96.74)”. Analysis showed some increasing trends of T2DM in Nepal which is of concern. Being our meta-analysis is a secondary analysis of the published literature, we do have some limitations due to primary studies variation. We have included our study limitations as “Our study had some limitations. There was heterogeneity in the studies due to variation in the T2DM diagnostic criteria, different demographics of the population, etc. Most of the included studies were based on specific areas such as provinces 1 and 3, and not enough studies have been done on a national scale. Finally, risk factors for T2DM were not reported in all the studies that were included.”"
}
]
},
{
"id": "91625",
"date": "13 Aug 2021",
"name": "Chudchawal Juntarawijit",
"expertise": [
"Reviewer Expertise Environmental health 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\nBackground:\nIn the introduction, more information about the prevalence and risk factors of diabetes should be presented and reorganized for easy reading. The research problem and hypothesis also need to be clearly articulated.\n\nThe rationale for the review was also not clearly described in the context of what is already known. As there have been few studies in Nepal, it was not a good reason for conducting meta-analysis. Doing a meta-analysis using a small number of studies might cause bias.\n\nMethods:\nStudy methods were poorly described and hard to read (see a good example study by Miller et al.1). To help readers replicate the study, the authors should provide more detailed information on electronic search strategy, methods of results synthesis, and sensitivity analysis.\n\nUsing only the global search engine, e.g. PubMed, Embase, Scopus, and Google Scholar might cause publication bias if there were some researches papers published locally or in other databases. In point had not been mention in the study limitation.\nResults:\nResults were inadequately described. In the qualitative summary, the authors should talk about the important features of the information in Table 1. In quantitative synthesis, information on how the pooled prevalence was calculated is also needed. In every figure, the total events should be indicated, and the figure legend should contain more information.\nDiscussion:\nIn the Discussion, more information should be provided and reorganized for an easy read.\n\nIn the study limitation, the authors mention T2DM diagnostic criteria and demographic data as a problem. However, the authors did not mention how the problems affect the results and how the study handled them.\n\nThe statement: “Our finds highlight the importance of exercise and a healthy diet to prevent the increased morbidity among individuals with T2DM in this country”, needs more justification. Was the information from the results of this study or from the literature?\n\nIn an attempt to identify diabetes risk factors, the study limited only those studies from Nepal. How this will affect the study results?\n\nConclusion:\n\nIn the conclusion statement, only obesity was claimed to cause diabetes. This conclusion might need more justification since obesity and other risk factors were not extensively discussed. This result was also in contrast to that observed by Jayawardena et al.2, a similar study using data from all countries in South Asia. In that study, family history, urban residency, age, higher BMI, sedentary lifestyle, hypertension, and waist-hip ratio were found to be associated with an increased risk of diabetes.\n\nThe conclusion statement should also provide study limitations and recommendations for public health use.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "7096",
"date": "06 Sep 2021",
"name": "Alok Atreya",
"role": "Author Response",
"response": "Background: In the introduction, more information about the prevalence and risk factors of diabetes should be presented and reorganized for easy reading. The research problem and hypothesis also need to be clearly articulated. Reply: Thank you for the comment. We have presented the situation of T2DM in a funnel pattern in the background giving an overview of global, regional, and national scenarios. We have rephrased and edited as per requirement by the reviewer’s comment to further clarify the rationale. The rationale for the review was also not clearly described in the context of what is already known. As there have been few studies in Nepal, it was not a good reason for conducting meta-analysis. Doing a meta-analysis using a small number of studies might cause bias. Reply: Thank you for the comment. We have edited the rationale as per requirement by the reviewer’s comment to further clarify the rationale. We included 15 prevalence-based studies with justifiable sample sizes and assessed the quality of those individual studies using the JBI bias tool to reduce the bias of including studies. Due to the urge of the evidence-based practice, we authors think pooling of the data from available individual studies to give pooled prevalence is justifiable. Methods: Study methods were poorly described and hard to read (see a good example study by Miller et al.1). To help readers replicate the study, the authors should provide more detailed information on electronic search strategy, methods of results synthesis, and sensitivity analysis. Reply: Thank you for the comment. We have conducted our study as per the standard guideline and abide by the MOOSE checklist for the meta-analysis of observational studies. Our electronic search details including the link, and additional sensitivity analysis are available in the extended data file and shared publicly. Using only the global search engine, e.g. PubMed, Embase, Scopus, and Google Scholar might cause publication bias if there were some researches papers published locally or in other databases. In point had not been mention in the study limitation. Reply: Thank you for the comment. We have conducted our study as per the standard guideline and abide by the MOOSE checklist for the meta-analysis of observational studies. In Nepal, almost all Nepalese local journals are listed in NEPJOL (Nepalese Journal Online), which is the common platform and all the published papers are available through Google scholar so we included the Google scholar database in our review, which is missed by some prior reviews. So, we authors believe including Google scholar and other standard global databases won’t miss published literature. Results: Results were inadequately described. In the qualitative summary, the authors should talk about the important features of the information in Table 1. In quantitative synthesis, information on how the pooled prevalence was calculated is also needed. In every figure, the total events should be indicated, and the figure legend should contain more information. Reply: Thank you for the comment. We elaborated qualitative summary as “A qualitative summary of all 15 individual studies is presented in (Table 2). Nine studies were done in a community setting while the rest six were done in the hospital setting. Two community-based studies and one hospital-based study included samples from different parts of Nepal to represent the country, while the rest were loco-regional studies.” For transparency of our work we made our data available in public data repository Figshare; link: https://doi.org/10.6084/m9.figshare.14706648.v1. Regarding data pooling methods, based on heterogeneity we used a random or fixed-effect model. And we mentioned the model used in every section before the description of the individual results and forest plot. Regarding total events, I agree with the reviewer, however, due to the default setting of the software CMA-3, we could not edit the figure. Discussion: In the Discussion, more information should be provided and reorganized for an easy read. In the study limitation, the authors mention T2DM diagnostic criteria and demographic data as a problem. However, the authors did not mention how the problems affect the results and how the study handled them. The statement: “Our finds highlight the importance of exercise and a healthy diet to prevent the increased morbidity among individuals with T2DM in this country”, needs more justification. Was the information from the results of this study or from the literature? Reply: Thank you for the comment. There are perceived barriers for the non-compliance for physician’s advice to a special diet and regular exercise as shown in a Nepalese study. We have added a reference to justify this statement. In an attempt to identify diabetes risk factors, the study limited only those studies from Nepal. How this will affect the study results? Reply: Thank you for the comment. Diabetes prevalence and risk differ across different societies and regions across the globe. This study is solely aimed to estimate prevalence and risk factors in the context of Nepal to build foundation evidence to make evidence-based practice in Nepal so may be different than other regions across the globe. Conclusion: In the conclusion statement, only obesity was claimed to cause diabetes. This conclusion might need more justification since obesity and other risk factors were not extensively discussed. This result was also in contrast to that observed by Jayawardena et al. 2, a similar study using data from all countries in South Asia. In that study, family history, urban residency, age, higher BMI, sedentary lifestyle, hypertension, and waist-hip ratio were found to be associated with an increased risk of diabetes. The conclusion statement should also provide study limitations and recommendations for public health use. Reply: Thank you for the comment. The conclusion statement states obesity as one of the many major risk factors for diabetes. We kindly apologize, but we have not claimed only obesity causes diabetes. The limitations have already been provided at the end of the discussion section, so due to fear of duplication, we did not include them in the conclusion section."
}
]
},
{
"id": "89248",
"date": "06 Sep 2021",
"name": "Prajwal Gyawali",
"expertise": [
"Reviewer Expertise Stroke"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nA) Background\nPlease check for sentence structure; \"In 2019, the International Diabetes Federation (IDF) estimated that 463 million adults worldwide had diabetes1. The statistics showed that these individuals were in the age range of 20 to 79, have diabetes, and 79.4% were from low- and middle-income countries.\"\n\nReference number 4 used in the background does not match with the authors' claim. This reference is more focused on foetal programming contributing to the prevalence of obesity in Nepal.\n\nThere are already two systematic reviews published in this sector, references 5 and 6:\nGyawali B, Sharma R, Neupane D, et al.: Prevalence of type 2 diabetes in Nepal: a systematic review and meta-analysis from 2000 to 20141.\nShrestha N, Mishra SR, Ghimire S, et al.: Burden of Diabetes and Prediabetes in Nepal: A Systematic Review and Meta-Analysis2.\n\nAuthors need to provide a valid reason for conducting this systematic review in the same area in the background section. Paper by Shrestha N. et al.2 was published less than 1 year ago and they have included 14 papers for the final analysis.\n\nB) Methods\nThe authors have reported the prevalence of impaired glucose tolerance and prediabetes. Why were these keywords not used in the search strategy? Likewise, have the authors used the terminology 'glucose' as a keyword in a search strategy?\nC) Discussion\nThe metanalysis published in 2020 by Shrestha N. et al.2 included 14 papers in the final analysis. All papers were after 2000. They reported the prevalence of pre-diabetes is much less than what the current paper has reported. The reason provided by the authors for this large difference is not properly addressed in the discussion. This is very important to address.\n\nThe papers should be discussed in sub-sections.\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? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-543
|
https://f1000research.com/articles/10-887/v1
|
03 Sep 21
|
{
"type": "Research Article",
"title": "Transformational entrepreneurship and its effect on readiness for change, psychological capital, and employee performance: evidence from an Indonesian bank",
"authors": [
"Michael Gunawan",
"Retno Wijayanti",
"Febri Nila Chrisanty",
"Budi W. Soetjipto",
"Ani Wahyu Rachmawati",
"Santi Rahmawati",
"Retno Wijayanti",
"Febri Nila Chrisanty",
"Budi W. Soetjipto",
"Ani Wahyu Rachmawati"
],
"abstract": "Continuing failures of financial capitalism across borders have led corporation to develop a more balanced economic growth model of transformational entrepreneurship that emphasises both short-term economic and longer-term social impacts. The model encourages entrepreneurial activities that bring major changes in the related markets and industries, as well as changes in society and culture. At the corporate level, transformational entrepreneurship prepares employees for any potential changes induced by a dynamic environment; it also improves the psychological capital of individual employees, and effective transformational entrepreneurship can eventually accelerate performance. The purpose of this study is to investigate (1) the direct and indirect effects of transformational entrepreneurship on readiness for change, psychological capital and employee performance, and (2) how the effects to readiness for change and psychological capital influence employee performance. The study data were collected using questionnaires completed by employees in 257 branches of a state-owned bank with locations throughout Indonesia. The data were analysed using the structural equation model. The results show that transformational entrepreneurship significantly and positively influences readiness for change, psychological capital, and employee performance and that readiness for change and psychological capital significantly and positively influences employee performance. Additionally, the effect of transformational entrepreneurship on employee performance is more significant if it is related to psychological capital than to readiness for change or to aspects of employee performance unrelated to transformational entrepreneurship. These findings enrich our understanding of transformational entrepreneurship and its value related to the direct and indirect effects on variables such as readiness for change, psychological capital and employee performance.",
"keywords": [
"transformational entrepreneurship",
"readiness to change",
"psychological capital",
"employee performance",
"structural equation model",
"banking industry"
],
"content": "Introduction\n\nTo sustain viability in a dynamic and turbulent environment, a company needs transformational leaders with high level of integrity and willingness to extend their employees’ efforts to achieve targets, which, in turn, will enhance the company's performance (Lafley, 2006). These characteristics closely relate to entrepreneurial qualities such as being innovative, proactive, and willing to take risks (Covin & Slevin, 1991; Miller & Friesen, 1982; Slevin & Covin, 1991). Bass (1985) and others (e.g., Howell & Avolio, 1993; Howell & Higgins, 1990) have suggested that transformational leadership is related to innovation in the organisation, while Bateman and Crant (1993) and others (e.g., Crant, 2000; Deluga, 1998) have found that transformational leadership is linked to proactive behaviour, an aspect of entrepreneurship.\n\nAs mentioned above, success in dealing with uncertain and unpredictable environments lies not only in survival but also in sustainability. For that reason, the company needs both (shorter-term) economic/financial result and (longer-term) social impacts, so the success of the company can cascade into the wealth of the society (Maas, Jones & Lockyer, 2019). A wealthy society has the economic power to support the company, continually allowing for the company's continuous growth into the future. Entrepreneurs have tried to accommodate such social impacts by developing the concept of social entrepreneurship. However, social entrepreneurship is more focused on the work of community, voluntary, and public organisations, as well as private firms working for social rather than for-profit objectives (Shaw & Carter, 2007, p. 419). Thus, “its impact has been limited to date as its solutions are rarely devised with scalability and true economic sustainability in mind” (Marmer, 2012, p.2).\n\nHence, there is a need for entrepreneurship that can successfully transform profit-motivated institutions. The concept of transformational entrepreneurship has been introduced, going beyond just combining transformational leadership and entrepreneurship. It encourages entrepreneurial progress by combining individuals, communities, and institutions that interact and collaborate to take advantage of current opportunities on a broader scale (Maas, et al., 2019; Schoar, 2010). Moreover, transformational entrepreneurship encourages entrepreneurial activities that bring major changes in the market and industry, as well as in social and cultural life (Marmer, 2012).\n\nEmbracing economic results and social impacts in its goals, the company must shift its perspective from an economic to a socio-economic standpoint. The shift requires the company and its employees to be ready for change. Being ready for change means the employees of such a company are dedicated and capable of implementing necessary change, through commitment and efficacy (Weiner, 2009). Moreover, embracing a socio-economic perspective means putting more emphasis on sustainability rather than mere survival. The socio-economic perspective gives employees hope for future success, growth optimism, and confidence (self-efficacy). Despite the challenges and adversities that employees are likely to face, they can persevere and remain resilient enough to succeed.\n\nHope, optimism, self-efficacy, and resilience are components of psychological capital (Luthans, Youssef & Avolio, 2018). As previously mentioned, the objective of adopting transformation entrepreneurship is for the company to sustain growth through continuously increasing employee performance. Referring to Pradhan and Jena (2017), employee performance includes task performance (performance related to the job description and/or employment contract), adaptive performance (performance related to dynamic work situations, such as technological changes), and contextual performance (performance related to maintaining and developing a team spirit). According to a review of the past literature, and to the best of the authors’ knowledge, there is a lack of research connecting transformational entrepreneurship to organisational readiness for change, psychological capital, and employee performance. Therefore, examining such organisational factors in relation to transformational entrepreneurship is the objective of this study.\n\nPrevious research does indicate that both organisational readiness for change and psychological capital can relate to employee performance. Weeks et al. (2004) found a positive and significant association between organisational readiness for change and job performance in sales organisations. Job performance examined in their study was essentially viewed as task performance. Meanwhile, Gooty et al. (2009) found a positive and significant association between psychological capital and job performance in an educational institution. They examined performance as in-role and extra-role performance, which refers to task and contextual performance. Peterson et al. (2011) also found that psychological capital was positively related to change in supervisor-rated performance and change in objective performance in a financial service organisation. Both of those performance categories are considered task performance. In short, there have been limited studies that connect both organisational readiness for change and psychological capital to performance, particularly simultaneously connecting to task performance, adaptive performance, and contextual performance. Consequently, examining such connections is the objective of this study.\n\nThis study took place in a large, state-owned bank in Indonesia. The business of banking was specifically chosen because it has long been known as a very competitive landscape, yet the industry is highly regulated. To compete successfully, each bank must be innovative, proactive, and risk-taking but remain within the boundaries of government laws and regulations. The emergence of digital technology has made the competition harsher than ever before, particularly with the presence of some tech start-ups that are able to launch without the support of banks. In other words, the banking industry is transforming itself into a more digital-savvy industry.\n\nOn the heels of the digital revolution, a transformational entrepreneurship within the banking industry is essential for banks to simultaneously enhance their economic and financial performance and increase positive social impacts by extending the scope of banking operations and, in turn, touching the lives of many more people. Individual bank branches comprise the frontline for banks’ transformational entrepreneurship practices. These are the business units that acquire and maintain customers for future revenue generation and engage with the local communities to create and maintain their social impacts. Such impacts are particularly crucial in a country like Indonesia, with more than 250 million people spread out over more than 17,000 islands. The banks that can create social impacts will generate wealth throughout the country, and this wealth will be fed back to the banks in terms of financial income. If successful, the wealth of the world's fourth most populous country will be more than enough to sustain banks’ growth for a very long time.\n\nAccording to Bass (1985) and Burns (2003), a transformational leader is one who can affect the evolution and growth of the character of an organisation, bringing it to a new, desired condition through dramatic changes. The leader can inspire their followers with challenging but achievable future vision and objectives. Moreover, as a role model, the leader can continuously motivate followers and intellectually encourage them to always look for creative and innovative ways to solve every problem they encounter. A transformational leader also often dedicates time to be with their followers to listen to their views, opinions, and feedback and provide guidance, support, and direction to take advantage of the opportunities that may arise.\n\nMeanwhile, Shane and Venkataraman (2000) defined entrepreneurship as individuals and processes that led to the discovery, evaluation, and exploitation of opportunities. Hsieh, Nickerson, and Zenger (2007) further argued that these opportunities existed or were created to fill the organisation's needs and wants. Such opportunities are then evaluated based on the organisation's desirability and feasibility before being exploited (McMullen & Shepherd, 2006; Shane & Venkataraman, 2000). A transformational leader can inspire, motivate, and guide their followers to be entrepreneurs. The leader first clarifies the future vision and objectives, then points out the gaps between the existing conditions and those necessary to achieve the vision by engaging in entrepreneurial behaviour. Along the way, a transformation leader urges his or her followers to be creative and innovative in identifying and creating opportunities.\n\nA transformational leader can extend his or her inspiration to include economic results and social impacts aligned with the organisation's vision statement and objectives. In this case, the leader is said to practice transformational entrepreneurship (Schoar, 2010; Virmani & Lepineux, 2016; Jones & Maas, 2019). Being a role model, a transformation leader expects his or her followers to be transformational entrepreneurs. They each have the basis of an entrepreneur but with greater concern for the well-being of society where their organisation operates and to which it serves. Removed from them is the ‘winner-takes-all’ mentality; instead, they operate with a ‘let’s-grow-together’ mentality. Basing their quest for opportunities using this new mentality can result in totally different solutions for filling in gaps and manifesting the desired future conditions. Their organisations may be more sustainable as they receive strong support from the society encompassing the organisation.\n\nThe successful inclusion of social impacts in an organisation's vision and objectives requires different behaviours. The behaviours’ essence is still entrepreneurship, but this entrepreneurship goes beyond merely finding and taking advantage of opportunities. Transformational entrepreneurship is expected to change and improve neighbouring communities. Prior to exerting actual effort to change such communities, however, the organisation and its employees must commit to it and be capable of implementing the necessary change. According to Weiner (2009), if an organisation and its employees already have change commitment and change efficacy, they are considered ‘ready’ for change. Armenakis, Harris and Mossholder (1993) further emphasised that this readiness must be collective and active, meaning that the whole organisation must be ready to participate in change. Correspondingly, we anticipated that:\n\nHypothesis (hereafter H) 1: Transformational entrepreneurship positively affects organisational readiness for change\n\nThe heart of entrepreneurship is opportunity. In transformational entrepreneurship, opportunities have a much wider scope, as an organisation touches the social and cultural lives of entire communities to gain their strong support. When carried out effectively, transformational entrepreneurship inspires the employee's hope and optimism about the organisation's sustained success. Moreover, obtaining a great deal of support from surrounding communities instils employees’ confidence and efficacy - they believe in their ability to succeed. Thereafter, if they encounter obstacles and adversities, they will show resiliency until they get over them. According to Luthans, Youssef, and Avolio (2018), hope, optimism, efficacy, and resiliency are the cornerstones of psychological capital. We, therefore, hypothesised the following:\n\nH2: Transformational entrepreneurship positively affects psychological capital\n\nWhen leaders practise transformational entrepreneurship effectively, their organisation can mobilise strong support from the communities (Maas, Jones & Lockyer, 2015; Sautet, 2013; Schoar, 2010). The support is a return favour for the organisation's improvement that can bring social and cultural life of the communities and be a potential economic power that can support back the organisation (Virmani and Lepineux, 2016). This economic power can be in the form of loyal customers who repeatedly buy or use organisation's products. These organisation's enthusiasts always speak highly of the organisation and its products. With this support at hand, the organisation and its employees will likely increase their performance. Accordingly, the below hypothesis is proposed:\n\nH3: Transformational entrepreneurship positively affects employee performance\n\nIn addition, Weeks et al., (2004) demonstrated a positive association between organisational readiness for change and employees’ performance. Employees who perceive the organisation for whom they work are ready to counter changes in the environment and believe that their organisation is committed to upgrading their capability to overcome any possible challenges and obstacles derived from change. These are the challenges and obstacles that can also impede their performance. In other words, organisations perceived to be ready for change helps and supports its employees to get over such changes and eventually perform. In conjunction with the previous notions, we formulate the following hypothesis:\n\nH4: Organisational readiness for change positively affects employee performance\n\nFurthermore, scholars like Peterson et al., (2011) and Luthans et al. (2007) found a positive relationship between psychological capital and employee performance. These findings are understandable, considering that employees with higher psychological capital use positive thinking have positive attitudes toward work. Thus, they are highly motivated and will exert great efforts to achieve their targets. Consistent with the above findings, we derived a further hypothesis as follows:\n\nH5: Psychological capital positively affects employee performance.\n\n\nMethods\n\nThis study uses a causal research design to assess the potential impact of transformational entrepreneurship on organisational readiness to change and psychological capital to produce employees’ superior performance. This study also follows the STROBE guidelines/checklist for cross-sectional studies.\n\nInitially, 462 bank branches were targeted. Our email to potential respondents consisted of a cover letter and a set of questionnaires. Follow-up telephone calls and emails were made to increase the response rate. If the written consent from respondents was not obtained, they were unable to participate in the study. The data from bank managers and their immediate subordinates were collected in April through May of 2020.\n\nTo access these employees for data collection, we received permission from the bank's board of directors. They provided their oral and written consent due to the good relationship between the researchers and the Board of Director (BoD) of the state-owned bank. Additionally, because one of the co-authors is a member of the BoD of a state-owned bank, we were permitted to do the research and conduct the survey in the bank's branches. However, the respondents involved were not informed that one of the BoD involved in the study. In addition, the survey responses were kept anonymous to ensure there is no conflict of interest in this research.\n\nWe collected data using a structured questionnaire adapted from previous research: Maas et al. (2019), Marmer, M. (2012), Schoar (2010), and Virmani and Lepineux (2016). We back-translated the questionnaire from English to Indonesian, but we also included both English and Indonesian in the questionnaire. A copy of the distributed questionnaire can be found in the Extended data (Gunawan et al., 2021b). Our respondents were branch managers of a state-owned bank and their immediate subordinates. The respondent's criteria are: 1) Active branch managers who already worked and served in the bank for more than 15 years; 2) Two persons (subordinates) who are directly under the branch managers’ chain of command and already worked in various assignment for the bank. Although the respondents are highly educated and understand English, they still had a better grasp of Indonesian. If they were confused by the language in any item, they could always refer to that particular item in the other language. We had language and industry experts check each item in the questionnaire during its development process to minimise confusion for participants.\n\nBefore distributing the questionnaire to the actual respondents, it was pre-tested with branch managers and their immediate subordinates from another bank. Based on the pre-test feedback, we refined and modified the wording of some items to ensure the reliability and validity of each variable meets the required standard. Survey items are answered using a Likert-type scale from 1 (strongly agree) to 7 (strongly disagree).\n\nThe items for the transformational entrepreneurship variable were adapted from Maas et al. (2019), Marmer, M. (2012), Schoar (2010), and Virmani and Lepineux (2016). This part of the survey includes three categories and 17 items. The categories are ‘Quality of Human Capital’ (six items). ‘Taking Risks and Opportunities in a New Market’ (six items), and ‘Evaluating Changing Conditions’ (five items)”.\n\nThe items for readiness for change variable were adopted from Armenakis et al. (1993). These items asked the respondents about the organisation's and its people's readiness for change, using terms such as ‘aligned business goals’, ‘improved job security and quality’, ‘trust’, ‘good communication’, ‘sufficient money, and training’, and ‘physical infrastructure availability’.\n\nThe items for the psychological capital variable were adopted from Luthans et al., (2018). These items asked the respondents about their hope, optimism, self-efficacy, and resiliency. The items for employee performance variable were adopted from Pradhan and Jena (2017). These items asked the respondents about their employees’ tasks and, adaptive and contextual performances.\n\nThis study follows a two-step statistical approach to testing the hypotheses by analysing the outer measurement model and the inner-structural model. First, we conducted a confirmatory factor analysis and dropped items with standardised factor loading below 0.50, which means such items are not valid for the respective construct (Flynn et al., 2010). The results provide the standardised factor loadings for the outer model ranging from 0.570 to 0.922. Next, we examined reliability. Table 1 shows that composite reliability (CR) values range from 0.84 to 0.95, while the Average Variance Extracted (AVE) values range from 0.51 to 0.74 suggesting reliability in our measurement model. Please note that one dimension (adaptive performance) in EP was dropped due to its standardised factor loading < 0.50.\n\nWe performed structural path analysis using covariance-based Structural Equation Modelling (CB-SEM) Lisrel 8.80 because we estimated research models with reflective measurement models or factor models (Rigdon, Sarstedt and Ringle, 2017). Lisrel 8.80 is proprietary software; however, there is alternative free software to perform the statistical such as the R project with the Lavaan package.\n\nThis study was approved by Universitas Wanita Internasional Ethical Clearance Committee (Protocol number: 675/SR/WAREK-2/UWI/IV/2020) after due consultation, consent letter had been provided by the researchers to all respondents. The written consent to participate from the head office of a state-owned bank was gained according to document B.738.e-BCU/OTD/LOP/03/2020. The written consent to participate was acquired from respondents through the state-owned bank's Branch Office Heads and Managers. Respondents had provided their consent without any force from anyone. Subsequently, in order to protect the rights and privacy of the respondents, all forms of data were acquired will remain confidential.\n\n\nResults\n\nBentler and Chou (1987) suggested that the sample size for CB-SEM must be five times the number of indicators in the research model. The model has 65 indicators, meaning that our sample is supposed to be 325 branches. However, our actual sample is 257 branches, which is below that standard. Consequently, we must simplify the indicators by parcelling (Rhemtulla 2016) and using latent variable scoring (Joreskog, Sorbom, & Yang-Wallentin, 2006). Next, the second-order confirmatory analysis model (indicators) was transformed parcelled into a first-order confirmatory analysis model (dimension or variable). Parcelling reduced the number of indicators to 50 to make our sample size more than adequate. Parcelling also results in a more stable estimation of parameters for a small sample (Bandalos, 2002) and enhances the model's fit. The model's fit indicators show that RMSEA = 0.039 (≤0.08**), NNFI = 0.99 (≥0.90**), CFI = 1.00 (≥0.90**), IFI = 1,00 (≥0.90**), RFI = 0.99 (≥0.90**), SRMR = 0.016 (≤0.05**), GFI = 0.97 (≥0.90**), and Norm = 1.38 (≤ 3), which all indicate that the model fits and represents the data.\n\nWe invited 462 branches of the state-owned bank to participate in the study survey. In the end we received returned responses from 462 branch managers, each from a different branch, and 1404 of the employees under their immediate supervision. Unfortunately, 205 branches returned incomplete responses, so the remaining 257 valid branch's responses provided a response rate of 56%. In this case, 257 valid branch responses are considered complete, meaning that all of them have been filled in by the branch manager and at least 1 (one) out of 2 (two) subordinates of the branch leadership under him. Table 2 provides the respondents’ characteristics.\n\n\n\n• Male: 96.11%\n\n• Female: 3.89%\n\n\n\n• Male: 82.46%\n\n• Female: 17.54%\n\n\n\n• Bachelor’s degree: 82.88%\n\n• Others: 17.12%\n\n\n\n• Bachelor’s degree: 88.94%\n\n• Others: 11.06%\n\n\n\n• Married: 96.11%\n\n• Others: 3.89%\n\n\n\n• Married: 94.31%\n\n• Others: 5.69%\n\n\n\n• <30 years old: 0%\n\n• 30-40 years old: 44.36%\n\n• >40-50 years old: 39.30%\n\n• >50 years: 16.34%\n\n\n\n• <30% years old: 0.47%\n\n• 30-40 years old: 34.44%\n\n• >40-50 years old: 38.86%\n\n• >50 years: 26.22%\n\n\n\n• <6 years: 0.39%\n\n• 6-10 years: 15.18%\n\n• 11-15 years: 26.46%\n\n• 16-20 years: 24.90%\n\n• >20 years: 33.07%\n\n\n\n• <6 years: 0.47%\n\n• 6-10 years: 24.17%\n\n• 11-15 years: 15.80%\n\n• 16-20 years: 26.86%\n\n• >20 years: 32.70%\n\n\n\n• 0-2 years: 91.05%\n\n• >2 years: 8.95%\n\n\n\n• 0-2 years: 81.52%\n\n• >2 years: 18.48%\n\nTo assess the potential for non-response bias, we compared the chi-square of responses from early and late respondents (the first and last 20% of responses received). The results indicate there is no significant difference between responses of early and late respondents on key measures.\n\nThe results of hypotheses testing given in Table 3 and Figure 1 support all the hypotheses. The results support our hypothesis that transformational entrepreneurship has significant positive effects on readiness for change (H1, p < 0.05), psychological capital (H2, p < 0.05), and employee performance (H3, p < 0.05). The path coefficients for the effects of both readiness for change and psychological capital on employee performance are also positive and significant (H4, p < 0.05; H5, p < 0.05). Furthermore, the structural model (Figure 1) demonstrates the direct and indirect effects of transformational entrepreneurship on employee performance.\n\nThe coefficient for direct effect is 0.18; for the indirect effect through readiness for change, it is 0.1206 (obtained by multiplying the coefficient of transformation entrepreneurship-readiness for change path and the coefficient of readiness for change-employee performance path = 0.18 × 0.67), and the indirect effect through psychological capital is 0.224 (obtained by multiplying the coefficient of transformation entrepreneurship-psychological capital path and the coefficient of psychological capital-employee performance path = 0.80 × 0.28). Based on such coefficients, we can conclude that the biggest effect of transformational entrepreneurship on employee performance was indirectly via psychological capital (0.224 > 0.18 > 0.1206). Nevertheless, in this study, the effect of transformational entrepreneurship on employee performance could be both direct and indirect (partially mediated).\n\n\nDiscussion\n\nAs previously mentioned, transformational entrepreneurship inherits the heart and soul of traditional entrepreneurship. These entrepreneurs are innovative, proactive, and risk-taking in creating and or taking advantage of opportunities in the market (Covin & Slevin, 1991; Miller & Friesen, 1982; Slevin & Covin, 1990); they also add sustainability for the sake of economic results and social impacts. Support for H1 indicates that with sustainability intact, transformational entrepreneurship can stimulate change within an organisation. Innovativeness, proactiveness, and risk-taking require employees to pursue opportunities even with unclear guidelines. It means employees must tolerate ambiguity, and ambiguity results from a changing environment. In other words, transformational entrepreneurship leads employees to accept that change is inevitable. However, the inevitable change has dual orientations—economic and social—and each has its own dynamics. Whether they like it or not, employees must be ready to acknowledge both dynamics, and they must be committed and able to adapt to them. Therefore, this study's finding enriches the literature on ‘change’ by adding a sustainability perspective, in that one way to achieve sustainability is to support change.\n\nFurthermore, with the emphasis on sustainability, transformational entrepreneurship gives employees hope and optimism for their organisation's longer-term success. Sustainability can gather support from surrounding communities, which, in turn, increases employees’ efficacy to perform and build resiliency to overcome obstacles and adversities. Support for H2 shows that transformational entrepreneurship indeed develops hope, optimism, efficacy, and resiliency, all of the cornerstones of psychological capital (Luthans, Youssef & Avolio, 2018). In addition, Avey (2014) identified four groups of antecedents of psychological capital. They are individual differences, leaders, job design, and pragmatism. Avey found that individual differences (i.e., proactive personality and self-esteem) account for 45% of the variance in psychological capital.\n\nIn contrast, leadership (i.e., authentic and ethical leadership) accounts for 32% of such variance. Hence, it is not surprising that we found that transformational entrepreneurship significantly and positively affects psychological capital. Practising transformation entrepreneurship leads employees to be different individuals; they will be more innovative, proactive, and confident in taking risk (Covin & Slevin, 1991; Miller & Friesen, 1982; Slevin & Covin, 1990). Transformation entrepreneurship also requires strong leadership support (Roth & DiBella, 2015). The findings of this study thus extend our comprehension of transformational entrepreneurship's contribution to the development of psychological capital: it includes individual differences and leadership.\n\nWhen practising transformational entrepreneurship effectively, an organisation can assemble solid support from communities (Maas, Jones & Lockyer, 2015; Sautet, 2013; Schoar, 2010). Such support is a reciprocal courtesy for the benefits the organisation conveys to them and are a potential economic strength that can sustain the organisation (Virmani & Lepineux, 2016). This economic strength includes plenty of opportunities the organisation can explore and take advantage of and the communities that are always receptive to, or even excited about, new ideas or new products offered by the organisation. Support for H3 corroborates this notion because to exploit opportunities and deliver new ideas, employees must give their maximum effort based on their ability and consistently do their best. This study's finding enhances our understanding of how to increase employee performance in a socially reciprocal way: it works from the inside out (the organisation provides benefits that impact the society), which leads to an outside-in benefit (the organisation reaps financial rewards from the society in return).\n\nIn addition, Weeks et al. (2004) found that an individual's perceptions regarding their organisation's readiness for change were significantly and positively related to their job or task performance. Such perceptions reflect their confidence that the organisation will thrive amidst change. This confidence is developed because individuals believe that by implementing change, job quality will be improved. Moreover, individuals can foresee good results from implementing change, hence leading them to understand the value of their performance. As an individual's confidence grows, so does the spirit to take advantage of the change to improve performance. Support for H4 is consistent with these notions. However, this study's finding extends the performance to include contextual performance, which essentially results from pro-social and voluntary behaviour directed at improving the performance of colleagues, teams, and/or the whole organisation (Pradhan & Jena, 2017). This behaviour goes beyond what is required by the individual's job description or task assignment. In other words, the findings of this study shed light on readiness for change that brings contagious benefits to others in the organisation; these benefits extend beyond any single individuals.\n\nScholars such as Peterson et al. (2011) and Luthans et al. (2007) have also found a positive relationship between psychological capital and employee performance. Employees with positive psychological capital usually have high levels of hope, which means having strong determination and conviction about their ability to achieve their goals despite all the hurdles they may face (Snyder, 2000). Meanwhile, being highly resilient means being able to overcome various unfavourable conditions (Luthans, Avey, Avolio, Norman, & Combs, 2006). Having high levels of (positive) psychological capital also relates to being highly optimistic; regarding their work, this indicates that an employee feels highly positive about their future (Tiger, 1979). Moreover, a high degree of self-efficacy refers to Bandura's social learning theory (1982, 1986), employees’ conviction of their abilities to get their tasks done. Employees who are highly hopeful, resilient, and optimistic and a high degree of self-efficacy are likely to have positive thoughts and attitudes towards work; thus, they have greater motivation and exert more effort to achieve their targets. Support for H5 is consistent with this statement, but psychological capital does not only affect an employee's own performance; the effect extends to the performance of their colleagues, teams, and organisations. This ripple or ‘contagion’ effect occurs because with high hope, resiliency, optimism, and self-efficacy, employees can inspire others; hence, it becomes a source of positivity that spreads psychological capital.\n\nThis effect may play a role in increasing the perceived value of psychological capital as an impactful mediator for transformational entrepreneurship and employee performance, as this study has found. Transformational entrepreneurship is characterised by a willingness to tolerate ambiguity and to take risks. It will lead employees to accrue positive psychological capital, particularly in terms of being highly determined to achieve their targets and having strong convictions about their ability to complete their tasks. It is because the employee does not see ambiguity and risks as obstacles. Instead, both are considered natural and, hence, inevitable.\n\nAmbiguity is an integral part of employees’ work, as there can never be full clarity about work, and working with ambiguity has an inherent risk they have to accept. Employees who have positive psychological capital will overcome challenges that comes from ambiguity and risks with their best ability to achieve the goals. Their determination and willingness to give their best effort are likely apparent to others and, thus, become contagious; more and more employees will follow their example. Subsequently, the majority of employees will become highly motivated and put forth their best efforts to achieve their goals. As a result, they will each improve their performance. The findings of this study, therefore, highlight that transformational entrepreneurship with inevitable ambiguity and risks triggers employee's determination and motivation to give their best efforts and seize those challenges. They also highlight how these attitudes are likely to become infectious due to the resulting improvements in employee performance. This infectious role of positive psychological capital may indicate that the direct effects of transformational entrepreneurship on employee performance are less powerful than the indirect effects via psychological capital.\n\nFinally, we are aware that there are some limitations for this research, such as: 1) The research was conducted in the branch office of the state-owned bank. Perhaps in the future, the research also can be done in head office level to gain data from the top management like Board of Directors and Vice President; 2) The study was done in cross-sectional type and the data was collected during the COVID-19 pandemic. The situation is full of uncertainty, so perhaps it may give effect to the result; 3) We got many data from 257 branches of one of the state-owned banks in Indonesia. Perhaps in the future the data can be taken from other state-owned banks in Indonesia. Because currently, Indonesia has four stated-owned banks.\n\nWe propose three major areas for further research. Firstly, further empirical studies are needed to extend the framework of this study. Variables related to technology, such as digital transformation and technology adoption capability, warrant consideration in future research models. Technology may help organisations reach and engage a broader community to create more and stronger social impacts. Technology has also been demonstrated to change an organisation's business model and products (Hess, Matt, Benlian & Wiesböck, 2016).\n\nSecondly, future research is needed to examine the organisational characteristic of transformational entrepreneurship at the level of the head office of the organisation, as this study was conducted in branch offices. Head office work is mainly at the policy level, so the view and impacts are, theoretically, greater. In addition, future research is needed in industries other than banks. It would be interesting and useful to know how transformational entrepreneurship is practised and how it changes companies in various industries, for example, manufacturing. Other industries’ characteristics are different from those banking, which is considered a service industry. Manufacturing industries produce actual goods, such as clothes, cars, and televisions. Thus, the social impacts and the products are affected by the people.\n\nThirdly, our research focuses on the consequences of transformational entrepreneurship. Hence transformational entrepreneurship precedes readiness for change and psychological capital when, in reality, their relationships could reciprocate over time. Transformational entrepreneurship, for instance, could be affected by readiness for change and psychological capital. We could not empirically examine reciprocal relationships using cross-sectional data and therefore encourage future longitudinal research employing existing variables with additional technology variables.\n\n\nData availability\n\nFigshare: Dataset of Questionnaire Result from the respondents of Transformational Entrepreneurship, Readiness to change, Psychological Capital, and Employee Performance. https://doi.org/10.6084/m9.figshare.14267393.v4 (Gunawan et al., 2021a).\n\nThis project contains the following underlying data:\n\n- Questionnaire results from 257 Indonesian bank branch managers.\n\nFigshare: List of questions and descriptions of the questionnaire - Transformational Entrepreneurship. https://doi.org/10.6084/m9.figshare.15091182.v3 (Gunawan et al., 2021b).\n\nThis project contains the following extended data:\n\n- A copy of the questionnaire\n\n- Data coding key\n\nFigshare: The Respondent characteristics of Transformational Entrepreneurship case of a state-owned bank in Indonesia. https://doi.org/10.6084/m9.figshare.14731905.v1 (Gunawan, et al., 2021c).\n\nThis project contains the following extended data:\n\n- Profile of respondents\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe author would like to thank the faculty members at the University of Indonesia for their support and providing a good research environment. Next, we would like to express our appreciation for the state-owned bank in Indonesia that participated in the study. Furthermore, ‘thank you’ to the Research Synergy Foundation for the recommendations and support in making this research more successful.\n\n\nReferences\n\nArmenakis AA, Harris SG, Mossholder KW: Creating readiness for organizational change. Human Relations. 1993; 1993(46): 681–703. Publisher Full Text\n\nBakker AB, Tims M, Derks D: Proactive personality and job performance: The role of job crafting and work engagement. Human Relations. 2012; Publisher Full Text Reference Source\n\nBandalos DL: The Effects of item parceling on Goodness-of-Fit and Parameter Estimate bias in Structureal Equation Modeling. Structural Equation Modeling. 2002; 9(1): 78–102. 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}
|
[
{
"id": "95755",
"date": "15 Oct 2021",
"name": "Gideon Maas",
"expertise": [
"Reviewer Expertise Entrepreneurship",
"family businesses"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe focus of this article is on transformational entrepreneurship. There is an active debate on the impact transformational entrepreneurship can play to support sustainable socio-economic development globally. This article contributes to this debate, where there are probably more questions than answers currently, by focusing specifically on the direct and indirect effects of transformational entrepreneurship on readiness for change, psychological capital and employee performance, and how the effects to readiness for change and psychological capital influence employee performance.\n\nThis article is contributing significantly to the debate on transformational entrepreneurship. I am looking forward to seeing what the impact of this study is on different economic sectors in future.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "97563",
"date": "22 Oct 2021",
"name": "Andreas Walmsley",
"expertise": [
"Reviewer Expertise Entrepreneurship",
"entrepreneurship 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\nI like the focus of the paper and believe it should be indexed. It was, on the whole, written clearly and there is some reasonable grounding in the literature. The notion of transformational entrepreneurship is receiving increased interest from scholars but there is still some way to go before we can talk of a substantial body of literature in this area and so on this basis I think the paper does make a valuable contribution to an emerging area of research. This is also however my main area of critique, i.e. specifically the operationalisation of transformational entrepreneurship should be clarified if the paper’s contribution is to be fully realised. If, as the authors argue, TE impacts certain outcome variables the strength of these claims rest on the validity of the TE construct. Unfortunately, it remains unclear how specifically the construct has been operationalised. The authors mention some sources, which are all relevant to defining TE, but as far as I am aware these studies do not operationalise the concept for statistical purposes. Furthermore, because the accompanying dataset was unavailable to me via the links provided I was unable to ascertain the precise nature of the TE as operationalised in the study. Whether I, or other reviewers for that matter, agree with the operationalisation of TE is less important than being able to determine how exactly the construct has been operationalised. Perhaps the authors could ensure this is clarified prior to indexing?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "98858",
"date": "12 Nov 2021",
"name": "Victor Atiase",
"expertise": [
"Reviewer Expertise Entrepreneurial Finance"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTransformational entrepreneurship is still an emerging area and I commend the authors for undertaking this research. However, I believe transformational entrepreneurship is better measured at the country level rather than the firm level. This is because the major goal of TE is scaling up to create mutually beneficial opportunities for everyone in the economy. Issues such as heuristics, systemic and holistic approaches are better identified using country-wide data rather than firm-level data. I, therefore, think the researchers should be measuring transformational leadership which is much more related to the firm rather than TE.\nMeasuring TE from the perspective of state-owned banks is just one side of the coin. What are the private sector players, regulators, technological drivers etc?\nHowever, since this is still an emerging area, I support this publication and I hope the authors will take this further.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "93537",
"date": "04 Jan 2022",
"name": "Paul Jones",
"expertise": [
"Reviewer Expertise Transformational Entrepreneurship",
"Entrepreneurship",
"small business management"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study offers an interesting analysis of transformational entrepreneurship in the context of change, psychological capital and employee performance in a developing world banking setting. The literature on transformational literature remains limited especially in a developing world context. So this study represents a welcome addition. This study is generally well executed and draws upon a decent sample of 250 respondents. The study is well written in the appropriate language and draws on a detailed and critical literature review. The study method is well executed using the appropriate method. The study would benefit from a distinct conclusion section which recognises the developing world context and its significance on 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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-887
|
https://f1000research.com/articles/10-886/v1
|
03 Sep 21
|
{
"type": "Research Article",
"title": "Case Report: Scientific Dissemination as a Mediator of the Research Consolidation Process: Proposals for Institutionalization",
"authors": [
"Tássia Galvão",
"Kamilla Assis Tavares",
"Michele Fernandes",
"José Carlos Moreira de Souza",
"Matias Noll",
"Tássia Galvão",
"Kamilla Assis Tavares",
"José Carlos Moreira de Souza"
],
"abstract": "Introduction Communicating science is one of the main steps in the research process. However, the method of communication must be aligned with the audience for the message. This is especially evident in institutions that promote teaching, research, and extension, especially when considering joint actions that promote a dialogue between themselves and the community. Methods\nIn light of this need, this study was conducted with the aim of analyzing the main documents guiding the policies and institutional actions related to research at the two federal institutes based in the state of Goiás/Brazil: Institution A and Institution B and proposing ways to include scientific dissemination as a mediator of the research consolidation process. This is a bibliographic, documentary study with a descriptive, qualitative approach based on a case study. Results and Discussion The analyses indicate that research must be consolidated as institutional policy and that a policy to encourage research must be implemented. This has yet to be achieved at these institutions, although scientific dissemination is explicitly addressed by institutional documents guiding the development and dissemination of pedagogical practices, especially in teaching and extension. Scientific journalism and scientific dissemination are mediators and facilitators of this endeavor.",
"keywords": [
"Scientific journalism",
"Popularization of science",
"Educational principles of research",
"Federal Institute of Education",
"Science",
"and Technology."
],
"content": "Introduction\n\nIn Brazil, the core principle of educational institutions, as conceptualized in the law and educational practices, is (or should be) to facilitate a joint effort to promote the development of projects and actions related to teaching, research, and extension. The existence of Federal Institutes of Education, Science, and Technology (IFs), like universities, is based on this premise. Thus, the dynamics of IFs should be considered. They were created with the enactment of Law No. 11.892/2008 on December 29, 2008, which later culminated in the creation of the Federal Network of Professional, Scientific, and Technological Education (Rede Federal de Educação Profissional, Científica e Tecnológica). According to this law the goal of an IF is to offer professional and technological education at all levels and modalities through an educational and investigative process, be a center of excellence in general and applied science teaching, develop scientific extension and dissemination programs, carry out and stimulate the development of applied research, and promote cultural production, entrepreneurship, cooperation, and scientific and technological development, among other objectives.\n\nThese institutes rely on documents and practices that consider the inseparability of teaching, research, and extension in the creation of policies. In line with the need to include research and extension in the educational environment, Stecanela and Williamson (2013) argue that discussing research facilitates the promotion of awareness, which, in turn, generates positive attitudes and experiences. This occurs through encouraging students to develop the ability to analyze and evaluate personal experiences, their social realities, and systematized knowledge. Thus, inquiries, hypotheses, and research based on texts from various genres allow the construction and development of argumentation, one of the characteristics of scientific research.\n\nThe education that students receive at IFs must necessarily be delivered with the aim of promoting the professional and personal independence of students and their comprehensive development as people as well as autonomy in building their learning experiences and personal histories (Gramsci, 2004). Indeed, this is also the path that must be followed by scientific journalists and communicators, who are at the other end of this dissemination process, when performing their work. The development of autonomy among these mediating professionals in writing and in their dialogue with internal and external communities is necessary. This challenge becomes apparent when they only rely on their scientific sources. Bueno (2019) criticizes this situation. In this scenario, argumentation is part of their journalistic work and, as such, must be emphasized in student training. Another aspect of this approach that should be emphasized is the use of questioning as an impetus for writing texts that present various aspects of a single fact without losing the fundamental characteristics of journalism (such as relevance, public interest, and social responsibility). These characteristics can be seen in high-quality information dissemination (Morgan et al., 2018).\n\nThus, when aiming to implement this approach, we must consider the interpretation of Manacorda (2007), who states that schools change as the nature and purpose of science change. In this context, the author argues that the process of personal development is transformed, changing the contents and means of everyday production “from the immediate instruments of writing to the types of texts and even the most complicated teaching machines. However, this is extremely slow with an inevitable delay in the transformations of science and technology directly related to production” (Manacorda, 2007, p. 27). New content is then incorporated into traditional structures and relationships. According to this author, schools remain undecided between fulfilling a duty to educate people with specialized knowledge or to cultivate disinterested consumers of culture.\n\nOne of the paths proposed in this analysis, which comports with the interpretation of Manacorda (2007), is the mediation of scientific content through printed and digital journalistic texts, internet platforms, social networks, contents, projects, and scientific dissemination activities. Such an approach includes using natural language, easy-to-understand words, dynamic activities, active methodologies in the classroom, and strategies for promoting the involvement of students with the context of the programs’ subject matter (Galvão et al., 2020). In this way, several strategies are used to facilitate the understanding of subjects often considered complicated and demotivating by students, especially those related to the traditional sciences, such as chemistry, physics, and biology. This approach can also arouse students’ curiosity and aid in encouraging student autonomy (Berbel, 2011; Valente, 2018; Boillos Pereira et al., 2019), when discussing active methodologies. Therefore, the question of how to include these strategies in the educational context arises.\n\nAmong the texts that must be used in the promotion of research in classrooms and informal educational spaces are those that belong to the scientific dissemination genre and those that embody the practices of scientific journalism. According to Bueno (2013), the concepts of scientific dissemination and scientific journalism involve communicating science to laypeople, who are part of a broad audience and often do not understand the basic sciences or may even have difficulty understanding the Portuguese language. The aim of such communication is also to popularize science in educational environments. Even in the joint interpretation and analysis of scientific journalism texts along with scientific texts meant for a broad audience, cooperation between the educator and the student is necessary. According to Targino (2001), Bueno (2010), and Caldas (2010), professors must strive to do more than merely reproduce content, acting as journalists or communicators at mainly public education and technology institutions, and avoid assuming the unique and exclusive role of scientific translators, since they are the mediators of the process.\n\nTherefore, some questions arise regarding which space scientific dissemination and scientific journalism occupy in the research guidelines of Institution A and Institution B and how to devise strategies to include them in the everyday educational context. Thus, this research was conducted with the aim of analyzing the presence of scientific dissemination and scientific journalism in institutional normative documents, especially those guiding scientific research at these institutions, as well as outlining proposals for including these practices in the teaching, extension, and research actions of these institutions.\n\nThis is a bibliographic, documentary study using a descriptive, qualitative approach based on a case study. According to Marconi and Lakatos (2018), documentary research is characterized by the collection of data from contemporary, primarily written, documents. In this study, the identification, analysis, and theoretical/conceptual treatment of the official and administrative publications of these institutions are prioritized. Therefore, this study was based on discussions among authors on scientific dissemination, scientific journalism, science communication, the curricula of these institutions, and the work of those who view research as an educational principle, such as Bueno (1985, 2010, 2013, 2019), Caldas (2010), Machado (2010), Ramos (2012), Stecanela and Williamson (2013), and Targino (2001). The articles used in the bibliographic research were mainly published between 2008 and 2018 and were collected from the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Capes) Journals Database (Capes Journals Platform).\n\nWhile conducting the documentary research, we identified the two key documents guiding institutional management: the Institutional Development Plan of Institution A (2019d) and the IDP of Institution B (2018). They were prepared and implemented according to legal guidelines on the creation of IDPs, including Law No. 9.394/1996 (LDB), Decree No. 5.773/2006, and Law No. 10.861/2004, in effect from 2019 to 2023. The Institutional Pedagogical Political Project (IPPP - Institution A) and the Institutional Pedagogical Project (IPP - Institution B) were updated in 2018. The research draft and graduate program policy as well as the norms of scientific initiation at these institutions were also analyzed. The aim was to identify the presence (or absence) of scientific dissemination in the form of pedagogical actions and practices focused on the dissemination of scientific knowledge and research to the general public in these documents. We also determined whether these practices, which must be developed by the academic community, and the work of the social communication sectors of these institutions had been integrated.\n\nWe also investigated whether the proposals in the documents of the IFs comported with the proposal for the popularization of science through the Action Plan in Science, Technology, and Innovation for Popularization of Science in Brazil (MCTIC, 2018). This document was selected because there is no national policy for promoting scientific dissemination, only documents meant to guide actions in this area. We also analyzed the statute of the Oswaldo Cruz Foundation (Decree No. 8.932/2016) because this entity contributes to scientific research and dissemination throughout the country.\n\nResearch allied with teaching is present in the ideals of those who seek an education that provides lasting benefits to students. As Machado (2010) and Ramos (2012) state, engaging in research that involves the problematization of a phenomenon, fact, or object leads students to perform a didactic action to “unveil its essence”, since such engagement by students requires the integration of the real world with educational content (Hanney and Skirkeviciutey, 2019). The problematization of phenomena lends itself to the development of an integrated curriculum, as it elucidates the scientific, technological, economic, and historical principles of the phenomena under investigation, contributing to the development of students who understand the parts that constitute the whole.\n\nThe study conducted by Ramnarain and Moleki (2017) on the use of newspaper articles by teachers in elementary-school classes in South Africa, a practice that also includes the integration of research and teaching, provides exciting implications. The results indicate that the use of scientific articles in the classroom is closely related to the construction of critical thinking skills and humanistic development among both teachers and students. This practice evens makes scientific content seem less abstract to students, leading them to become more invested in science, technology, and the needs of society. Moreover, this approach changes the role of the teacher from that of a transmitter of knowledge to that of a facilitator of learning.\n\nResearch is present in both informal educational contexts, such as museums and fairs, and in formal spaces, such as public and private educational institutions and scientific events. In the free, public education offered by federal institutions, research traverses scientific, technological, and cultural knowledge. This view is in line with that of Gouvêa (2015), who states that the dissemination and integration of knowledge by society are necessary to transform social relations.\n\nIn this context, we consider scientific dissemination and one of its branches, scientific journalism, important tools in the efforts to include research in the everyday educational context, making subjects considered difficult more palatable to students and stimulating their interest in science. According to Bueno (1985), scientific journalism has six functions: informative (disseminating facts and information about science and technology); educational (presupposing that journalists must serve the needs of society and including the functions of informing, training, and raising the awareness of the public); social (situating information about science, technology, and innovation (ST&I) in broad contexts); cultural (acting in favor of the preservation and enhancement of national culture); economic (enhancing the relationship between scientific development and the productive sector); and political–ideological (aiding in the establishment of a national policy of knowledge generation). Although this research serves diverse purposes, social and educational perspectives are prioritized throughout it.\n\nThus, scientific dissemination is a way of returning not only material investments but knowledge of the benefits and harms of scientific discoveries from academia to people’s everyday lives. It is a way to democratize access to scientific knowledge and increase the scientific literacy of individuals (MCTIC, 2018). It also allows the entire research process to gain support through the recognition of knowledge that must be disclosed to society, making it an indispensable element of research. This joint work between researchers and society requires a constant dialogue to facilitate the learning process, the development of research projects with well-defined objectives, and the participation of professors and students in research. Texts, journalistic articles and reports, and scientific dissemination and journalism articles are necessary instruments for presenting scientific knowledge to the public. The aim of scientific dissemination is to share knowledge, developing the public’s ability to question information, which, for Demo (2011), is the primary characteristic of science. According to this author, if one does not question findings, he or she does not understand material and merely reproduces it. Therefore, we present the inclusion of science communication in the educational environment as an indicator of the institutionalization of scientific dissemination in IFs in the state of Goiás.\n\n\nWhere is scientific dissemination in the official documents?\n\nOne of the first proposals to institutionalize scientific journalism and scientific dissemination in the public educational institutions that were analyzed called for the inclusion of these two practices in the official documents guiding IFs and in the normative documents of research, which are as important as the former, strengthening the research actions and work performed in the everyday educational context. Thus, these factors must be considered in the development of a policy so that proposals and actions can be implemented effectively, especially when such communication acts as a mediator in the teaching-learning process of science-related content.\n\nThis intermediation is a viable option among young people since, according to a recent study titled What do young Brazilians think of science and technology? (Massarani, Castelfranchi, Fagundes, Moreira and Mendes, 2019), they are interested in issues related to science and technology. In this study, the public perception of science is considered an important factor in identifying processes of dissemination and appropriation of technical and scientific knowledge and seeking mechanisms for promoting citizen participation in ST&I (Massarani et al., 2019). This was the first study to include measurements of more than opinions, including information about access to knowledge and perceptions of “fake news” and controversial scientific theories. Throughout the country, 2,206 young people aged 15 to 24 years participated in the study.\n\nThe most relevant findings were that the environment (80%), medicine, and health (74%) are the science-related subjects that arouse the most interest among young people. Issues related to S&T (science and technology) are also more interesting to them than sports. A total of 67% of the participants reported being “very interested” in these subjects (Massarani et al., 2019). When asked about people with whom they discussed topics related to S&T, 44% answered that they first exchanged ideas with their teachers or professors. This may indicate that the school environment plays a decisive role in the exchange of information and knowledge of S&T by students and encourages the development of scientific research by young people. In response to this question, friends ranked second (41%), followed by other relatives (21%).\n\nThe question of how young people consume science-related content remained. Most of them reported doing so using digital means, such as Google (79%), followed by videos posted on YouTube (73%) and WhatsApp (50%), with the last channel considered the least reliable option by the respondents. Professors and teachers were considered the most reliable source, selected by half of the students, followed by doctors (37.2%) and scientists at universities or public research institutes (36.7%). Journalists ranked fourth, selected by 24.2% of respondents. The level of interest among young people in science-related professions is promising: 84% of them reported that they consider this profession “very attractive” or “attractive.” Despite their interest, they consider pursuing this profession “difficult” or “very difficult” (93%).\n\nThese data show the importance of professors and teachers in encouraging scientific research, as they appropriate and disseminate reliable content in the field of scientific research, promote dialogue with young people, and act as the main channels for disseminating information. It is undeniable that the process of searching for information currently takes place mainly through digital media, but such information must necessarily pass through channels that have credibility, be they institutional ones or individuals who are considered credible by young people. Thus, we can infer from these results that the misconception that becoming a scientist is impossible is far from being overcome, as this belief seems to endure. Therefore, programs, projects, and actions aimed at bringing knowledge of science to the public must show not only what is being produced, but how, what the role of scientists is, and how to conduct research, as well as the positive and negative aspects and the successes and failures of the scientific process. This would debunk a belief that is deeply rooted in our society: that becoming a scientist is unattainable. As Noy and O'Brien (2019) state, the more science is discussed in education, the more society tends to trust it. Similarly, scientific activities are strengthened as the relationship between education and science is strengthened.\n\nTherefore, scientific dissemination and, consequently, scientific journalism can contribute in two main ways to consolidating research at federal institutes and bringing knowledge of science to young people: by encouraging the use of journalistic articles, magazines, television programs, internet sources, videos, and scientific journalism content in the classroom and enhancing media coverage of science and technology (Bueno, 2013). We believe that guidelines must be officially outlined in the documents analyzed in the present article for this to occur incisively and systematically and to ensure that this approach is linked to outcomes and that attention is paid to these issues when formulating institutional policies, projects, and actions.\n\nThe initial results published in this study were obtained through qualitative analysis of the occurrence of the terms “communication/communicational”, “disseminate/dissemination”, “scientific dissemination”, “knowledge diffusion”, “scientific knowledge dissemination”, “scientific knowledge”, and “scientific journalism”. We searched for these terms in the IDP and IPPP that were updated in 2018; drafts of the Research, Innovation, and Graduate Policies (2019a, 2019b, 2019c); and the regulations of the Scientific Initiation, Technology, and Innovation Scholarships Program (SITISP) of Institution A (2016). After completing our first evaluation of the frequency of their occurrence, we synthesized the significance and meanings associated with these phrases, determining in which titles and passages of the documents they were present. We focused on searching for proposals that included scientific dissemination that would result in the emergence of actions and integrative practices in the everyday contexts of IFs so that we could propose strategies to encourage such practices. These initial points are not extensively addressed in this study, but this is the first step in establishing connections between teaching, research, extension, scientific dissemination/journalism, and the popularization of science. We present in Table 1 the frequency of occurrence of the terms mentioned above, and, in Table 2, we present their significance to Institution A.\n\nBased on the items shown above, we can conclude that there may be some difficulty in understanding what constitutes a work of scientific journalism or an example of scientific dissemination aimed at the general public, or, rather, what constitutes scientific production for specialized audiences, like scientific articles, journals, and scientific journals. Therefore, we could not delimit the concept of “popularization of science” as we had first envisioned.\n\nWhen searching for “diffusion/dissemination of knowledge/knowing/scientific process” and “scientific knowledge” in the IDP, we found 15 instances. These terms appear in references to the social function of the institution, consolidation of the institution as a center for production and dissemination of knowledge, the objectives of the institution, research and extension activities, the Center for Technological Innovation, events, the institution’s policies, actions in the research field, academic facilities, collaboration with scientific journals, the relationship between research and extension, and partnerships with other institutions.\n\nThese terms also appear in the communication policy, with the strengthening of the institutional image linking it to a commitment to educational, scientific, and technological development, among other objectives. To this category, we can assign actions related to scientific journalism and scientific dissemination, even if they are not directly mentioned. There is room to develop this into more specific programs and projects mentioned in the institutional document, thus strengthening the institution’s actions in this area. In general terms, we can say that the IDP can accommodate more consistent scientific dissemination projects and practices, scientific journalism, science communication products for internal and external audiences, and the creation of specialized channels. However, a more comprehensive study addressing the possibilities of integrating the communication sector with the sectors that promote and manage institutional research and promoting dialogue with the academic community is necessary. The terms “scientific dissemination” and “scientific journalism” did not appear explicitly in this plan.\n\nSince the IPPP is a document that addresses education explicitly, few occurrences of “communication/communicational” and “dissemination/disseminate” were found. In the former case, there were only seven occurrences, and not all referred to social communication, with most of them addressing communication as a field of speech and language, as shown in Table 2. In this first part of the document, the term “communication for the dissemination of science” is absent. Language referring to “diffusion/dissemination of knowing/knowledge/scientific process” is predominant in the IPPP. There were 37 instances of these terms, and they are present in several passages. The main references to these terms in the context of this research are shown in Table 2.\n\nHere, we understand that the documents guiding research activities at the institutions we analyzed are still in the drafting and discussion stage and will be finalized later. It is noteworthy that there is no relevant mention of any of the terms we searched for in the regulations regarding scientific initiation, with the proposals addressing the subjects only superficially. They do not even disclose the final work of the research report, whose delivery is mandatory at the end of the IC program through the presentation of an abstract that is clear and is written in accessible language.\n\nAn example of language related to scientific dissemination in an official document appears in the statute of the Oswaldo Cruz Foundation (Fiocruz), which is a historically well-known Brazilian institution dating back to 1970 that assigns greater importance to this area than other institutions. Fiocruz’s Canal Saúde is responsible for “promoting public debate, social participation, and the dissemination of projects and activities of interest in the areas of health, the environment, science, and technology in healthcare” It is also responsible for the following:\n\nplanning, coordinating, supervising, and executing activities related to the development of studies and research related to the history, scientific dissemination, and cultural heritage of health, science, technology, and other related fields, as well as dissemination and education in science, technology, and health (Fiocruz, 2016, p. 7).\n\nTherefore, it is possible to conclude that scientific dissemination can be included in macro documents linked to institutional competences as well as in various areas and actions related to teaching, research, and extension. The aim of including such language in official documents is to guide the development of specific policies and programs for the dissemination and popularization of science by outlining requirements and commitments, always considering the dialogue between communication sectors and the academic community in the dean’s office and on campuses.\n\nJust as in Institution A documents, we searched for the terms “communication/communicational”, “disseminate/dissemination”, “scientific dissemination”, “knowledge diffusion”, “scientific knowledge dissemination”, “scientific knowledge”, and “scientific journalism” in the IDP, IPP, the general regulations of graduate and specialization programs, and in the scientific initiation programs at Institution B. We must note that the searches and analyses of the first two documents were performed together, considering that the “plan” and “project” were included in a single file divided into chapters. Table 3 shows the frequency of occurrence of the terms in the documents, and Table 4 shows their main contexts.\n\nWe found that explicit language related to scientific dissemination was present in the documents that were analyzed, unlike in those pertaining to Institution A, from which such references could only be inferred. Although there are only two occurrences of this term in the documents, it is noteworthy that its importance is recognized in the institutional history of the IDP and in the charter of the Library System (IPP), which stipulates the development of scientific dissemination programs. In other words, this requirement is mentioned at the beginning of the first document, and it could not be disregarded by the management or academic body of the institution when establishing actions or goals over the years. Despite this fact, there is no objective delimitation of activities that comply with this stipulation for the next five years, not even in the section related to prediction of the implementation of the institution’s communication policy. The only references to scientific dissemination actions that can be inferred from the language in the IDP and IPP are implicitly expressed in the titles.\n\nAs already mentioned, scientific dissemination in actions taken in consideration of the inseparability of teaching and research, or research and extension, or teaching, research, and extension, can be included in the next update to these documents. This can be accommodated in the competences and actions of the Dean of Research, Graduate Programs, and Innovation of the SIBi; policies; and the programs and projects of teaching, research, extension, and communication, among others. A notable fact that we consider positive is the presence, even if only in the title of the SIBi, of the Division of Communication, Training, and Culture (DGT&C). The IPP describes this sector as being responsible for communicating science mainly in a specialized and restricted way that is different from the scientific dissemination that we advocate in this study. Nevertheless, this issue could be further explored in the joint work between the communication sectors of the institution and the SIBi team to transpose and expand scientific communication (SC) to scientific dissemination.\n\nLike Bueno (2010), we understand that SC necessarily forms part of scientific dissemination-related actions, which means that the two are intertwined. One depends on the other to fulfill the objective of communicating science to society. One of the purposes of the DGT&C is to “promote cultural and scientific dissemination activities” (https://suap.ifgoiano.edu.br). The existence of a specific sector for addressing what we advocate in this study can have a significant impact on such efforts if we think about actions that can be integrated into various institutional sectors because they transcend the communication sector. Journalists and communicators specialized in the discourse of scientific dissemination and scientific journalism can also be framed in this context, whether in the form of partnerships or by helping institutions to achieve their educational and social purposes, among other objectives.\n\nA second characteristic of Institution B’s documents that is worth mentioning is the way they were prepared, that is, the methodology used by the academic community in executing their preparation. The IDP has technical-bureaucratic content, essentially, with some administrative information; thus, we can infer from this analysis that the institution is organized adequately from an academic point of view. The IPP is the base document for institutional management, which effectively outlines Institution B’s policies. We can infer that “all” the actions must be connected even if this is not mentioned in the pedagogical project of the institution. This is a means of addressing the formulation of programs and activities, even if they are not directly linked to the teaching sector, as is the case of the scientific dissemination- and communication-related actions to be developed in these areas. Although such nuances may be difficult to perceive, when we analyze the two institutes in depth, we can capture them and observe important, implicit details.\n\nAmong the terms that appear most frequently in the documents, the IDP and IPP, are “communication” with 77 occurrences, “scientific knowledge/knowing/process” with 40 occurrences, and “dissemination/disseminate” with 22 occurrences. Most of these terms were present in the IPP. In the IDP, communication appears between courses to be offered at the Ceres and Trindade campuses and between strategic objectives and performance indicators and improvements in internal and external communication flows. Other references are included in the communication policy, such as in the definition of strategies, improvement in information flows, and the delimitation of communication products.\n\nAmong the phrases related to “scientific knowledge/knowing/process” and “knowledge diffusion/dissemination” are democratization, socialization of knowledge to contribute to an ethical and solidarity-driven society (historical), and the integration of technical and technological knowledge with pedagogical practices. We emphasize the importance of a humanistic view for the world, promoting the sharing of scientific and cultural knowledge, which can be seen in the description of the role of Institution B and IFs in the documents. In this way, we can infer that there is concern for socializing information and disseminating science, not only through translation but also through knowledge generation. This can also be observed in initial and continuing education courses (ICE), which require attention to be paid to the demands of training (teaching) and scientific and technological knowledge (research) in line with local and regional realities.\n\nInitially in the IPP, a document that shows adequate consideration of institutional policies, scientific dissemination is included in several areas, such as Research, Graduate Programs, and Innovation policies, which provide a stimulus to the socialization and internal and external dissemination of the scientific production of Institution B. Here, we can perceive the consideration given to establishing policies that promote scientific dissemination. The general inclusion of actions aimed at promoting scientific dissemination to the general public and the identification and improvement of forms of institutional dissemination is also present in extension programs and events. There is a requirement in the research actions, under the aegis of the Dean of Research, Graduate Programs, and Innovation, to “support and monitor the dissemination of research results in the internal and external community and scientific events” (https://suap.ifgoiano.edu.br). At this point, it would be appropriate to expand this dissemination to aspects of science other than results, including details of the production process and continuous communication actions related to each research project. Other actions mentioned in the IPP regarding this topic include contributing to fostering and strengthening the dissemination of research at Institution B, encouraging the guidance of the coordinators and directors of campuses in the production, execution, and monitoring of research programs, and disseminating the resulting scientific production. The other instances refer to the SIBi and the specification of its services.\n\nTherefore, explicit stimuli to the development of actions related to scientific dissemination are enumerated, especially in relation to the topics addressed in this study. We found that the integration of these actions with the work of the social communication sector was lacking and that this sector could enrich and contribute to such activities by making institutional research accessible to several audiences. The development of a program or project promoting a dialogue between the communication and research sectors under the dean and representatives of science departments could represent a concrete means of uniting the academic community and the scientific field. It would also be possible to hold science fairs for the public, allowing students to familiarize themselves with laboratories and ongoing research through exposure to scientific equipment and lectures and external exhibitions in public places in cities, such as parks, zoos, and bars. It would also be possible to hold meetings between journalists, communicators, and researchers; form working groups for creating communicational products showing what is done at institutions and its relevance to people’s lives; and disseminate materials in public and private spaces, such as medical and dental offices and places with a lot of foot traffic. A critical advertising medium that generates good results, especially in inland cities, is the “sound car.” It would also be possible, through short texts, to disseminate science-related actions and scientific events, among other things, to the public.\n\nIt is important to observe the significance of the meanings associated with the word “scientific” (knowledge, knowing, and others) to the role of Institution B in the sharing of scientific and cultural knowledge. The implications of this concept can also be observed in its extension policies, through the construction of bonds with society via the exchange of knowledge and experiences, research development, teaching, and extension and in the inseparability of these areas, along with actions in the areas of scientific, technological, social, artistic, and cultural innovation. Moreover, such practices would provide an increased stimulus to produce scientific articles for congresses, seminars, and science-related events. In this context, it is apparent that a path of dissemination and scientific journalism should be followed, complementing what is set out in the institution’s documents. It is evident in this part of the plan and project that this message is directed at researchers and scientists without the intent of reaching the lay public.\n\nWhen we talk about the “communication” present in the IPP, we seek the meanings that directly concern the institution’s dialogue with society in an expanded form. Despite this term having the largest number of occurrences, not all refer to the communicational form that is addressed in this study. Many were found in the titles of methodologies, which pertain to information and communication technologies or refer to the education policies addressing the interpersonal communication or communication between professors and students, and communication courses to be offered, among other such things, or to the competences of the institutional communication sectors. Thus, such titles refer to general requirements and not to science communication inside or outside the institution.\n\nFinally, when we consider scientific dissemination integrated with teaching, the documents of the two institutions do not address the work of scientific dissemination directly. Instead, there are implied forms of a direct link between teaching and research activities. Although this inseparability can be seen in the guiding documents of the policies, programs, projects, and actions in the academic environment of these institutions, the language that is used is not directly related to the use of instruments of scientific journalism or scientific dissemination in the classroom. These two expressions are not found in the IPPP, IDP, or other Institution A documents. They appear twice in Institution B’s documents, but in a restricted way, as has already been mentioned in the analysis of Institution B. Nevertheless, there seems to be room to insert these practices into the norms and guidelines of teaching, especially in relation to the topics referring to research and its direct connection with educational practices and the intersection between teaching and research, between research and extension, and between teaching, research, and extension.\n\nBy drawing a parallel with the Action Plan in Science, Technology, and Innovation for Popularization and Dissemination of Science and Technology (MCTIC, 2018), we can observe that, despite the fact that mechanisms such as including technological projects in extension activities (IFG, 2019e) and holding fairs and exhibitions as extension activities of the IF Goiano are present in the IPPP and IPP it is necessary to further develop the teaching, research and extension triad. This would allow the execution of the proposed plan and the appropriation of science and technology by students of these federal institutes.\n\nThe objective of the plan, which must be translated into a policy that relates scientific dissemination to institutional priority areas, is to popularize science in the educational context, enabling citizens to improve their lives and generating a more participatory society. In this context, the assumption that scientific dissemination and scientific journalism are practices aimed at returning the resources used in research to the public is fundamental. It can aid in overcoming the quality crisis in Brazilian education. Scientific dissemination is the appropriation of science and technology by Brazilians and it is a cross-sectional action encompassing all federal states (MCTIC, 2018).\n\nWe do not intend to present an exhaustive discussion in this documentary study but rather to promote the understanding that scientific dissemination, scientific journalism, curricula, and research development are inseparable and essential for the consolidation of research at federal institutes throughout the country. Thus, among the data collected from the official documents of Institution A and Institution B, we observed that discreet actions related to scientific journalism tended to be implied in language related to topics that referred to scientific dissemination. Although the term was not explicitly mentioned (in Institution A), we can infer that the institution recognizes the existence and importance of disseminating research results, since this theme is included in titles throughout the IDP and IPPP. Nevertheless, we have concluded that forthcoming editions of these documents must clarify, or at least initiate, a discussion about programs, projects, and actions that associate the process of dissemination with the results of scientific research. Including specific topics related to scientific dissemination in the titles of media, teaching, research, and extension in the documents of the two institutions is also necessary. We also propose that a research group bringing together Institution A and Institution B, which could advance this discussion, as well as a formal network connecting the journalists, communicators, and researchers of these IFs, should be created, thereby broadening the flow of communication with the local, regional, and national press.\n\nWe understand that such dissemination efforts should always be aimed at a lay audience. This means that the proper treatment of information will be necessary; therefore, even in the initial stages, it will be essential to establish a dialogue and joint effort between journalists, communicators, and researchers through such official plans. Therefore, we suggest that in-depth studies be conducted on this subject so that our suggestions can be implemented in updates to the documents of Institution A and Institution B. It is important to consider officially documenting the guidelines to be followed and policies to be formulated and putting them into practice. This would allow the inclusion of the culture and practices of scientific journalism and science dissemination and publicize the work of these institutions and the other public educational institutions of the Federal Network of Professional, Scientific, and Technological Education, exposing the public to the scientific work they are carrying out.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "References\n\nBerbel NAN: As metodologias ativas e a promoção da autonomia de estudantes. 2011.[Active methodologies and the promotion of student autonomy]. Semina: Ciências Sociais e Humanas. 2011; 32(1): 25–40.Reference Source\n\nBoillos Pereira M, Pérez-Izaguirre E, Apaolaza-Llorente D: Systems of Augmentative and Alternative Communication (SAACs) in Spain: A Systematic Review of the Educational Practices Conducted in the Last Decade. Social Sciences. 2019; 8(1), 15. Publisher Full Text\n\nBueno WC: Jornalismo científico: conceitos e funções.[Scientific journalism: concepts and functions]. Ciência e Cultura. 1985; 37(9): 1421–1427. Reference Source\n\nBueno Wc: Comunicação científica e divulgação científica: aproximações e rupturas conceituais.[Special Issue] [Scientific communication and scientific dissemination: conceptual approaches and ruptures]. Informação e Informação. 2010; 15(1), 1–12. Reference Source\n\nBueno WC: A formação do jornalista científico: além da competência técnica. [The formation of the scientific journalist: beyond the technical competence]. In: Porto CM, Bortoliero S (Eds.). Jornalismo, ciência e educação: interfaces. 2013; (pp. 13–24). Salvador, BA: EDUFBA.\n\nBueno WC: O jornalismo científico no século XXI: desafios e tendências.Scientific journalism in the 21st century: challenges and trends.2019. São Paulo, SP: Curso de Jornalismo Científico. Comtexto Comunicação e Jornalismo a Distância. Reference Source\n\nCaldas G: Divulgação científica e relações de poder.[Special Issue] [Scientific dissemination and power relations]. Informação e Informação. 2010; 15(1), 31–42. Reference Source\n\nDemo P: Educar pela pesquisa. [Educate through research]. Campinas, SP: Autores Associados; 2011.\n\nGalvão T, Felicio CM, Ferreira JC, et al.: Scientific Journalism as an Educational Practice: An Experience Report of the Collective Construction of a “Science Clothesline”. Science Communication. 2020; 00(0), 1–12. Publisher Full Text\n\nGouvêa G: A divulgação da ciência, da técnica e cidadania em sala de aula. [The dissemination of science, technique and citizenship in the classroom]. In: Giordan M, Cunha MB (Eds.). Divulgação Científica na Sala de Aula. 2015; pp. 13–41. São Paulo, SP: Unijuí.\n\nGramsci A: Cadernos do Cárcere. Volume 2: Os Intelectuais. O Princípio Educativo. Jornalismo. [Jail Notebooks. Volume 2: The Intellectuals. The Educational Principle. Journalism]. Translation Nelson Coutinho. Rio de Janeiro, RJ: Civilização Brasileira; 2004.\n\nHanney R, Skirkeviciutey G: Reflection, identity, community: Affordances of blogging for social interaction and reflective dialogue. Education and Information Technologies. 2019. Publisher Full Text\n\nMachado L: Ensino médio e técnico com currículos integrados: propostas de ação didática para uma relação não fantasiosa. [High school and technical with integrated curricula: proposals for didactic action for a non-fanciful relationship]. In: Moll J (Ed.). Educação Profissional e Tecnológica no Brasil Contemporâneo. 2010; (pp. 80–95). Porto Alegre, RS: Artmed.\n\nManacorda MA: Marx e a pedagogia moderna. [Marx and modern pedagogy]. Translation Newton Ramos de Oliveira. Campinas, SP: Alínea; 2007.\n\nde Marconi MA, Lakatos EM: Fundamentos de Metodologia Científica. [Fundamentals of Scientific Methodology]. São Paulo, SP: Atlas; 2018.\n\nMassarani L, Castelfranchi Y, Fagundes V, et al.: O que os jovens brasileiros pensam da ciência e da tecnologia?[What do young Brazilians think of science and technology? (Resumo Executivo).Rio de Janeiro, RJ: Instituto Nacional de Ciência e Tecnologia em Comunicação Pública da Ciência e Tecnologia (INCT-CPCT - Brazil); 2019. Reference Source\n\nMorgan M, Collins W, Sparks G, et al.: Identifying Relevant Anti-Science Perceptions to Improve Science-Based Communication: The Negative Perceptions of Science Scale. Social Sciences. 2018; 7(4): 64. Publisher Full Text\n\nNoy S, O’Brien TL: Science for good? The effects of education and national context on perceptions of science. Public Understanding of Science. 2019; 28(8): 897–916. Reference Source\n\nRamnarain U, Moleki B: Teachers’ Use of Newspaper Articles in Promoting a Humanistic Perspective of Science in South Africa. J Science Teacher Education. 2017; 28(2): 205–217. Publisher Full Text\n\nRamos M: Possibilidades e desafios na organização do currículo integrado. [Possibilities and challenges in organizing the integrated curriculum]. In: Frigotto G, Ciavatta M, Ramos M (Eds.). Ensino Médio Integrado: Concepção e Contradições. 2012; (pp. 107–128). São Paulo, SP: Cortez.\n\nStecanela N, Williamson G: A educação básica e a pesquisa em sala de aula.[Basic education and classroom research]. Acta Scientiarum Education. 2013; 35(2): 283–292. Reference Source\n\nTargino MG: Divulgação de resultados como expressão da função social do pesquisador.[Dissemination of results as an expression of the researcher's social function]. Intercom: Revista Brasileira de Ciências da Comunicação. 2001; 24(1): 11–35. Reference Source\n\nValente JA: A sala de aula invertida e a possibilidade do ensino personalizado: uma experiência com a graduação em midialogia.[The inverted classroom and the possibility of personalized teaching: an experience with graduation in medialogy]. In: Bacich L, Moran L (Eds.) Metodologias ativas para uma educação inovadora: uma abordagem teórico-prática. 2018; (pp. 26–44). Porto Alegre, RS: Penso."
}
|
[
{
"id": "269033",
"date": "09 Sep 2024",
"name": "Thiago Magela Rodrigues Dias",
"expertise": [
"Reviewer Expertise Bibliometrics",
"scientometrics",
"Information Retrieval",
"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\nThe work is relevant and addresses an important issue in the context of teaching and research institutions in the scientific dissemination process.\nThe work is adequate.\nSome comments to improve the text of the article:\nThe Rationale for the work could present the scope of the Federal Institutes in more detail. In addition, the Network's numbers and its growth history could be presented. Still in the justification, some more recent references could be included.\nIn the Methodology, it would be important to better contextualize the research locus and also detail some laws and guiding documents for those who are not accustomed to Brazil's educational policy.\nSome quantitative data from the Results section could be presented in graphs so that the section is not so descriptive.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "269029",
"date": "19 Sep 2024",
"name": "Md Nurul Islam",
"expertise": [
"Reviewer Expertise Bibliometrics",
"Library and Information Science",
"Education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nRecommendations for Improvement\nImplementation Strategies: Offer concrete steps and examples of how institutions can implement the proposed changes. Stakeholder Engagement: Discuss the role of different stakeholders in the process and how they can be involved in institutionalizing scientific dissemination. Expand Theoretical Framework: Include more recent studies and theories related to science communication to update and deepen the theoretical discussion. References to recent literature could be updated to enhance the context of the discussion.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-886
|
https://f1000research.com/articles/10-246/v1
|
26 Mar 21
|
{
"type": "Software Tool Article",
"title": "An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates",
"authors": [
"Ann M. Mc Cartney",
"Medhat Mahmoud",
"Michael Jochum",
"Daniel Paiva Agustinho",
"Barry Zorman",
"Ahmad Al Khleifat",
"Fawaz Dabbaghie",
"Rupesh K Kesharwani",
"Moritz Smolka",
"Moez Dawood",
"Dreycey Albin",
"Elbay Aliyev",
"Hakeem Almabrazi",
"Ahmed Arslan",
"Advait Balaji",
"Sairam Behera",
"Kimberley Billingsley",
"Daniel L Cameron",
"Joyjit Daw",
"Eric T. Dawson",
"Wouter De Coster",
"Haowei Du",
"Christopher Dunn",
"Rocio Esteban",
"Angad Jolly",
"Divya Kalra",
"Chunxiao Liao",
"Yunxi Liu",
"Tsung-Yu Lu",
"James M Havrilla",
"Michael M Khayat",
"Maximillian Marin",
"Jean Monlong",
"Stephen Price",
"Alejandro Rafael Gener",
"Jingwen Ren",
"Sagayamary Sagayaradj",
"Nicolae Sapoval",
"Claude Sinner",
"Daniela C. Soto",
"Arda Soylev",
"Arun Subramaniyan",
"Najeeb Syed",
"Neha Tadimeti",
"Pamella Tater",
"Pankaj Vats",
"Justin Vaughn",
"Kimberly Walker",
"Gaojianyong Wang",
"Qiandong Zeng",
"Shangzhe Zhang",
"Tingting Zhao",
"Bryce Kille",
"Evan Biederstedt",
"Mark Chaisson",
"Adam English",
"Zev Kronenberg",
"Todd J. Treangen",
"Timothy Hefferon",
"Chen-Shan Chin",
"Ben Busby",
"Fritz J Sedlazeck",
"Medhat Mahmoud",
"Michael Jochum",
"Daniel Paiva Agustinho",
"Barry Zorman",
"Ahmad Al Khleifat",
"Fawaz Dabbaghie",
"Rupesh K Kesharwani",
"Moritz Smolka",
"Moez Dawood",
"Dreycey Albin",
"Elbay Aliyev",
"Hakeem Almabrazi",
"Ahmed Arslan",
"Advait Balaji",
"Sairam Behera",
"Kimberley Billingsley",
"Daniel L Cameron",
"Joyjit Daw",
"Eric T. Dawson",
"Wouter De Coster",
"Haowei Du",
"Christopher Dunn",
"Rocio Esteban",
"Angad Jolly",
"Divya Kalra",
"Chunxiao Liao",
"Yunxi Liu",
"Tsung-Yu Lu",
"James M Havrilla",
"Michael M Khayat",
"Maximillian Marin",
"Jean Monlong",
"Stephen Price",
"Alejandro Rafael Gener",
"Jingwen Ren",
"Sagayamary Sagayaradj",
"Nicolae Sapoval",
"Claude Sinner",
"Daniela C. Soto",
"Arda Soylev",
"Arun Subramaniyan",
"Najeeb Syed",
"Neha Tadimeti",
"Pamella Tater",
"Pankaj Vats",
"Justin Vaughn",
"Kimberly Walker",
"Gaojianyong Wang",
"Qiandong Zeng",
"Shangzhe Zhang",
"Tingting Zhao",
"Bryce Kille",
"Evan Biederstedt",
"Mark Chaisson",
"Adam English",
"Zev Kronenberg",
"Todd J. Treangen",
"Chen-Shan Chin"
],
"abstract": "In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research.\n\nThe overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.",
"keywords": [
"Structural variant",
"CNV",
"SARS-CoV-2",
"NextGeneration Sequencing"
],
"content": "Introduction\n\nStructural variants (SVs) comprise a number of genomic imbalances including copy number variations (CNVs), insertions (INS), deletions (DELs), inversions (INVs), duplications (DUPs), and inter-chromosomal translocations.1–3 SVs have been implicated as clinically significant mutations with proven associations to multiple diseases.4,5 Despite next-generation sequencing becoming increasingly common within the field of biomedical research, several practical challenges exist for comprehensively detecting and evaluating SVs particularly in regard to the high false positive or negative rate along with the accuracy of breakpoint prediction.6,7 While SV detection with genotyping arrays remains the most commonly used method, the toolbox for SV detection is expanding to incorporate the advancements in third generation sequencing technologies provided by Pacific BioSciences,8 Oxford Nanopore Technologies,9,10 optical mapping and NanoString11 to name a few. These advancements offer potential for solving previously unresolved structural variants.\n\nIn October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on SV, Pan-genomes, and SARS-CoV-2 related research. Consequently, this international structural variation hackathon meeting focused on eight themes: 1.) efficiently genotyping vast quantities of SVs; 2.) mapping CNVs to SV types; 3.) detecting and validating SVs for SARS-CoV-2; 4.) filtering high-confidence SV calls for clinical genomics; 5.) SV read-based phasing for haplotype analysis; 6.) genome graph generation without a reference; 7.) machine learning approaches to predict lab-of-origin of a sample.; and 8.) gene-centric data browsing for SV analysis.\n\nOverall, this manuscript details our tools’ objectives, value-add, implementations, and applications and sets the foundation for further concept development beyond. In this article we present 10 software tools that were the results of this hackathon.\n\nNibbleSV: efficient genotyping of SVs from short read datasets. Detection of SVs longer than a short-read (<500bp) DNA trace is very challenging as the SV allele becomes split across multiple reads. To this end, long read sequencing technology is preferential for overcoming this challenge however, although long read sequencing has proven more accurate in SV identification, obtaining accurate allele frequencies across a population is important in order to rank and identify potential pathogenic variations.\n\nThus, it is still important to genotype SV events in pre-existing short read datasets such as those provided by the 1000 genomes project, Topmed, CCDG, etc. Recently, two main approaches, Paragraph12 and VG,13 have achieved this with high accuracy even for insertion SV events. However, these methods are computationally expensive particularly when the number of SVs to be genotyped per sample increases. Furthermore, and maybe more crucially, both methods rely on precise breakpoints that do not change in other samples, an assumption that is potentially flawed particularly over repetitive regions. NibbleSV is a software package able to efficiently genotype vast quantities of SVs whilst also using a kmer catalogue of SVs in order to circumvent the need for re-mapping the same dataset to different versions of the same reference genome (e.g. hg19 vs. GRCH38 vs. CHM13), again aiding computational efficiency (Figure 1).\n\nCNV2SV: supplement CNV calling in SV detection. CNVs are a subset of SV consisting of deletions and duplications. One common challenge is mapping CNVs to specific SV types. Automatically linking these events together will improve our understanding and interpretation of regions where large CNVs occur and potentially also lead to improvements in breakpoint accuracy and thus resolution if the breakpoints are more complex (i.e. including other SV events, e.g. inversions). Here, we demonstrate CNV2SV using the haploid human genome of T2T CHM13 and will showcase CNV2SV on additional diploid, publicly available samples (Figure 2).\n\nCoronaSV: SV pipeline for SARS-CoV-2. While deletions have been reported in several SARS-CoV-2 genomes at consensus level,14,15 the confidence in how these deletions are detected has not yet thoroughly been evaluated. Existing methods for detecting SV at the individual read level often suffer from false positive calls.16,17 Additionally, analyses with different variant calling pipelines often result in inconsistent calls.18,19 To examine the landscape and extent of SV across SARS-Cov-2 genomes, a method for generating accurate and trustworthy SV calls is needed. With this in mind, we developed the CoronaSV bioinformatics pipeline.\n\nCoronaSV is a SV detection and SV validation pipeline for SARS-CoV-2 that combines an ensemble SV calling approach that relies on both long read and short read sequencing technologies (Figure 3). Both assembly-based and read based SV detection methods are used by CoronaSV. By combining different sequencing technologies and variant detection approaches, we can identify both a) confident SV call set and b) artifacts that may result from specific technologies + computational approaches.\n\nCleanSV: Filtering High-quality SVs. Short-read sequencing is performed within clinical genomics to both inform and directly guide patient care. This has been immensely successful for various Mendelian disorders, where patients now routinely have their genomes sequenced to detect high-quality variants. Indeed, this approach has been utilized within clinical genomics for close to a decade,20 often to correct misdiagnoses (see21 for a recent example).\n\nWithin precision oncology, short-read sequencing (normally targeted sequencing or whole exome sequencing (WES)) has proved successful not only illuminating the nature of specific cancers, but also guiding novel drug development. Today routine sequencing is used to apply therapies for specific cancer subtypes, and influence the treatment of individual patients.22,23 For clinical work, samples from tumors are sequenced for somatic variants in well-studied oncogenes/tumor suppressor genes. Bioinformaticians will then manually investigate the variant calls within IGV in order to validate how accurate they are, and finally send reports summarizing these data to clinicians.\n\nHowever, SV calling using short-read data is marred by high false positive (FP) call rates, sometimes up to 90% with modern callers.10,24,25 As a result, manual curation for each patient proves oppressively time-consuming for the needs of modern precision care and is prone to human error. Even though aneuploidy has been long studied for its role in tumor progression (see26 for a recent review), due to algorithmic uncertainties, routine inclusion of high-confidence SVs within clinical reports is often infeasible today.\n\nTherefore, there exists a pressing need within bioinformatics to develop methods to remove false positives from the outputs commonly used SV callers, and benchmark their performance across a variety of assays (including a range of sequencing depths and tumor purities). Individual SV callers rely upon specific strategies to detect SVs, which makes the nature of the false positives algorithm-specific. Having access to a call set with a lower false positive rate would certainly not eliminate the requirements of manual curation, but it would make the problem more tractable.\n\nThe goal of this project was to develop a set of publicly available filters tailored for cancer genomics which have been measured to perform reliably across popular SV callers, as the filters must be specific to the SV caller used. Using a large cohort of high-quality normal whole genome sequencing (WGS) samples, we perform systematic false positive filtering. SVs labeled by the algorithm as somatic have evidence as actually being germline, while others are algorithmic artifacts. With such filters, bioinformaticians would have access to a set of high-quality somatic calls to manually curate, which could finally result in more robust clinical reports.\n\nSniphles: Phasing SVs with parallel programming. Phasing infers the correct cis or trans relationship between different heterozygous variations facilitating accurate haplotype reconstruction.27 Protocols and programs utilizing molecular phasing (chromosomal separation at the bench before sequencing), pedigree-based phasing (matching parental and offspring genotypes to understand the haplotype), population-based phasing (using genotype data from large cohorts to infer haplotypes), and read-based phasing (mapping sequencing reads with the same variants to construct a haplotype) are all successful approaches to phasing next-generation sequencing data.28 The long-reads of third generation sequencing have bolstered our ability to phase longer and more comprehensive haplotype blocks.29 More comprehensive haplotype blocks increase our ability to accurately phase structural variants.\n\nThe goal of this project is to develop a wrapper script around the Sniffles SV caller10 to properly phase SV and augment the ability of Sniffles to accurately call SV (Figure 5). This result is obtained by using phased reads generated by SNV phasing tools such as WhatsHap or LongShot,27,30 and subsequently call SVs on the haploid phase blocks separately using temporary files before finally merging both haplotypes to obtain a single VCF file. As this algorithm processes each phase block separately this is attractive for parallelization. Our wrapper script additionally makes Sniphles compatible with alignments in the CRAM format.\n\nSwagg: Structural Variation With Annotated Graph Genomes (Swagg). Most graphical approaches to variant calling only use genome graphs. While this information helps illustrate variation on a genomic level, it does not show variation on the individual protein level. To help leverage the power of graph approaches for SV calling, we introduce a pipeline that delivers both protein and genome graphs.\n\nSwagg is a pipeline that enables the construction of genome graphs from read data (Figure 6). The input into the pipeline is sequence reads with or without a reference genome(s). Reads can be short reads or preprocessed (basecalled) long reads. These reads are then assembled into longer contigs which are mapped back to the reference genome to highlight discrepancies with the reference genome. These discrepancies can be caused by real mutations or sequencing artifacts and easily identified using SV tools, which output VCF files for each read set. These VCF files are taken together to make the genome graph at the end of the pipeline. The overall pipeline and intertwined modules are shown below. In addition to the pipeline for creating graph genome and graph proteins, we also have a module for simulating reads based on an input reference genome.\n\nPanOriginSV: detecting lab-of-origin. The advent of novel synthetic biology methods and organic bench-top synthesis toolkits like CRISPR31 has enabled rapid developments in genetic engineering. However, this progress has also introduced biosafety concerns surrounding the intentional or unintentional misuse of these tools. In order to increase accountability, the lab-of-origin studies attempt to map a set of plasmids to their lab-of-origin. Subsequently, the Genetic Engineering Attribution Challenge (GEAC) was announced, inviting open source tools from the community that could best predict the lab-of-origin.\n\nPrevious methods have employed machine learning or deep learning-based approaches that despite their promise, suffer from sub-optimal accuracy, long training times as well as explainability issues. Recently, a new alignment based tool PlasmidHawk32 reported higher accuracy than machine learning tools. PlasmidHawk relies on linear pangenome constructs to align query sequences to a pangenome in order to best determine the Top-1 and Top-10 candidate labs. Though PlasmidHawk has a higher accuracy, the runtimes to create the linear plasmid are non-scalable to larger datasets. Another drawback being the linear pangenome doesn’t incorporate SV, which could be important to predict hard-to-classify sequences. To address some of these challenges, we propose a tool PanOriginSV that combines machine learning approaches with graphical pangenome based alignment to predict lab-of-origin (Figure 7).\n\nPanOriginSV creates multiple pangenome graphs from similar training sequences using BCALM33 creating a variation graph that incorporates SV and aligns the sequences back to the graph using GraphAligner.34 The most similar training sequences for graph construction are clustered using MMSEQ2.33,35 After this, top alignments, scores to the pangenome and sequence metadata are considered as features for a downstream machine learning model towards lab-of-origin prediction.\n\nGeneVar: SV Browser. Next-generation sequencing provides the ability to sequence extended genomic regions or a whole-genome relatively cheaply and rapidly, making it a powerful technique to uncover the genetic architecture of diseases. However, significant challenges remain, including interpreting and prioritizing the identified variants and setting up the appropriate analysis pipeline to cover the necessary spectrum of genetic factors, which includes expansions, repeats, insertions/deletions (indels), SV and point mutations. For those outside the immediate field of genetics, a group that includes researchers, hospital staff, general practitioners, and increasingly, patients who have paid to have their genome sequenced privately, the interpretation of findings is particularly challenging. Although various tools are available to predict the pathogenicity of a protein-changing variant, they do not always agree, further compounding the problem. Furthermore, with the increasing availability of next-generation sequencing data, non-specialists, including health care professionals and patients, are obtaining their genomic information without a corresponding ability to analyse and interpret it as the relevance of novel or existing variants in genes is not always apparent. Similarly SV analysis36,37 and its interpretation requires care in regard to sample and platform selection, quality control, statistical analysis, results prioritisation, and replication strategy.\n\nHere we present GeneVar, an open access, gene centric data browser for SV analysis (Figure 8). GeneVar takes as input a gene name or ID and produces a report that informs the user of all SVs overlapping the gene and any non-coding regulatory elements affecting expression of the gene. The tool is intended to have a clinical focus, informing the interpretation of SV pertaining to a gene name provided by the user.\n\nSVTeaser: simulated data for SV benchmarking. SV detection tools often have a large number of wrongly detected variations16,24 requiring benchmarking to assess method quality before finalizing a workflow. Few tools are currently available to simulate data for SV benchmarking. SVTeaser is a tool for rapid assessment of SV calling fidelity with two main use-cases: 1) genotyping a set of pre-ascertained SVs and 2) benchmarking a new algorithm against pre-existing tools across a range of parameters. Users simply supply SVTeaser with a reference sequence file (.fasta) and, optionally, a set of SVs (.vcf). SVTeaser outputs simulated reads across a range of read lengths and depths and provides a downstream dataframe based analysis framework for evaluating accuracy (Figure 9). SVTeaser achieves rapid assessment by downsampling the full reference to a subset of numerous 10kb samples to which it adds SVs.\n\nXSVLen: haplotype-resolved assemblies for benchmarking SVs. Since the development of a “gold standard” SV set, sequencing technologies and assembly algorithms have improved to enable nearly complete haplotype-resolved assemblies of human genomes. XSVLen is a framework (Figure 10) to use haplotype-resolved assemblies for benchmarking SV detection algorithms. Each variant call may be considered an operation to be applied to the reference genome. Our framework for benchmarking SV callsets is to apply SV operations to the reference genome and compare the modified reference against the haplotype-resolved assemblies. This approach allows for SV calls that are different but produce similar sequences due to the repetitive nature of the genome to be scored as valid. In this manner, all variants in a region that is accurately assembled in both haplotypes may be benchmarked using this approach. We demonstrate the effectiveness of this approach by scoring SV calls generated from Oxford Nanopore reads on the HG002 genome38 using CuteSV39 and comparing against gold-standard calls by Truvari (https://github.com/spiralgenetics/truvari). This approach can be extended to use any haplotype-resolved assembly to benchmark SV callsets in additional genomes, enabling benchmarks as a distribution across call sets.\n\n\nMethods\n\nNibbleSV: NibbleSV is a lightweight, scalable and easy to apply method to identify the frequency of SV events across short read data sets. As such, NibbleSV extracts kmers that are informative if an SV is present or if an SV is absent given the breakpoints of the previous predicted SV. Subsequently, NibbleSV scans the short read bam or fastq file for the presence of these k-mers and counts their number of occurrences. In the end, NibbleSV extends the VCF file with tags holding information about the number of times an SV is supported by kmers or not (Figure 1).\n\nCNV2SV: CNV2SV is a tool developed to identify CNVs in the context of a whole genome sequence (Figure 2). CNV2SV requires three input files which is a BED or VCF formats (from Parliament2,40 Control-FREEC,41 a putative SVs from genome-genome alignment (vcf format, from dipcall) and assembled reference files (fasta files) from both the reference and the assembled sample. In addition, we require preinstalled packages such as intervaltree, mappy, pyfaidx together with python v.3.8.* or higher. The visualisation for CNV2SV requires the installment of R together with the circularlize package, matplotlib, seaborn and pandas. CNV2SV currently relies on an installation of Control-FREEC which is needed for the CNV calling from short reads. The main output of CNV2SV (cnvlink.py) comprises the best matching linked SV for each CNV call, with summary statistics including alignment overlap, mismatches, respective start and end positions useful for evaluating e.g. the quality/resolution of breakpoints identified by the CNV callers. Furthermore, all additionally identified adjacent and distant SVs are reported separately for each CNV. The raw output can be further visualized to show the CNV-SV links identified across the genome in a circular plot, as well as summary statistics for the linking results (Figure 2).\n\nCoronaSV: CoronaSV is a method developed for generating accurate and trustworthy SV calls across SARS-Cov-2 genomes. The tool utilises available SRA data from SARS-CoV-2 isolates that have been sequenced with both Illumina and ONT platforms. CoronaSV utilizes a combination of three different approaches: read-based SV detection with paired-end Illumina reads and ONT long-reads, as well as assembly-based SV detection using both short and long-reads (Figure 3). All the software packages used by CoronaSV can be installed via the Conda package manager (https://github.com/conda/conda).\n\nCleanSV: The goal of the hackathon project was to develop filters and QC checks to remove false positive calls from common SV callers. Currently, within clinical genomics, it’s exceptionally difficult to categorize true positives from false positives, thus making accurate diagnoses virtually impossible. The situation is even more complicated within clinical oncology, as researchers need to precisely separate true somatic calls from false positives and (potential) germline calls. In order to aid with precision SV calling, the team wrote a set of scripts to be used with short-read SV callers, allowing researchers to better generate a set of high-quality SVs to further investigate manually (Figure 4).\n\nFor cancer genomics, groups normally develop in-house filters to improve the precision of SV calling. The scripts developed for this project accept as input GRIDSS,42 Manta,43 DELLY,44 and SvABA45 calls from short-read WGS data, along with a manually-curated reference set of calls designated as ground truth. The reference set was curated using a paired melanoma and normal lymphoblastoid COLO829 cell lines using four different technologies (Illumina HiSeq, Oxford Nanopore, Pacific Biosciences and 10x Genomics), along with extensive external validation.46 Using the reference set, we proceeded to investigate the presence and nature of false positives from the initial callsets. (Note that we focused on WGS for this hackathon, but a similar approach could be applied to other assays such as WES.) Samplot47 visualization of read data allowed manual curation of parameters associated with FP calls, and associations between AnnotSV47,48 annotated parameters and FPR helped identify additional FP-associated SV parameters (Figure 4). Along with the manually-curated reference set, the panel of normal (PON) used for further filtering was generated from a compiled set of high-quality germline calls using 3,782 normal samples freshly-sequenced at a median depth of 38x by the Hartwig Medical Foundation.49,50\n\nSniphles: The main idea is to phase the identified SVs. We use two approaches; the first is to extract the tagged reads from the bam file and use these reads to phase the SVs if not conflicted. The second approach is to split the haplotype bam file based on the haplotype tag, using each split bam file to call SVs separately, this method called (Sniphles). Sniphles utilize information impeded in haplotypes, bam file and reads info support SVs. This method phases structural variants and augments the ability of Sniphles to accurately call SVs (Figure 5). Sniphles is implemented in Python 3, and it takes a haplotyped bam, and a SV VCF file as input and produces a phased vcf file as output.\n\nSwagg: Structural Variation with Annotated Graph Genomes (SWAGG) is a pipeline to make genome graphs from read data. The input into the pipeline is reads either with or without reference genome(s). Reads can be short-reads or preprocessed (basecalled) long-reads. Reads are assembled into longer contigs, and contigs are mapped back to the reference genome to look for discrepancies with the reference genome. These discrepancies can be either real mutations or sequencing artifacts, and are found using structural variant tools which output VCF files for each read set. These VCF files are taken together to make the genome graph at the end of the pipeline (Figure 6).\n\nPanOriginSV: This tool is a lab-of-origin prediction tool that combines machine learning approaches with graphical pangenome based alignment to predict lab-of-origin (Figure 7). PanOriginSV is implemented in Python 3 and uses the scikit-learn package for deploying machine learning models. PanOriginSV also relies on MMSEQ2 for clustering, BCALM for graph construction and minigraph for graph alignment. Given a training set of engineered plasmids and their source labs, this software can predict the lab of origin of a test set of plasmids.\n\nGeneVar: The GeneVar tool was developed to help inform the clinical interpretation of structural variants pertaining to a user-provided gene. This software is an open access, gene-centric data browser for SV analysis. GeneVar is a web page application (Figure 8). After entering the gene name (HGNC, Ensembl gene (ENSG), or transcript (ENST) identifier) in the search box on the homepage, the user is directed to the summary of the gene-specific page. GeneVar is available on GitHub (https://github.com/collaborativebioinformatics/GeneVar). The repository provides detailed instructions for tool usage and installation. A bash script for automated installation of the required dependencies is also provided.\n\nSVTeaser: SVTeaser is a tool for rapid assessment of SV call fidelity created for geneticists designing experiments to genotype a set of pre-ascertained SVs and bioinformaticians benchmarking a new algorithm against pre-existing tools across a range of parameters (Figure 9). Users are required to supply SVTeaser with a reference sequence file (.fasta) and, optionally, a set of SVs (.vcf). SVTeaser outputs assorted statistical metrics across a range of read lengths and depths. SVTeaser achieves rapid assessment by downsampling the full reference to a subset of numerous 10kb samples to which it adds SVs.\n\nXSVLen: This software is a framework for haplotype-resolved assemblies for benchmarking SV detection algorithms (Figure 10). XSVLen takes a cuteSV or Sniffles10 VCF output file and using reference coordinates will produce modified sequences having included inserted sequences or deleted sequences within the reference sequence. By creating these modified sequences, we could check for the presence of the predicted variants in haplotype-resolved assemblies. All methods are open-source licensed and have been made available on GitHub: https://github.com/collaborativebioinformatics.\n\nNibbleSV: NibbleSV requires a reference genome and VCF file that includes all the SV that should be genotyped (Figure 1). Next, allele kmers for the reference and alternative are extracted. The extraction process includes each site’s flanking regions. Subsequently, the occurrence of these k-mers in the reference fasta file are counted. This step is necessary to prevent k-mer miscounting between reference vs. alternative allele. To enable scaling of NibbleSV for large data sets, the results of these two steps are written into a temporary file, which is all that is needed for the actual genotyping step. During the genotyping step, NibbleSV uses this small temporary file and the bam/cram file of the sample and identifies the presence/absence of the reference and alternative k-mer across the entire sample. This is very fast and requires only minimal resources of memory as the number of k-mers is limited. On completion of NibbleSV a scanning of the bam/cram file is carried out reporting which SV have been re-identified by adding a tag in the output VCF file of this sample (Figure 1). The VCF per sample can then be merged to obtain population frequencies. The VCF per sample can then be merged to obtain population frequencies. NibbleSV requires 4Gb of memory, a single core and around 2GB hard disk space to store its index from e.g. GIAB HG002.\n\nOverview of NibbleSV workflow that utilises an input reference genome and file containing variant calls to generate a list of genotyped alleles using a kmer based strategy.\n\nCNV2SV: An overview of the CNV2SV workflow is illustrated in Figure 2. CNV/SV are called from short read datasets using Parliament.51,52 Locations of duplications are determined using CNVnator53 individual calls and combined calls. Copy number estimation for regions across the genomes is implemented by Control-FREEC that is converted into BED and VCF files. The genomes to be compared are aligned using dipcall,dot plots of the alignment constructed to identify potential regions of interest and extracted to VCF output. Calls for both short read and assembly based CNV/SV calls are merged to locate regions in which the duplication events overlap. Visualization scripts will be made available in future versions. Here, each called CNV from the short read dataset is compared to SVs identified from the genome-genome alignment. This is achieved in two steps: First, CNVs are queried against an interval tree structure containing the SVs from the genome-genome alignment to find adjacent CNV-SV pairs (<1000bp apart, putative tandem duplication events). For CNVs for which no matching SV can be identified in this way, the search is then extended to the whole genome (putative translocation events). All potential CNV-SV links are evaluated by sequence alignment using mappy (Python binding for minimap2,54 https://pypi.org/project/mappy/, with a standard sequence identity threshold of 0.8. A quick-start example using CHM13 and GRCh38 data is available on our GitHub page. In addition, we hosted a detailed description of the output data on the GitHub page.\n\nCNV2SV software pipeline that utilises both short and long read data as input to calculate the frequency of copy number variants across complete genomes.\n\nSystem requirements (see GitHub for more information): CNV2SV has been tested to work on a desktop system on the CHM13 data set with an Intel® i7-6700K Processor (4.00Ghz quad-core), 32GB RAM (less may be required), 50GB free disk space and running Unix-like operating system (e.g. Ubuntu-based distribution) or Windows subsystem for Linux running Ubuntu. The initial genome-genome alignment (CHM13 vs GRCh38) was computed on a cloud-based platform (DNANexus). CNV2SV requires Python (3.8 or newer). A full list of package dependencies is available on the GitHub page.\n\nCoronaSV: All software packages used by CoronaSV can be installed via the Conda package manager. Additionally, the CoronaSV workflow is defined using Snakemake. Running the CoronaSV.smk snakemake pipeline handles downloading all specified data and processing of sequencing data to variant calls. Each step of the CoronaSV pipeline (Figure 3) has a defined conda environment with exact versions of software specified for easy installation. CoronaSV utilizes three approaches that includes 1) read-based SV detection with paired-end Illumina reads, 2) ONT long-reads and 3) assembly-based SV detection. Illumina paired-end short-reads are trimmed using trimmomatic55 and mapped to the SARS-CoV-2 reference using bwa mem.56 After mapping, PCR duplicates are removed with Picard MarkDuplicates (http://broadinstitute.github.io/picard). Structural variants are identified then using Delly,44 Manta,43 Lumpy,57 and Tardis.58 Nanopore long-reads are filtered using Nanofilt and mapped to SARS-CoV-2 reference using minimap2 with default parameters. SVs are then called using Sniffles, SVIM, and CuteSV. Read quality assessment is carried out by NanoPlot. In order to integrate assembly based methods, de novo SARS-CoV-2 assemblies were generated using Unicycler for short-read sequencing and Flye for ONT long-reads. NucDiff and SVanalyzer tools are used for assembly-to-assembly comparisons. Followup comparative analyses across callsets is implemented by SURVIVOR59 (Figure 3).\n\nIllustration of the CoronaSV package workflow that takes SARS-CoV-2 short and long read data types along with a SARS-CoV-2 reference genome as input and generates a set of commonly found SVs.\n\nSystem requirements: CoronaSV is tested on Linux-based systems with multiple illumina and nanopore sequencing data (see GitHub for full list of the testing data). The RAM usage of CoronaSV depends on the size of input data. Peak RAM usage appears during de novo assembly using Unicycler, and 16 GB of RAM is sufficient for the pipeline to run on 8 CPU cores with additional 50Gb of disk space. CoronaSV requires python (version 3.6 or newer) and snakemake. Required tools and package dependencies can be found on GitHub page.\n\nCleanSV: The methods adopted to construct the CleanSVs filtration protocols are shown in Figure 4. In order to generate the data required to develop adequate filters, structural variants (SVs) were called on Illumina short reads using novoalign hs37d5 HG002 BAM (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz) and Illumina short-read HiSeqX Ten hg19 COLO829 BAM (https://nextcloud.hartwigmedicalfoundation.nl/s/LTiKTd8XxBqwaiC?path=%2FHMFTools-Resources%2FGRIDSS-Purple-Linx-Docker) using GRIDSS,42 Delly,44 and Manta.43 In HG002, the SV truthset (6) was used to determine the false positive (FP) SV calls in the short read dataset. Any SV calls that were found outside of the truthset Tier1 bed regions were then filtered. In the sample COLO829, the SV truthset (2) was used to determine the FP SV calls in the short-read dataset. Calls were inspected through manual curation by samplot (7). Generated samplots were annotated with UCSC table browser repeat tracks (8) and converted using vcfanno (9) as well as GC content by bedops file conversion from wig to bed (10).\n\nCleanSV pipeline highlighting methods used to generate adequate filters that can be utilised by clinicians to filter false positive and mislabeled SV calls from short-read cancer datasets.\n\nWe then compiled a set of high-quality germline calls using 3,782 normal samples freshly-sequenced at a median depth of 38x by the Hartwig Medical Foundation.49,50 We intiial hypothesized that such a large cohort could be used to both perform systematic FP filtering and possibly detect calls simply incorrectly labeled as somatic. The calls were filtered if a match within 2bp of the breakpoint was found in the PON. System requirements: The scripts to filter SV calls with either VCF or BEDPE format require R version 3.6.0 or higher, which is available for Linux, Mac OS, and Windows. The analyses within were run on R version 4.0.3, with Biocondcutor version 3.12. For running SV callers, it is recommended to use a HPC environment on Linux.\n\nSniphles: The Sniphles workflow (Figure 5) requires the following dependencies: Python >= 3.6, Pysam (Version 0.16.0) (https://github.com/pysam-developers/pysam), Cyvcf2 (Version 0.30.2),60 Sniffles (Version 1.12),10,39 SURVIVOR (Version 1.0.7),59 Mosdepth (Version 0.2.6),61 Bcftools (Version 1.9)65, tabix (Version 1.8).62 The workflow partitions reads in the bam file into groups based on phase blocks and phase status, which enables parallel analysis of the data. The read coverage at each block and each phase is computed with Mosdepth and used to estimate the parameters for calling SVs by Sniffles. Next, the identified SVs per haplotype are concatenated using bcftools. SVs of two haplotypes are combined using SURVIVOR with option “1000 1 0 0 0 0” to merge SVs within 1 kbp between each other and to allow for different types of variants to be considered on different haplotypes. SVs are then force called with Sniffles using this combined vcf file. Force called SVs from each haplotype are combined with SVs of unphased regions as the final output (Figure 5). To facilitate workflow testing, Princess (https://github.com/MeHelmy/princess) was used to align, detect and phase SNVs and SVs from PacBio HiFi reads. The produced Bam from the previous step is the input for Sniphles, where pysam was used for alignment.\n\nIllustration of methodology utilized by Sniphles to produce a phased structural variant call set. An overview of the Sniphles pipeline demonstrating how a haplotyped input bam file is used to generate a phased structural variant call set.\n\nSwagg: The minimal system requirements for SWAGG are 8Gb RAM, 1 CPU and 10Gb of storage. Figure 6 demonstrates the implementation and operation of the SWAGG software package. Protein graphs are generated using a multiple sequence alignment of the proteins, then using the tool msa_to_gfa (https://github.com/fawaz-dabbaghieh/msa_to_gfa) after which this multiple sequence alignment is converted into a graph file in GFA format, with the original sequences embedded as paths in the graph for visualization. This tool is tested with Python 3 and does not require any extra libraries or dependencies. New sequences can be aligned to these graphs using Partial Order Alignment algorithm for example.\n\nIllustration of the SWAGG pipeline that utilises both long and short read datasets for the construction of graph genomes.\n\nPanOriginSV: PanOriginSV has three additional open source dependencies which are MMSEQ2 (for clustering), BCALM (pangenome creation) and GraphAligner (for sequence-to-graph alignment). MMSEQ2 is the most memory intensive step, and MMSEQ2 requires roughly 1 byte per sequence residue. An overview of the pipeline utilised by this tool is highlighted in Figure 7. PanOriginSV performs lab-of-origin prediction in three distinct steps. Firstly, during the training phase PanOriginSV clusters similar sequences using MMSEQ2. Further, the most similar clusters having a predefined number of representative lab labels are selected for the pangenome creation. Second, in order to incorporate SV information into the pangenome a graphical pangenome is created using BCALM for each of the clusters identified in the first step. These pangenomes reflect sequence-level structural variation that reveal important differences in highly similar sequences that could belong to different labs thereby reducing the possibility of false positives. The training sequences are then mapped back to their corresponding pangenome graph to obtain important alignment information including but not limited to number of hits and percentage identity of alignment. These are then collated and embedded into a feature vector that is passed on to a machine learning model for prediction.\n\nPipeline demonstrating the PanOriginSV software package that’s implementation determines that lab-of-origin input sequencing data.\n\nThirdly, features from the alignment steps are combined with sequence metadata and input into a random forest classifier that is trained to predict lab-of-origin in a multiclass classification task. Both the top-1 and top-10 predictions are output and compared to previous literature and Genetic Engineering Attribution Challenge (GEAC) benchmarks.\n\nGeneVar: Figure 8 shows the different components of GeneVar, which is a web browser application. The webpage, including data storage, requires only one core with 1 Gb RAM and requires less than 1 Gb of storage. After entering the gene name (HGNC, Ensembl gene (ENSG), or transcript (ENST) identifier) in the search box on the homepage, you will be directed to the gene-specific page containing: 1) Gene-level summary with number of SVs, number of clinical SVs or SVs overlapping clinical SNVs, 2) Links to the gene's page on OMIM, GTEx, gnomAD, 3) A dynamic table with the annotated variants overlapping the gene, 4) A graph with the distribution of the allele frequency for variants matched with gnomAD-SV (50% reciprocal overlap). The profile of the SV to consider, such as type and size range, can be specified on the side bar. Each column in the dynamic table can be \"searched\" into or reordered dynamically. All data used by the app will be available for download in tab-delimited files. By default, allele frequency is reported based on dbVar63 and gnomAD genomes and exomes. Furthermore, GeneVar utilises dbVar database and links SV to genes and annotate gene impact, allele frequency, and the overlap with clinically-relevant SVs, SNVs and indels. All data, are available for download in a tab-delimited file. Each variant has been extensively annotated and aggregated in a customizable table. GeneVar is available on GitHub (https://github.com/collaborativebioinformatics/GeneVar). The repository provides detailed instructions for tool usage.\n\nA graphical representation of the pipeline used by GeneVar in order to provide clinicians with a comprehensive summary of SVs associated with a user provided gene name.\n\nSVTeaser: SVTeaser generates regions from a user provided reference and adds in a structural variant into each region using one of two methods - 1) a call to SURVIVOR simSV59 which generates random, simulated SVs by introducing variation (deletions (DEL) and insertions (INS) type of SV breakpoints) in DNA sequences, or 2) automatic spike-in of a known SV from an input SV VCF file. Resultant altered reference sequences are then used for Illumina short-read simulation using ART.64 Parameters controlling simulated sequencing read-length, insert-size, and depth parameters can be altered. Simulated reads can then be mapped to the original, unaltered reference with any mapper of choice; here, BWA was used. Resultant BAM files can then be used to detect SVs using any mapping-based SV caller of choice; here, Parliament240 was used to generate calls with manta, breakseq,65 cnvnator, and lumpy. The resultant VCFs are then matched to the simulated SVs’ VCFs using Truvari and output is parsed into a pandas dataframe for report generation. SVTeaser requires installation of Python 3.7, Truvari, SURVIVOR,59 Vcftools and ART read simulator. The components of SVTeaser are shown in Figure 9.\n\nSVTeaser software implementation showing how by using a reference genome a set of SVs can be simulated to benchmark SV calling tools to inform experimental design decisions prior to analyses.\n\nXSVLen: The XSVLen workflow requires Python3, Minimap2, Nextflow, and R >=3.5.0. As demonstrated in Figure 10, XSVLen takes as input a haplotype-resolved de novo assembly, and a VCF file (generated by cuteSV39 or sniffles10) of variants including only insertion and deletion calls. For each insertion or deletion call within the vcf file, a modified reference genome is generated. This modified reference will contain a 1.5kb flanking sequence that either has the sequence removed if a deletion call, or the alternate sequence added between the flanking sequences if an insertion call. The resulting ‘query’ sequences are then mapped using minimap2 to both haplotypes. Each aligned query gives rise to a map of aligned bases P={(q1,t1), … , (qn,tn)}. To score each variant call, we find two indexes i, j. These index the end of the prefix, and beginning of the suffix in the query. When the call is valid, (P [j][0] - P [i][0]) - (P [j][1] - P [j][0]) is equal to 0. To account for differences in alignment, we iteratively search for an (iopt, jopt) combination, with iopt ≤ i and j ≤ jopt that gives the smallest difference. Variants are reported as valid if the difference is less than 10 bases or the intervals defined between P [iopt] and P [jopt] are within 95% length in either haplotype. A summary report is then produced using an R script.\n\nA graphical representation of the XSVLen software pipeline showing the utilisation of haplotype-resolved de novo assembly and a VCF file to benchmarking SV detection algorithms.\n\nNibbleSV:\n\nWe benchmarked NibbleSV over the GIAB HG002 SV call set66. In summary, this call set was created using multiple long and short read technologies and underwent manual validation across multiple groups to ensure an overall high quality and accuracy. Using an Illumina data set from (2x250 GIAB HG002) we benchmarked true positives (i.e. SV that should be present), false positives (i.e. parental only SV that should not be present in the proband HG002), and false negatives (i.e. SV that should be present in HG002 but were not found). Using only chr 22 from HG002, NibbleSV with a kmer size of 23 takes around 2-4 minutes on a single thread with a 80gb bam file and the provided VCF file. We assessed our recall at different k-mer sizes which increases with the kmer size. For example, k=21 (2min 3sec) achieves 0.59 recall with a precision of 0.83. Interestingly, for insertions the recall rate increases to 0.86 with a precision of 0.86.\n\nCNV2SV:\n\nFigure 11a shows the best links (based on the alignment identity score) between CNVs identified by CNVnator and duplication SVs inferred from the dipcall alignment of CHM13 and GRCh38. The genomic areas surrounding four selected adjacent duplication events are further highlighted using dot plots, revealing the architecture of the corresponding variation in the context of the genome-genome alignment. In Figure 11b, all CNV-SV links meeting a default alignment identity threshold are shown, further revealing events corresponding to putative copy number increases of greater than two. We further explored the reason why some CNV and SV could not be linked, through statistical analysis of the raw SV calls as shown in Figure 12.\n\nCNV2SV results using CHM13 in comparison to GRCh38. (A) The diagram connects the genomic location of individual CNV calls on GRCh38 (broad ends) to the location of their linked SV identified in the GRCh38-CHM13 genome-genome alignment (thin ends). The diagram reveals a number of underlying putative translocation events identified for the called CNVs. Adjacent CNV-SV links (putative tandem duplications) are shown as streaks at the respective genomic position. For four select CNV-SV links, the genome-genome alignment for the underlying SV is further shown as a dot plot on the outside of the diagram. Only the best matching SV link (thin end) identified for each CNV call (broad end), as determined by sequence alignment score between both events, is shown here. (B) Similar to A, but displaying all potential CNV-SV links that meet the default alignment identity threshold of 0.8. CNVs with multiple matching duplication SV events identified in the genome-genome alignment can be explained by copy numbers greater than two occuring in distant locations, and alternatively may suggest the involvement of complex genomic rearrangements including transposable elements.\n\nIn terms of linkage statistics, the majority of the CNVs identified have not been linked to a SV event, as indicated by A. One of the main reasons for the unsuccessful linking is the length disparity between the called CNV events and SV events as shown in B. Overall, among linked CNV and SV events, the distribution of three major categories are shown in C: adjacent events, distant events, and events spanning multiple chromosomes. Distant events are called in the case when the linked SV is at least 1Kbp away from the CNV call (either upstream or downstream). Details of the distribution of the adjacent and distant events per CNV call are given in D and E shows that alignment quality is better for adjacent matches when compared to more distant SV matches. While most links for a single CNV event are unanimously distant or adjacent, we observed an event in which a CNV was linked to both an adjacent and a distant SV which occurs on chromosome 7 (F: adjacent: chr7:100997804 length 8325 and distant: chr7:100994092 length 3249).\n\nCoronaSV: We processed more than 200 SARS-CoV-2 SRA runs with CoronaSV, and Figure 13 shows the high confidence SVs generated with SURVIVOR59 by taking a majority vote across multiple SV callers. We also looked for shared SVs across multiple samples. There were only a few inversions identified that were consistently and reliably called between samples. We believe those inversions are related to the transcriptional landscape of SARS-CoV-2. These inversions are small (less than 1Kb), and five of them were found in ORF1ab and one on ORF M.\n\nHistogram showing size of the SVs and the total number of SVs across multiple Nanopore and Illumina datasets. The y-axis of the histogram is log compressed.\n\nCleanSV: We investigated filtering SV calls using both the curated reference set and a high-quality panel of normals (PON). The PON was created using GRIDSS calls from 3,782 normal samples freshly-sequenced at a median depth of 38x by the Hartwig Medical Foundation49,50. Using this PON consisting of GRIDSS calls from 3,792 freshly-sequenced normal WGS samples, we explored how the percentage of calls from short-read SV callers which were incorrectly labeled as true somatic calls, either due to being algorithmic artifacts or germline calls. Our results show the promise of such an approach. (Figure 14). Note that this is not only a check for false positives: we know a priori that many calls from somatic SV callers are mislabeled as somatic when they’re actually germline. This is a known algorithmic error: SVs are normally first called in the normal sample and labeled as “germline”, and then the resulting SVs called using the tumor sample (separately or jointly with against the normal) are labeled as “somatic”. While such an approach is common for short-read SV callers, this frequently leads to mislabeled results, often for the simple reason that the normal sample is sequenced at a much lower coverage than the tumor sample.\n\nUsing a cohort of 3,792 freshly-sequenced WGS normal samples to create a Panel of Normals (PON) from GRIDSS calls and a set of curated calls from sample COLO829 to classify false positives, we discover that a sizeable number of false positives were found within the panel of normals, suggesting that these were miscategorized due to algorithmic errors. PON filtering based on GRIDSS calls is effective for the modern callers such as GRIDSS, Manta and SvABA which (partially) rely upon localized assembly.\n\nWe plan to continue to explore whether the false positives found exhibit distinct features which we could use for future filters to distribute to the community. With these insights, given that clinical genomics still overwhelmingly relies upon short-read sequencing, our goal would be to also apply filters to all variants (e.g. the case of Mendelian diseases).\n\nSniphles:We used Princess (https://github.com/MeHelmy/princess) to align, detect and phase SNVs and SVs from PacBio HiFi reads 32x coverage. The produced Bam from the previous step is the input for Sniphles, where pysam (https://github.com/pysam-developers/pysam) was used for alignment. For each phase block we used the mosdepth61 to detect coverage. Later, we called SVs using Sniffles10,39 with the adequate numbers of reads to support SV. The identified SVs per phase block were sorted and concatenated using bcftools version 1.967, and both the haplotypes were merged using SURVIVOR.\n\nSwagg: The main results from the Swagg package includes the development of the graph module and the protein graphical application (Figure 15). The graph module is able to retrieve basic statistics from a pangenome graph in GFA format from either reference-based (fasta + VCF) or a set of assemblies (fasta), followed by conducting a pairwise comparison of all paths in the graph, and outputting a matrix in TSV format with the path names and corresponding samples in the first position. After creating the pairwise matrix, the module can plot an SV pileup over any path in the graph, counting the number of other paths that contain an SV overlapping each position. In addition to utilizing the pairwise comparisons where hotspots are references to a given sample, this approach also allows for graphs derived from vcf files. The objective from the protein graph mapping application was to show if the variants introduce new amino acids or stop a stop codon. Similarly, a pangenome graph can be constructed from DNA sequences as panproteome graphs can be built from different amino acid sequences of a protein. These graphs can then help visualize the variants between the sequences and show the paths each sequence take through the graph. Another layer of information can be added to the nodes, e.g. does a node represent a conserved or a non-conserved side, does a path divergence in the graph has any significant phenotypic characteristics, relating genome-wide association studies to these proteins graph68. Therefore, when aligning a new sequence to the graph, one can check the path the new sequence took in the graph and what information are related to this path.69 Figure 15 shows an example of an annotated graph of the Nucleocapsid Phosphoprotein in SARS-COV-2.\n\nProtein graph with paths representing the original sample. This graph here is a directed acyclic graph of an MSA of 26 “N” gene (Nucleocapsid Phosphoprotein) generated from 26 SARS-COV-2. Visualized using gfaviz.70\n\nPanOriginSV: It became apparent that the quality and representation of the clusters was a main factor in prediction accuracy. To this end, we tested PanOriginSV on a range of clusters of at least 500 sequences and only considered cases where the test sequence had a training representative in the assigned cluster. The CPU time used by PanOriginSV was 10-50x less than the linear model (depending on the cluster). We observed a range of results, with the linear prediction model outperforming PanOriginSV by up to 5% in some clusters and PanOriginSV outperforming the linear model by up to 6% in others (Table 1). With deeper analysis of the input data, we hope to achieve better clusters and thus better prediction results with the graph model. It is also worth noting that our graph construction method can be improved using more recent pangenome graph construction tools.\n\nBenchmarking results on large clusters obtained from MMSEQ2. For a single cluster, 25% of sequences were held out and used as the testing set. The accuracy of the top predicted lab was consistently higher in PanOriginSV compared to PlasmidHawk, however the accuracy when testing against the top 5 predictions for both tools was comparable.\n\nGeneVar: Databrowser. Upon querying a gene or transcript, the data browser will visualize a rare-variant burden test, allele frequency distribution, and variant level information for known SVs within dbVar. The data browser does not have a login requirement and integrates multiple public resources (Figure 16). To illustrate whether a particular gene/transcript or exon has been adequately covered to detect variation, the average depth of coverage is graphically represented. An additional panel shows gene expression levels across all general tissues included in GTEx71. Report summary. Analysis results are enriched with information from several widely used databases such as ClinVar72 and gnomAD,73 as well as graphical visualization utilities integrated in the pipeline as part of GeneVar. Resulting variants are reported in a tab delimited format to favor practical use of worksheet software such as iWork Number, Microsoft Excel or Google Spreadsheets. All information can be downloaded in tabular form.\n\nA description of the elementary transcript details for the gene of interest. This includes the Ensembl transcript ID, Ensembl Gene ID, number of exons and genomic coordinates as described in the GRCh38 build.\n\nSVTeaser: SVTeaser was able to simulate SV data on average 14 min per sample when tested on chromosome two. SVTeaser output includes organized VCF results of true positive, false positive, and false negative from evaluated SV callers. Furthermore, performance scores are reported alongside automated plots for quick visual evaluation of SV callers (Figure 17). SVTeaser is able to simulate sequencing for known deletions and insertions with various coverage, read length, and insert length. This enabled thorough evaluation for understanding the strengths and boundaries of the SV callers in question (Figure 18).\n\nA report generated from benchmarking a real HG002 Manta 30x Illumina sample against GIAB Tier1 SVs. A) Counts of SVs by SVType and their intersection state with GIAB Tier1 benchmark SVs. B) Summary table of benchmarking performance.\n\nC) Proportions of SV intersection states with the benchmark by SV size bin.\n\nCount of False Positives, False Negatives, and True Positives from four SV callers (columns) against chromosome 2 deletions through multiple simulated coverages (rows). SV callers: breakseq, lumpy, manta, cnvnator. Coverages: 10x, 20x, 30x.\n\nXSVLen: A diploid assembly of the MHC locus of HG002 from Nurk et al74 was used to benchmark variants. The assembly has an N50 of 16.1 and 18.0 Mb per haplotype. Variants were called using 50-fold coverage of ONT reads using CuteSV version v1.0.8. The number of INS and DEL per SV size can be observed in Table 2. The number of INS/DEL overlapping with the haplotype-resolved assemblies are shown in Table 2 as well as a comparison of assembly-based calls and gold-standard Truvari calls.\n\nInsertion and deletion events are compared according to structural variant size and number and overlaps with 1) haplotyped assemblies and 2) Truvari callsets are counted.\n\n\nConclusion\n\nThe results of the 2020 Baylor College of Medicine/DNANexus hackathon described here represent novel work that pushes the field forward for human genome SV detection but also for Covid related research. Both are needed to further current findings about diversity and the complexity of organisms and their genotypes. To further facilitate this progress in a FAIR-compliant manner, 80 people came together from across the world in October 2020 completed 10 groundbreaking prototypes. Hackathons like these not only represent short bursts of prototype development, but are essential to form groups and communities, inspire communication across countries and research institutions, and form novel collaboration networks. As such, this year’s hackathon not only sparked the projects described here, but also highlighted the need for unified databases for SVs and other genomic features hosted on DNAnexus, Anvil, and other platforms as well as larger standards and references (e.g. GIAB, UKBB). This is essential to ensure quality standards for benchmarking and comparability, which will further advance the science and medical research.\n\nRapidly switching to a completely remote hackathon that enabled increased international participation was made necessary by the COVID-19 pandemic. This allowed for an open science effort across an even more diverse population of individuals and professional backgrounds. That diversity made it possible to complete 10 projects, which spearheaded novel insights in the understanding of structural variants in humans, as well as COVID19 genome structure. More importantly, it led to new synergies among participants, an active online community, and new friendships across borders.\n\n\nData availability\n\nAssociated code is available at: DOI 10.17605/OSF.IO/ME62X\n\nData sources utilized:\n\nNibbleSV: Genome in a Bottle, HG002, SV callset (ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb/)\n\nCNV2SV: CHM13 (https://github.com/nanopore-wgs-consortium/CHM13#telomere-to-telomere-consortium) and GRCh38\n\nCoronaSV: Data sources available on https://github.com/collaborativebioinformatics/coronasv\n\nCleanSV: hs37d5 HG002 BAM (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz), hg19 COLO829 BAM (https://nextcloud.hartwigmedicalfoundation.nl/s/LTiKTd8XxBqwaiC?path=%2FHMFTools-Resources%2FGRIDSS-Purple-Linx-Docker)\n\nSWAGG: Data sources available on https://github.com/collaborativebioinformatics/swagg/blob/main/sample_manifest.tsv\n\nXSVLen: MHC locus of HG002 (74)\n\nGeneVar: Data sources available on https://github.com/collaborativebioinformatics/GeneVar\n\nPanOriginSV: genetic engineering attribution challenge (GEAC)\n\nhttps://www.drivendata.org/competitions/63/genetic-engineering-attribution/\n\nSVTeaser: All data utilized was based on simulations\n\nSniphles: Genome in a Bottle, HG002, SV callset (ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb/)\n\n\nSoftware availability\n\nNibbleSV\n\nSource code available from: https://github.com/collaborativebioinformatics/nibSV\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nCNVSV\n\nSource code available from: https://github.com/collaborativebioinformatics/CNV2SV\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nCoronaSV\n\nSource code available from: https://github.com/collaborativebioinformatics/coronasv\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nCleanSV\n\nSource code available from: https://github.com/collaborativebioinformatics/CleanSV\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nSniphles\n\nSource code available from: https://github.com/collaborativebioinformatics/Sniphles\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nSwagg\n\nSource code available from: https://github.com/collaborativebioinformatics/swagg\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nPanOriginSV\n\nSource code available from: https://github.com/collaborativebioinformatics/PanOriginSV\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nGeneVar\n\nSource code available from: https://github.com/collaborativebioinformatics/GeneVar\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nSVTeaser\n\nSource code available from: https://github.com/collaborativebioinformatics/SVTeaser\n\nArchived source code at time of publication:\n\nLicense: MIT license\n\nXVSLen\n\nSource code available from: https://github.com/collaborativebioinformatics/The_X_team\n\nArchived source code at time of publication:\n\nLicense: MIT license",
"appendix": "Acknowledgements\n\nThe authors like to thank Richard Gibbs, Aaron Wenger and Stephen Rudd for their helpful discussions during the hackathon. In addition, Gerald Wright and Brenton Pyle for helping with advertisement and organising. DNA nexus provided computational resources for the hackathon. The authors would also like to thank Oxford Nanopore Technologies and Pacific Biosciences for sponsored prizes.\n\n\nReferences\n\nHo SS, Urban AE, Mills RE: Structural variation in the sequencing era. Nat Rev Genet. 2020 Mar; 21(3): 171–89. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFeuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet. 2006 Feb; 7(2): 85–97. PubMed Abstract | Publisher Full Text\n\nAlkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nat Rev Genet. 2011 May; 12(5): 363–76. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoffman EA, McCulley A, Haarer B, et al.: Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription. Genome Res. 2015 Mar; 25(3): 402–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZook JM, Hansen NF, Olson ND, et al.: A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020 Nov; 38(11): 1347–55. PubMed Abstract | Publisher Full Text\n\nLi H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15; 25(16): 2078–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJaillard M, Lima L, Tournoud M, et al.: A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet. 2018 Nov; 14(11): e1007758. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs. Bioinformatics. 2002 Mar; 18(3): 452–64. PubMed Abstract | Publisher Full Text\n\nGonnella G, Niehus N, Kurtz S: GfaViz: flexible and interactive visualization of GFA sequence graphs. Bioinformatics. 2019 Aug 15; 35(16): 2853–5. PubMed Abstract | Publisher Full Text\n\nGTEx Consortium: The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013 Jun; 45(6): 580–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLandrum MJ, Chitipiralla S, Brown GR, et al.: ClinVar: improvements to accessing data. Nucleic Acids Res. 2020 Jan 8; 48(D1): D835–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarczewski KJ, Francioli LC, Tiao G, et al.: The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May; 581(7809): 434–43. 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}
|
[
{
"id": "83791",
"date": "11 May 2021",
"name": "Francois Sabot",
"expertise": [
"Reviewer Expertise Genomics",
"bioinformatics",
"evolution"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Pangenome Hackathon paper lead by A. McCartney and FJ Sedlazeck was a great moment of intellectual development and findings for pangenomics research on human and coronavirus, pandemics time \"oblige\". Ten softwares/methods were developed, some being even released, some being more in alpha state. All these tools are of interest, in their targeted human-related field but also in non-human fields (working on plants, I am interested in more than one of them).\nThe paper has been written collectively, each software participants writing their part, and while of high interest in terms of opening, it is the main limit in the manuscript, in my opinion.\nIndeed there is no homogeneity in the way tools are described (global aim, method, implementation, figure, results/tests), and thus it is quite difficult to have a global idea of the different level of development. An initial table with level of advancement (alpha, beta, ready for use, in testing, etc or something like it) would be useful. In addition, a final reformatting by a single writer would smooth the reading.\nIn details, going for each tools:\nNibbleSV: what is the impact of SNP on the detection through k-mers? I mean if the individual has more than a very low level of variation, it may increase the FP rate? what is the RAM usage per sample? why providing info of time for 23mers but results of recall/precision with 21.\nCNV2SV: page 8, output of CNV2SV is said to be a python script (envlink.py)? Why computing the pre-alignment on DNAnexus? Which stats methods are used?\nCORONASV: are the three approaches (SR, LR, assembly) required in all analyses or you can choose? Why does Flye not represented in Figure 3?\nCleanSV: on page 6, I cannot see the link with aneuploidy in this specific case. Can you estimate the false negative rate? Do you have an idea of the RAM usage?\nSniphles: \"the produced BAM from the previous step\" is the one produced by Princess? The first sentence of results is the same as in the method. It missed also here a short summary of the results.\nSwagg: the implementation text is almost the same as in the introduction of the tool. The implementation part is quite short and the fig 6 did not shown any info about the protein graph possibility. Finally, what is the advantage of having the protein graph compared to an alignment showing the variation?\nPanOriginSV: What are the alignment information included in the training part? Which 'more recent pangenome graph construction tool' are you thinking about?\nGeneVar: a really interesting tool for praticians. My only question is will it be possible to add new informations about variations outside of strandard DB?\nSVteaser: do you have any information of time per SV? What are the size of variations you can include? Can we add also translocations or SNP?\nXSVLen: the figure 10 is quite drafty and would need to be improved for more information. Do you have any information about the recall/precision?\nIn conclusion, I was very impressed by the high number of tools and of their quality and think this paper is really worthy.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6799",
"date": "03 Sep 2021",
"name": "Ann Mc Cartney",
"role": "Author Response",
"response": "We would like to thank Francois Sabot for their time on giving the authors of this manuscript feedback and comments. Upon receiving these comments the corresponding authors reached out to the developers of each of the tools developed as part of this hackathon, each of which have highly appreciated your work and thoughtful comments. The responses to each of the reviewers comments are outlined below in bold and italic. General Comment 1: The Pangenome Hackathon paper led by A. McCartney and FJ Sedlazeck was a great moment of intellectual development and findings for pangenomics research on human and coronavirus, pandemics time \"oblige\". Ten softwares/methods were developed, some being even released, some being more in alpha state. All these tools are of interest, in their targeted human-related field but also in non-human fields (working on plants, I am interested in more than one of them). The paper has been written collectively, each software participant writing their part, and while of high interest in terms of opening, it is the main limit in the manuscript, in my opinion. Indeed there is no homogeneity in the way tools are described (global aim, method, implementation, figure, results/tests), and thus it is quite difficult to have a global idea of the different levels of development. An initial table with level of advancement (alpha, beta, ready for use, in testing, etc or something like it) would be useful. In addition, a final reformatting by a single writer would smooth the reading. Response: We thank the reviewer for this suggestion. Indeed we also struggled as this manuscript has over 50 authors. The tools have so far only been developed within a few days in the context of a remote hackathon and thus represent more prototypes / proof of concepts than production ready methods. Comment 2: For NibbleSV Developers: “what is the impact of SNP on the detection through k-mers? I mean if the individual has more than a very low level of variation, it may increase the FP rate? What is the RAM usage per sample? why providing info of time for 23mers but results of recall/precision with 21. Response: That's a great question. We predict that the impact of SNP is minimal because the SNV must be directly within +/- e.g. 10bp of the SV breakpoint on either side. If there is a SNV it will lower our recall rate. We have further experimented with spaced kmers, that would help in this regard. RAM usage is ~4Gbp per sample. Comment 3: For CNV2SV Developers: page 8, output of CNV2SV is said to be a python script (envlink.py)? Why computing the pre-alignment on DNAnexus? Which stats methods are used? Response: Thank you for your question. The CNV2SV script performs the CNV-SV linking steps independently of the tools used to generate the three input files (2 .vcf files containing SV calls and CNV calls, respectively, as well as the reference genome as .fasta). In the scope of the Hackathon, we generated the test input VCF files using dipcall (genome-genome-alignment for SVs) and CNVnator (a CNV caller), for a human data set. These steps were executed on DNANexus, since unlike the actual CNV2SV script itself, high processing power and working memory were required, especially for the genome-genome alignment for the two human genome versions. Users can use VCF files as generated by tools and parameters of their choice as input for CNV2SV. While we expect output from most relevant tools that produce calls in VCF format to be compatible, we specifically tested the before mentioned tools in the scope of the Hackathon. While the statistics applied to generate the input SV/CNV calls vary based on the tools used, CNV2SV itself performs the linking using default cutoff values for parameters such as minimum CNV length, minimum alignment identity and maximum distance for adjacent duplication events. Furthermore, basic statistics are recorded for matched CNV-SV pairs as well as the failure reasons for CNVs that could not be linked to a corresponding SV. In response to the final question \"Which stats methods are used?\" the developers were not sure about which stat this is in reference to. Comment 4: For the CORONASV Developers: are the three approaches (SR, LR, assembly) required in all analyses or you can choose? Why is Flye not represented in Figure 3? Response: We thank the reviewer for catching this; we have updated the text to indicate that long read assembly with Flye is not currently supported for such a small genome with default parameters. Specifically, we have modified \"In order to integrate assembly based methods, de novo SARS-CoV-2 assemblies were generated using Unicycler for short-read sequencing and Flye for ONT long-reads.\" to instead read \" In order to integrate assembly based methods, de novo SARS-CoV-2 assemblies were generated using Unicycler for short-read sequencing\". Comment 5: For the CleanSV Developers: Can you estimate the false negative rate? Do you have an idea of the RAM usage? Response: Here we refer to the presence of somatic structural variations to be synonymous with “aneuploidy”. Aneuploidy itself is an umbrella term used within oncology to refer to somatic abnormalities of a cell’s chromosomes. We try to clarify this with a sentence in the manuscript. In terms of the false negative rate, so far this has been estimated with simulated benchmarks, which surely don’t reflect the complexities of actual clinical data---any real data will be of variable tumor content (purity) and coverage. The best source of collective knowledge within the field is probably the results of DREAM challenges. Indeed, the question of false negatives is one of the deeper questions for all variant calling methods used within cancer genomics. Systematically investigating this problem would require benchmarks from real data, which don’t exist---even robustly characterized cell lines would not be realistic enough. With that in mind, we also wish to emphasize that clinicians are primarily concerned with the presence of false positives. These are potential therapeutic biomarkers which, if missed/ignored by bioinformatic methods, could result in overlooked therapeutic interventions. In terms of RAM usage, the tool provided uses standard functions in R, and will not be memory intensive. Comment 6: For the Sniphles Developers: \"the produced BAM from the previous step\" is the one produced by Princess? The first sentence of results is the same as in the method. I also missed a short summary of the results. Response: We would like to thank the reviewer, a change was made accordingly in the manuscript. Comment 7: For the Swagg Developers: the implementation text is almost the same as in the introduction of the tool. The implementation part is quite short and the fig 6 did not show any info about the protein graph possibility. Finally, what is the advantage of having the protein graph compared to an alignment showing the variation? Response: Generating the graphs out of the amino acid has a visualization factor, as different sequences can be represented as different paths in the graph, conserved sequences in the MSA will show up as a single node and bubbles are generated from the variations. One can extend this be aligning new sequences to the graph, e.g. using a modified Smith-Waterman algorithm after topologically sorting the graph, this way, the alignment can tell us quickly which path this new sequence takes through this graph, moreover, one can add another layer of data to the paths, for example in bacteria, certain mutations or conserved sequences in the protein are related to antibiotic resistance. Comment 8: For the PanOriginSV Developers: What is the alignment information included in the training part? Which 'more recent pangenome graph construction tool' are you thinking about? Response: We’d first like to thank the reviewer for their questions. We thread/align the query sequences to the pangenome graph created using BCALM. The nodes that are hit are used as the features for machine learning. We have experimented with other information as well such as alignment length, %id, etc, but overfitting is an issue that requires further work. Minigraph would be a more recent pangenome graph construction tool that we could use. Comment 9: For the GeneVar Developers: a really interesting tool for practitioners. My only question is will it be possible to add new information about variations outside of standard DB? Response: Thank you reviewer, for the question. At this time, we don’t plan to support non-standard data types. However, if you have a specific use case in mind, the developers would be open to a collaboration. Comment 10: For the SVteaser Developers: do you have any information of time per SV? What are the sizes of variations you can include? Can we also add translocations or SNP? Response: Thank you to the reviewer for the feedback. In terms of running time per SV, this correlates with the size of SV simulated and the nature of the SV (e.g. translocations being more difficult). However, these operations are relatively straightforward operations manipulating the strings from the FASTA file. Users are able to set the size of SVs within the simulation framework, and in principle could handle any organism. Yes, translocations and SNPs are possible. Comment 11: For the XSVLen Developers: the figure 10 is quite drafty and would need to be improved for more information. Do you have any information about the recall/precision? Response: Many thanks for the suggestion and the interest, the figure is intended to give an overview of the method and not a detailed explanation of the pipeline. Regarding precision/recall numbers, we did not check this specifically but in Table 2 the number of TP and FP are summarized for the assembly calls."
}
]
},
{
"id": "83792",
"date": "17 May 2021",
"name": "Kamil S. Jaron",
"expertise": [
"Reviewer Expertise Genomics",
"evolutionary biology",
"bioinfromatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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\nThis manuscript is a write-up report of an apparently very successful hackathon. Authors present an overview of 10 different approaches to solve various issues in the genomics world of structural variants, some of then sound really promising. I appreciated the modest tone authors haven chosen when describing the current state of each tools. All the tools have at least some exploratory value, and all of them are publicly available, therefore I have no major objections for the manuscript to be indexed.\nThis being said, I do agree with the first reviewer, I would greatly appreciate if before diving into details of individual methods, a big picture overview would be provided, for example a table with short descriptions, urls and development stages would be really handy. Disclosing the development stages would be particularly useful for a reader to know what to expect if proceeding further in reading.\nI do think this manuscript will spark a lot of ideas in the SV community, so I also wondered, what are the contribution policies to individual tools? Many of the tools have some future plans and are not yet production ready. Who would be the people to contact if someone would be interested in contributing and helping out with finishing a tool that would be particularly helpful for their research project?\nThe manuscript could benefit immensely from a big reorganisation. I do believe that classical Intro/Meth/Results organisation is not doing this manuscript a favour. It was really hard for me to keep track of ten threads in parallel and at some point I just gave up on top-bottom reading. I ended up scrolling back and forth between different sections to get information regarding one tool I tried to understand at the time. I also think most of the people will be mostly interested in one of the tools only when opening the manuscript for reading, therefore I would propose to keep the common Introduction and Conclusion sections but restructure the rest of the paper paper on per method basis.\nI also appreciated authors' effort to comply with FAIR principles. Although I have not check every tool, those I did were neatly documented. Thoughts regarding individual tools are listed bellow.\nNibblerSV\nIf I understand right. The genotyping using NibblerSV is done in two phases - 1. calculating a dictionary of specific kmers for each allele, I would call those diagnostic kmers (e.g. allele specific kmers absent in the reference genome) and 2. matching kmers of resequencing data to the diagnostic kmers. I did find the idea very clearly explained.\nThe part I did not understand is how it's decided if a sample does or does not carry a variant. Does it need to have all the diagnostic kmers at a certain coverage? Or at least some proportion? What if the sample contains kmers of multiple diagnostic markers? Is it possible to genotype a heterozygous SV? Is there any measure of confidence in genotyped alleles? I personally would prefer to read more about these details over technical aspect such as different types of temporary files that the software is producing that actually are mentioned.\nI also wondered, given the approach of generating catalogues of SV-diagnostic kmers, I would anticipate very variable power to detect SVs of different sizes and types. For example, recent inversions will be identified only through very few kmers found at the edge of the inversion, compared to large scale insertions that will probably harbour many diagnostic kmers and clearer signal. Did you look at the sensitivity/precision in respect to size/type? Would that be a consideration one should have when deciding if to use nibSV or paragraph or VG?\nCNV2SV\nThis tool has the least intuitive motivation of all the tools presented. I would naturally assume all loci with CNV should also be called as SVs, hence I was not sure why it is interesting at all getting the same information twice. However, the results of this analysis proved my intuition wrong. Only very few CNVs are linked to SVs. However, the suggested explanation with length disparity was a bit dissatisfying to me. How comes that the SV and CNV callers call variants of so different size? Which are shorter/longer? Do you think the CNV/SV reconcilation could be more overlapping with a different choice of SV/CNV caller?\nThis software has absolutely outstanding description on the GitHub repository.\nMinor comments:\nFigure 12, panel B has a cropped y-axis label.\nIn the Methods the text \"formats (from Parliament\" has an opening bracket that is never closed.\nCoronaSV\nI did appreciate the idea of scalable pipeline for conservative analyses of SARS-CoV-2 genomes. Authors made many unjustified choices. For example, why did you chose in particular Manta, Delly, Lumpy and Tardis to detect SV using short reads? But I suppose it is understandable why it would be challenging justify every choice in limited time of a hackathon.\nThe step of the analysis I am worried about is the merging by SURVIVOR, it also happens to be the only one that does not seem to be included in the GitHub repository. What parameters were used for individual merging steps using SURVIVOR? Given the genome of SARS-CoV-2 is really small, I believe that the outcome of this pipeline will be very sensitive to the chosen thresholds for merging variants.\nThis project aims to get \"trustworthy SV calls across SARS-Cov-2\", but there was only very little effort in validation of the SV set detected as far as I can tell. I was honestly quite surprised to see how many deletions that are >20k long you reported as confident. Is it really possible for SARS-CoV-2 to lose more than 2/3 of its genome? Could they represent some SV calling artefacts? One way how to check the quality of called SVs would be compare phylogenetic relationships of the analysed viruses that are probably available for all the sequenced data anyway and verify that the common SVs are shared within monophyletic clusters.\nFinally, the provided data frame with the input data contains various types of libraries. How does SV calling works on RNA-seq data? To be honest, I am not even sure what \"RNA-seq\" means in the context of RNA viruses, but I do find strange that all the libraries seem to be treated the same. Could some of those huge deletion be simply the selection process of the non-WGS libraries?\nI understand this is a hackathon paper, and therefore it would be unreasonable to ask for more analyses, but I do believe that the wording of this tool should be toned down a lot. I think this is a good first draft for this ambitious pipeline, but loads of work and thought should be given to it before the called SV sets are called trustworthy.\nCleanSV\nThe idea here is to figure out empirical filtering thresholds to minimise false positives on called SVs. This is a great idea and it's desperately needed to have a better community resources to reduce the need for manual curation.\nI am also very sure that these thresholds would have great applicability in other species and germline SV calling. Is there any chance of more general applicability?\nGiven authors have decided not to share the filtering thresholds, I think it should be clearly stated early on that this is only a conceptual description of the workflow and results are not provided yet.\nMinor comments:\nI resume hs37d5 in \"Illumina short reads using novoalign hs37d5 HG002 BAM\" means it a human data, but I do think it should be explicitly mentioned.\nA bunch of citations are in a different format, something like \"(7)\" and without actual reference.\nSniphles\nAgain, a very timely contribution. Phasing of SVs will me more and more important as long read technologies are more and more available even for population genomics studies.\nI found the idea very clear, and sound. I did wonder, however, about the merging step. Technically, SVs from different halplotype need to be merged as if only the SV is homozygous in the alternative allele, therefore I wonder if it is appropriate to lump together everything that is closer than 1000 bases from each other. How many such variants were detected?\nThat's kind of related to the only thing I was missing - results. The test case of this method is basically a more confusing repetition of what is already written in methods without any actual numbers of phased SVs. How successful was phasing? How many and how long blocks were phased? If unavailable yet, you should be explicit that it's untested approach.\nAlthough I have not tried to install the software, I appreciated that the GitHub repository was very neat and the code very well organised.\nSwagg\nThis was another tool with rather difficult text and figure. It is still not very clear to me how using protein graph should help SV calling.\nI was also rather confused about the construction of protein graph. In methods the you write, \"Protein graphs are generated using a multiple sequence alignment of the protein\", but what is \"the protein\"? I originally imagined SWAGG would use genome annotation, where the multiple sequence alignment comes into play? I got it lot better from the presentation I found on the GitHub, but I am still not 100% sure how it's done. The presented figure is very pretty, but I did not understand at all what I was supposed to look at.\nI just think it's pity, it does look like a loads of work with a really interesting idea. I would recommend to spend more effort on explanation of the reasoning behind and general clarity of the text.\nI also wondered, is the protein information used for SV calling in the end? If no, why is not the input to your software a vcf file with SVs? Why it's important they are called by GATK and deepVariant? That was another confusing bit for me.\nPanOriginSV\nA machine learning approach that takes genome variation graph that includes both SNVs and SVs and determines lab of origin. First, I would like to disclaim I am a bit out of my depth reviewing this method, as I never worked with lab strains and genetically modified organisms or thought about the problem of lab attribution.\nI was a bit confused about the benchmarking. The Genetic Engineering Attribution Challenge seem to have plenty of approaches with really successful prediction algorithm, why is the approach compared to a single method (PlasmidHawk) that does not seem to be compared to the other approaches in the challenge? I also wondered why the results were shown in per-cluster basis, not overall accuracy, so they could be comparable to the approaches from the Genetic Engineering Attribution Challenge.\nPerhaps a silly thought, but do you think that machine learning approach is scalable? Having comparable training dataset to the unclassified dataset is essential for meaningful prediction, would the approach work for novel strains?\nMinor comments:\nThis sentence \"PanOriginSV has three additional open source dependencies which are MMSEQ2 (for clustering), BCALM (pangenome creation) and GraphAligner (for sequence-to-graph alignment)\" should probably contain references to respective software.\n\"10-50x less than the linear model (depending on the cluster).\" Less than PlasmidHawk?\nGeneVar\nThis tool has a functional prototype and it works! It allows a user to browse variants related to any human gene, which is fun. However, I do think it should be called \"human SV browser\" (I originally imagined the intend is to make a generic SV browser).\nI appreciated to attempt of making information about human SVs accessible to more general public, but I do wonder how close to the goal authors got. I don't think allele frequency spectrum is an easy plot for a user without background in genetics. Also, there are loads of variants shown for every gene, would it be possible in future to somehow prioritise to the \"most likely relevant\" variants? What you think could be done to improve accessibility of the tool by for example GPs?\nMinor comment:\nIn the app, it's a bit confusing that SV length is filtered on the panel on left, while all the remaining variables are filtered by clicking on the empty \"all\" fields bellow column names.\nSVTeaser\nI really like this idea for a framework for simulating reads and benchmarking SV callers. Beside previously utilised approach of generating insilco generated SVs, SVTeaser also allows a lexicon based generation of SVs. I also found the writing and description of this method very nice and understandable.\nOne of the main general problems of simulating sequencing reads is that it is very hard to take into consideration all biases of real life sequencing. For example, cross sample or bacterial contamination are really hard to consider. As a consequence, benchmarking using simulations is (probably) always overly optimistic. Would it be useful to attempt to quantify the optimism? For example by simulating reads from a sequenced genome with known SVs? Then the precision and recall of SVs could be compared between the simulated and real sequencing data.\nXSVLen\nSound approach, but took me while to see any added value compared to the original study by Chin et al. (2020)1. Do I understand right that what was done on MHC locus you generalised in a framework for any region with haplotype-resolved assemblies? I think it should be more clearly stated what was done by by Chin et al. before and how your approach differs. Also, in the text you refer to Nurk et al., although the reference is Chin et al. (I think it was confused with this other paper presenting HiCanu2).\n\nIn the table, the second row says \"Number of these calls that overlap assembly contigs\". First, how can be any variant called outside of an assembly contig? Do you mean overlapping with haplotype-resolved contigs? You also write \"these calls\", which made me think it's a subset of the first row, but insertions >50bp seems to have a higher number in the first row (14942 vs 17481). Actually, I did not really understand the third row either, where the \"Number of truvari\" come from? Are these cuteSV compared to the gold standard? If so, how comes the FP and TP do not sum up to the same number as the first row?\nSimilarly to SWAGG, I think this could be a useful tool and you seem to do loads of work on the coding part. However, the text was very confusing to me and I do think with more effort in it you could reach much wider readership.\nMinor comments:\nThis sentence is hard to read \"This software is a framework for haplotype-resolved assemblies for benchmarking SV detection algorithms (Figure 10).\", what about \"This software is a framework for benchmarking SV detection algorithms against haplotype-resolved assemblies (Figure 10).\"?\n\"All methods are open-source licensed and have been made available on GitHub: https://github.com/collaborativebioinformatics.\" is an unnecessary statement as FAIR principles are disclosed for all 10 tools and all the links are provided at the bottom.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6767",
"date": "03 Sep 2021",
"name": "Ann Mc Cartney",
"role": "Author Response",
"response": "We would like to thank Kamil Jaron for his time on giving the authors of this manuscript feedback and comments. Upon receiving these comments the corresponding authors reached out to the developers of each of the tools developed as part of this hackathon, each of which have done their utmost to respond to each comment or question. The responses to each of the reviewer's comments are outlined below in bold and italic. Comment 1: General: This manuscript is a write-up report of an apparently very successful hackathon. Authors present an overview of 10 different approaches to solve various issues in the genomics world of structural variants, some of them sound really promising. I appreciated the modest tone authors have chosen when describing the current state of each tool. All the tools have at least some exploratory value, and all of them are publicly available, therefore I have no major objections for the manuscript to be indexed. This being said, I do agree with the first reviewer, I would greatly appreciate it if before diving into details of individual methods, a big picture overview would be provided, for example a table with short descriptions, urls and development stages would be really handy. Disclosing the development stages would be particularly useful for a reader to know what to expect if proceeding further in reading.I do think this manuscript will spark a lot of ideas in the SV community, so I also wondered, what are the contribution policies to individual tools? Many of the tools have some future plans and are not yet production ready. Who would be the people to contact if someone would be interested in contributing and helping out with finishing a tool that would be particularly helpful for their research project? Response: This is a great question. In general the tools are provided as is. The individual authors are part of their github pages. Furthermore these tools might be extended in future hackathons. Some tools are still being worked on (e.g. NibSV). In terms of contacting authors, please contact the authors associated with each tool; this should be listed in each README of the respective tool. Naturally, feel free to contact the lead authors of this paper as well. Comment 2: General: The manuscript could benefit immensely from a big reorganization. I do believe that the classical Intro/Meth/Results organization is not doing this manuscript a favor. It was really hard for me to keep track of ten threads in parallel and at some point I just gave up on top-bottom reading. I ended up scrolling back and forth between different sections to get information regarding one tool I tried to understand at the time. I also think most of the people will be mostly interested in one of the tools only when opening the manuscript for reading, therefore I would propose to keep the common Introduction and Conclusion sections but restructure the rest of the paper on a per method basis. Response: While we agree, this is a given from the journal for hackathons. We are following this format. Comment 3: General: I also appreciated the authors' effort to comply with FAIR principles. Although I have not checked every tool, those I did were neatly documented. Thoughts regarding individual tools are listed below. Response: We thank the reviewer for going over these and highly appreciate the feedback. Comment 4: For the NibblerSV Developers:If I understand right. The genotyping using NibblerSV is done in two phases - 1. calculating a dictionary of specific kmers for each allele, I would call those diagnostic kmers (e.g. allele specific kmers absent in the reference genome) and 2. matching kmers of resequencing data to the diagnostic kmers. I did find the idea very clearly explained. The part I did not understand is how it's decided if a sample does or does not carry a variant. Does it need to have all the diagnostic kmers at a certain coverage? Or at least some proportion? What if the sample contains kmers of multiple diagnostic markers? Is it possible to genotype a heterozygous SV? Is there any measure of confidence in genotyped alleles? I personally would prefer to read more about these details over technical aspects such as different types of temporary files that the software is producing that actually are mentioned. Response: NibSV currently screens the diagnostic kmers against the reference genome. Right now if one of these kmers are found in the reads it is reported that the SV is found in general. This can be improved upon easily (e.g. weight with reference allele kmers) but that is the current state. NibSV does not include a genotyping model nor ref alleles at the moment. Still the early results are very promising. The tests were done using GIAB Tier 1 v0.6 truth SV set and alignment file of illumina 2x250 bp dataset for HG002 sample . The true positive count is the number of genotyped SVs that are not parental SVs i.e. HG2count > 0 and the FP count is the parental SVs i.e. HG2count=0. The parental SVs that are not genotyped are counted as TNs and the non-parental SVs that are not genotyped by nibSV are counted as FN. The following metrics are used to evaluate performance of NibSV: Recall = TP/ (TP+FN); Precision = TP/(TP+FP); Accuracy = (TP+TN)/(TP+FP+FN+TN); False discovery rate = FP/(TP+FP).We have compared the performance of nibSV with SVTyper (will update the results in the manuscript). The Paragraph tools required to add the padding bases to the SVs in the truth set. We could not successfully run paragraph without making any changes to the truth set. Therefore, we have not included the paragraph tool in this result. Comment 5: For NibSV Developers: I also wondered, given the approach of generating catalogues of SV-diagnostic kmers, I would anticipate very variable power to detect SVs of different sizes and types. For example, recent inversions will be identified only through very few kmers found at the edge of the inversion, compared to large scale insertions that will probably harbour many diagnostic kmers and clearer signals. Did you look at the sensitivity/precision in respect to size/type? Would that be a consideration one should have when deciding if to use nibSV or paragraph or VG? Response: This is again an excellent point. We only focused on insertion and deletions at this moment. Indeed we see a higher recall on insertion compared to deletions. This is also driven by the fact that we see a deletion more often within repeats. Nevertheless, nibSV does not consider the entire length of an insertion but rather only the breakpoints. We think that nibSV has some advantages over runtime and its not reliant over the genome version of the reads. However, Paragraph etc. will likely have more control of different insertions at the same region. Comment 6: For the CNV2SV Developers: This tool has the least intuitive motivation of all the tools presented. I would naturally assume all loci with CNV should also be called as SVs, hence I was not sure why it is interesting at all getting the same information twice. However, the results of this analysis proved my intuition wrong. Only very few CNVs are linked to SVs. However, the suggested explanation with length disparity was a bit dissatisfying to me. How come that the SV and CNV callers call variants of so different sizes? Which are shorter/longer? Do you think the CNV/SV reconciliation could be more overlapping with a different choice of SV/CNV caller? This software has an absolutely outstanding description on the GitHub repository. Minor comments: Figure 12, panel B has a cropped y-axis label. In the Methods the text \"formats (from Parliament\" has an opening bracket that is never closed. Response: Typically CNV is called against a locus on a reference genome. We take the view that a CNV is caused by one or more SVs but most CNV callers do not identify a specific SV (insertions or deletions with the coordinate associated.) For example, if we know there are additional copies for region A. A CNV caller will call an additional copy of A in the reference coordinate, but one would not know where the additional copy really is and what the exact sequences and the inserted locus. CNV2SV is partially developed to understand the spectrum of CNV. By connecting the CNV calls for SV calls from de novo assembly results, we get a chance to understand the nature of CNVs is the light full de novo assembly results. The differences of the sizes from the different CNV caller and SV caller actually reflects that we still need more work to understand the relationship of CNVs and SVs. (Most CNV callers use short read data with coverage statistics. This is fundamentally different from calling SVs from assembly-assembly alignment in terms of detection methodology.) We anticipate more de novo assemblies of human genomes will help us eventually get better pictures. Comment 7: For the CoronaSV Developers: I did appreciate the idea of a scalable pipeline for conservative analyses of SARS-CoV-2 genomes. Authors made many unjustified choices. For example, why did you choose in particular Manta, Delly, Lumpy and Tardis to detect SV using short reads? But I suppose it is understandable why it would be challenging to justify every choice in the limited time of a hackathon. The step of the analysis I am worried about is the merging by SURVIVOR, it also happens to be the only one that does not seem to be included in the GitHub repository. What parameters were used for individual merging steps using SURVIVOR? Given the genome of SARS-CoV-2 is really small, I believe that the outcome of this pipeline will be very sensitive to the chosen thresholds for merging variants. This project aims to get \"trustworthy SV calls across SARS-Cov-2\", but there was only very little effort in validation of the SV set detected as far as I can tell. I was honestly quite surprised to see how many deletions that are >20k long you reported as confident. Is it really possible for SARS-CoV-2 to lose more than 2/3 of its genome? Could they represent some SV calling artefacts? One way to check the quality of called SVs would be to compare phylogenetic relationships of the analysed viruses that are probably available for all the sequenced data anyway and verify that the common SVs are shared within monophyletic clusters. Finally, the provided data frame with the input data contains various types of libraries. How does SV calling work on RNA-seq data? To be honest, I am not even sure what \"RNA-seq\" means in the context of RNA viruses, but I do find it strange that all the libraries seem to be treated the same. Could some of those huge deletions be simply the selection process of the non-WGS libraries? I understand this is a hackathon paper, and therefore it would be unreasonable to ask for more analyses, but I do believe that the wording of this tool should be toned down a lot. I think this is a good first draft for this ambitious pipeline, but loads of work and thought should be given to it before the SV sets are called trustworthy. Response: The reviewer makes several helpful points. To the first point, we selected a handful popular SV callers from short reads suitable for the task, and given the short duration of the hackathon, we unfortunately were unable to evaluate a more comprehensive set. To the general point of do we expect to see such large SVs, given SARS-CoV-2 is sequenced from an intrahost population, which often is from metatranscriptomes (RNA-seq applied to a microbiome sample) containing subgenomic RNAs, large SVs can be observed as it captures the transcriptional landscape of SARS-CoV-2. And we have added details of SURVIVOR to the Github repository, thank you for pointing this out. Comment 8: For the CleanSV Developers: The idea here is to figure out empirical filtering thresholds to minimise false positives on called SVs. This is a great idea and it's desperately needed to have better community resources to reduce the need for manual curation. I am also very sure that these thresholds would have great applicability in other species and germline SV calling. Is there any chance of more general applicability? Response: We thank the reviewer for the assessment and insightful question. In terms of more general applicability, we agree with the reviewer entirely. However, in order to release these filters/thresholds to the larger community for general use, the optimal approach would be to focus on a particular use of SV calling (e.g. translational genomics in oncology) with a particular assay of a certain average coverage and tumor purity. These filters need to be tailored specifically for these parameters. We suspect generating filters per SV caller for general use would result in minimal quality control; this is especially true within cancer genomics in terms of calling somatic and germline SVs accurately. As for focusing on other species (even within a germline context), the main impediment is that we would need a sufficient number of samples from species X at a specific time in order to create these filters. Comment 9: For the CleanSV Developers: Given authors have decided not to share the filtering thresholds, I think it should be clearly stated early on that this is only a conceptual description of the workflow and results are not provided yet. Response: We agree with this assessment, and have tried to clarify this in the manuscript. This paper is the result of a hackathon, and the ideas within are largely proof of concepts which have value outside of a more comprehensive paper. Comment 10: For the CleanSV Developers: Minor comments: I resume hs37d5 in \"Illumina short reads using novoalign hs37d5 HG002 BAM\" means it is human data, but I do think it should be explicitly mentioned. A bunch of citations are in a different format, something like \"(7)\" and without actual reference. Response: We have clarified and fixed these issues in the manuscript. Comment 11: For the Sniphles Developers: Again, a very timely contribution. Phasing of SVs will be more and more important as long read technologies are more and more available even for population genomics studies. I found the idea very clear, and sound. I did wonder, however, about the merging step. Technically, SVs from different haplotype need to be merged as if only the SV is homozygous in the alternative allele, therefore I wonder if it is appropriate to lump together everything that is closer than 1000 bases from each other. How many such variants were detected? That's kind of related to the only thing I was missing - results. The test case of this method is basically a more confusing repetition of what is already written in methods without any actual numbers of phased SVs. How successful was phasing? How many and how long blocks were phased? If unavailable yet, you should be explicit that it's an untested approach. Although I have not tried to install the software, I appreciated that the GitHub repository was very neat and the code very well organised. Response: We would like to thank the reviewer for the ideas and suggestions. Also, we would like to mention that, this is a prototype of the ideas, and we opened an issue regarding the suggestions. We shall implement a parameter to set the minimum accepted length to identify 2 heterozygote SVs as one. “How many such variants were detected? That's kind of related to the only thing I was missing - results.” We used chromosome 20, it contained 652 SVs with minimum 13 to support SVs. 239 SVs are heterozygote we managed to phase 182 of those (76.15%) in 76 phase blocks using the first method. For the second method, while we completed the tool, and it worked as expected, but sadly it did not give the expected results, we still need to work on debugging and enhancing the second method. Comment 12: For the Sniphles Developers: “I did wonder, however, about the merging step. Technically, SVs from different halplotype need to be merged as if only the SV is homozygous in the alternative allele, therefore I wonder if it is appropriate to lump together everything that is closer than 1000 bases from each other.” Response: We agree with the suggestion, we shall implement a parameter that takes as an input the maximum distance to merge heterozygote SVs. Comment 13: For the Sniphles Developers: “The test case of this method is basically a more confusing repetition of what is already written in methods without any actual numbers of phased SVs.” Response: We changed it accordingly. Comment 14: For the Sniphles Developers: “How successful was phasing? How many and how long blocks were phased? If unavailable yet, you should be explicit that it's an untested approach.” Response: This is a prototype we worked only on chromosome 20 using HiFi data, we still need to develop our method, we updated the manuscript to state that. Comment 15: For the Swagg Developers: This was another tool with rather difficult text and figure. It is still not very clear to me how using a protein graph should help SV calling. I was also rather confused about the construction of the protein graph. In the methods you write, \"Protein graphs are generated using a multiple sequence alignment of the protein\", but what is \"the protein\"? I originally imagined SWAGG would use genome annotation, where the multiple sequence alignment comes into play? I got it a lot better from the presentation I found on GitHub, but I am still not 100% sure how it's done. The presented figure is very pretty, but I did not understand at all what I was supposed to look at. I just think it's a pity, it does look like a load of work with a really interesting idea. I would recommend spending more effort on explanation of the reasoning behind and general clarity of the text. I also wondered, is the protein information used for SV calling in the end? If not, why is not the input to your software a vcf file with SVs? Why is it important that they are called by GATK and deepVariant? That was another confusing bit for me. Response: We would like to thank the reviewer for their comments and questions, specifically with respect to why we should build a variation graph and not just keep variations in a VCF file. Building graphs from amino acid sequences can be used to align new amino acid sequences to these graphs, thereby finding similarities to other sequences. A modified Smith-Waterman algorithm that works for DAGs (Directed Acyclic Graphs) can be used for this job. Due to how proteins work and fold, it is possible to have a gene between two samples from two different genres in bacteria that are very distant (20-30% sequence similarity), however, due to nonsense mutations, the amino acid sequence similarity is higher (50-60%). For example, in Myxobacteria, looking at two different samples from two different genres or families, building a pangenome graph out of the DNA is not really feasible due to the amount of variations between them. However, looking at amino acid sequences, more similarities can be found. Therefore, with building a graph out of the amino acid, paths can be labeled with metadata (certain conserved nodes for example are associated with antibiotic resistance, aligning a new sequence to this graph, can also tell us about this new sequence). This can additionally be accomplished via HMM modeling, but, building a graph adds a visualization element, and with the recent optimizations in graphical mapping algorithms, it may be faster at aligning a sequence to a graph than using some HMM model. Building on the idea that we can add metadata to paths in the graph, looking at this paper for example, \"Jaillard et al. (2018). “A Fast and Agnostic Method for Bacterial Genome-Wide Association Studies: Bridging the Gap between K-Mers and Genetic Events.” We see how from looking at the graphs, certain nodes can be associated with resistance. However, for example, this method breaks down when the similarity between the sequence we're looking at drops, as it's hard to find shared k-mers then. However, going to amino acid space, the similarity increase and similar methods and algorithms can then be used but with the amino acid alphabet. Comment 16: For the PanOriginSV Developers: A machine learning approach that takes a genome variation graph that includes both SNVs and SVs and determines lab of origin. First, I would like to disclaim I am a bit out of my depth reviewing this method, as I never worked with lab strains and genetically modified organisms or thought about the problem of lab attribution. I was a bit confused about the benchmarking. The Genetic Engineering Attribution Challenge seems to have plenty of approaches with really successful prediction algorithms, why is the approach compared to a single method (PlasmidHawk) that does not seem to be compared to the other approaches in the challenge? I also wondered why the results were shown on a per-cluster basis, not overall accuracy, so they could be comparable to the approaches from the Genetic Engineering Attribution Challenge. Perhaps a silly thought, but do you think that machine learning approach is scalable? Having a comparable training dataset to the unclassified dataset is essential for meaningful prediction, would the approach work for novel strains? Minor comments: This sentence \"PanOriginSV has three additional open source dependencies which are MMSEQ2 (for clustering), BCALM (pangenome creation) and GraphAligner (for sequence-to-graph alignment)\" should probably contain references to respective software. \"10-50x less than the linear model (depending on the cluster).\" Less than PlasmidHawk? Response: We’d first like to thank the reviewer for their feedback and questions. While other tools have been developed for the same problem, Plasmidhawk was recently shown to outperform the other state-of-the-art methods while also being more straightforward to run. Additionally, Plasmidhawk does not require a GPU in order to train efficiently. The main reason for showing per-cluster accuracy was to show the performance of our method on large groups of highly similar sequences. In addition, machine learning methods are not well suited for small cluster scenarios due to the lack of training data. Unfortunately, the code for all other methods in the GEAC was unavailable, therefore we were unable to compare results without submitting to the challenge. However, we do think that machine learning is scalable, although the preprocessing of the data will become more important as the dataset grows. For novel strains that have no similarity to the database, our method would not work but we are confident that no other method would. However, for novel strains that have “signatures” in the database, these would be represented by nodes in the pangenome that are relatively unique to certain labs. Comment 17: For the GeneVar Developers: This tool has a functional prototype and it works! It allows a user to browse variants related to any human gene, which is fun. However, I do think it should be called a \"human SV browser\" (I originally imagined the intent is to make a generic SV browser). I appreciated the attempt to make information about human SVs accessible to the general public, but I do wonder how close to the goal the authors got. I don't think the allele frequency spectrum is an easy plot for a user without a background in genetics. Also, there are loads of variants shown for every gene, would it be possible in future to somehow prioritise to the \"most likely relevant\" variants? What you think could be done to improve accessibility of the tool by for example GPs? Minor comment: In the app, it's a bit confusing that SV length is filtered on the panel on the left, while all the remaining variables are filtered by clicking on the empty \"all\" fields below column names. Response: Thank you reviewer for your thoughts and questions. We agree that ranking the variants shown could be helpful for genes with a lot of variants. While right now a long list of variants suggest more filtering needed by the user, it would be better to have the most impactful SVs shown first by default. In terms of improving accessibility of the tool to GPs, etc. We think adding documentation and tutorials to the tool would be helpful, for example to interpret the frequency histogram, and will be added as the tool matures. We are also keen on receiving feedback directly from clinicians and GPs. We are exploring ways to reach out to them to learn what should be changed, improved, or added. Comment 18: From the SVTeaser Developers: I really like this idea for a framework for simulating reads and benchmarking SV callers. Beside the previously utilised approach of generating insilco generated SVs, SVTeaser also allows a lexicon based generation of SVs. I also found the writing and description of this method very nice and understandable. One of the main general problems of simulating sequencing reads is that it is very hard to take into consideration all biases of real life sequencing. For example, cross sample or bacterial contamination are really hard to consider. As a consequence, benchmarking using simulations is (probably) always overly optimistic. Would it be useful to attempt to quantify optimism? For example by simulating reads from a sequenced genome with known SVs? Then the precision and recall of SVs could be compared between the simulated and real sequencing data. Response: We agree that benchmarking against simulated data is overly optimistic and that it’s hard to accurately replicate library preparation errors such as what you have described. A primary goal of SVTeaser is to assist developers of SV calling algorithms with assessing how their tool would perform without needing to quantify their algorithm’s problems versus their sequencing’s problems. A well benchmarked, production-ready tool shouldn’t rely on only SVTeaser and would always have real data to test against. However, should someone want to simulate more realistic sequencing experiments by adding batch effects such as cross-sample contamination, it would be possible for them to run SVTeaser twice - once over their target sample’s SVs at e.g. 28x coverage and again with a second sample’s SVs at e.g. 2x coverage. Then, simply concatenating the sets of generated reads prior to read-mapping would create a simplistic simulation of ~5% cross-sample contamination. While SVTeaser doesn’t currently automate this kind of operation, we will strongly consider how best to incorporate the functionality. Comment 19: For the developers of XSVLen: Sound approach, but took me a while to see any added value compared to the original study by Chin et al. (2020)1. Do I understand right that what was done on MHC locus you generalised in a framework for any region with haplotype-resolved assemblies? I think it should be more clearly stated what was done by Chin et al. before and how your approach differs. Also, in the text you refer to Nurk et al., although the reference is Chin et al. (I think it was confused with this other paper presenting HiCanu2). In the table, the second row says \"Number of these calls that overlap assembly contigs\". First, how can there be any variant called outside of an assembly contig? Do you mean overlapping with haplotype-resolved contigs? You also write \"these calls\", which makes me think it's a subset of the first row, but insertions >50bp seems to have a higher number in the first row (14942 vs 17481). Actually, I did not really understand the third row either, where does the \"Number of truvari\" come from? Are these cuteSV compared to the gold standard? If so, how come the FP and TP do not sum up to the same number as the first row? Similarly to SWAGG, I think this could be a useful tool and you seem to do loads of work on the coding part. However, the text was very confusing to me and I do think with more effort in it you could reach much wider readership.Minor comments: This sentence is hard to read \"This software is a framework for haplotype-resolved assemblies for benchmarking SV detection algorithms (Figure 10).\", what about \"This software is a framework for benchmarking SV detection algorithms against haplotype-resolved assemblies (Figure 10).\" Response: Many thanks for the comments and all the interest about the work we performed. The assembly we used for benchmarking is the one generated by Wenger et al. 2020 (NCBI Assembly with accessions GCA_004796485.2 (maternal) and GCA_004796285.1 (paternal) - so we worked with the whole-genome and not only CHM. The reference of CHM locus has been removed from the text and we included the right reference. We have updated the methods section for improving comprehension on the approach we implement. Here, we benchmarked sequence-resolved variants by checking their presence in a haplotype-resolved assembly available and so it works on top of an haplotype-resolved assembly. We have also updated the main table to include the correct numbers and also to help comprehension of categories. The \"Number of these calls that overlap assembly contigs\" row makes reference to SV called by cuteSV (sequence-resolved SV calling) that would be found also in the assembly by the approach we tested (construct SV query and map queries back to assembly). In the \"Number of truvari” (updated to Number of overlapping calls classified with truvari) row we include the classification obtained using truvari – we compare the cuteSV calls and GIAB truth set). This was due to a bug in the annotation script that has been fixed. The minor suggested change has been applied to the text. Again, we thank the reviewer for his thoughtful comments, suggestions and feedback and hope that the following responses have clarified any queries or concerns."
}
]
},
{
"id": "83790",
"date": "20 May 2021",
"name": "Ricardo Assunção Vialle",
"expertise": [
"Reviewer Expertise Bioinformatics",
"genomics",
"genetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes ten Structural Variation related software tools developed at the Second Baylor College of Medicine & DNAnexus hackathon. These tools successfully cover relevant topics in the SV field and certainly will be appreciated by the scientific community. As other reviewers pointed out, my primary concerns are that the text still needs some work to improve readability and fix inconsistencies (e.g., American vs. British spelling). Also, a table summarizing all tools described will be very welcome. There are also some issues specific to some tools that should be addressed. Comments for each tool are described below.\nNibbleSV: The tool seems great, performs efficiently, and the results are impressive. I just have few comments that would be interesting to see. First, the authors could add more details about the tests using the HG002. If I understood right, the GiaB tier 1 v0.6 was used as candidates to genotyping using the Illumina reads (250bp), is that correct? Also, how was the evaluation done? Second, if possible, it would be interesting to see how NibbleSV compares with other tools (e.g., paragraph). Finally, it would be nice to see how it performs in more complicated regions (e.g., segmental duplications). I wonder if NibbleSV could help filter artifact SVs found by misalignment in those regions.\nCNV2SV: The motivation and the tool description must be improved in the manuscript. Also, the results are not well described and discussed, being restricted to the legends of Figures 11 and 12.\nMinor: In the methods, CNV2SV circularlize should be circlize to refer to the R package. Missing description of letter C in figure 11 legends.\nCoronaSV: The method proposes a Snakemake pipeline for SV discovery in SARS-CoV-2 genomes. It integrates short and long reads SV discovery tools, as well as assembly-based methods. CoronaSV also handles downloading sequencing data from SRA for variant calling. As a use case, the pipeline was applied to over 200 genomes, and a basic report of the results was shown. I’m not familiar with viral genomes, but I’m wondering what is the actual gain of applying such complex pipeline instead of performing de novo assembly and getting the SVs from it instead.\nCleanSV: The tool proposes a systematic way for filtering false-positive somatic SVs in cancer genomics. The approach uses germline SVs identified in normal tissue samples to find the best filtering thresholds for specific SV callers. There is no description of how to run the tool, and an example dataset could be added to the GitHub page.\nSniphles: More details could be added to the diagram of the pipeline, the calling and merging steps are oversimplified. Is there a reason why Sniffles need Mosdepth to estimate its parameters? It would be great to see how it compares with the “first” approach of phasing mentioned by the authors, using tagged reads to phase SVs.\nSwagg: The motivation and methods are not very clear in the manuscript. It seems to me that the protein-graph is basically capturing small-variants. Where SVs fit in this context? The example showed in Figure 15 needs a more detailed explanation (e.g., what the color mean? Is there any SV affecting this protein?). Also, some phrases are repeated in the introduction and methods sections.\nPanOriginSV: I’m unfamiliar with the topic addressed by this tool. For the little information I could get, the proposal seems very relevant, and the results look promising. In the introduction, the authors discuss the drawbacks of using machine learning approaches and highlight PlasmidHawk advantages, but in the end, propose another machine learning method? What is different in this method compared to existing ones? I’m wondering if extending that tool to work non-linear pangenomes would be possible. Also, it would be nice to see the same benchmarking against PlasmidHawk.\nGeneVar: The proposal of GeneVar seems interesting and novel. However, not all features described in the manuscript seemed to be implemented. For instance, the authors state that a rare-variant burden test is performed but, I could not find that on the demo website. Also, the annotations are still very basic, the presentation of the overlap is not user-friendly. I would suggest improving how information is shown, with more summarized information about the overlap.\nSVTeaser: SVTeaser is a framework for benchmarking SVs using simulations. Simulations are performed using SURVIVOR. Overall, the method seems well developed, and the contribution is relevant for the field.\nXSVLen: The methods sound truly relevant and novel. I’m very interested in applying this method in the future. I’m wondering if a more refined report could be implemented. It would be interesting to see results summarized for each haplotype separately. In the manuscript, the results table is hard to understand. For example, the first row shows 14942 INS >=50, while the second row shows a higher number when I would expect just a subset based on the description.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6800",
"date": "03 Sep 2021",
"name": "Ann Mc Cartney",
"role": "Author Response",
"response": "We would like to thank Ricardo for their time on giving the authors of this manuscript feedback and comments. Upon receiving these comments the corresponding authors reached out to the developers of each of the tools developed as part of this hackathon, each of which have done their utmost to respond to each comment or question. Comment 1: General: This manuscript describes ten Structural Variation related software tools developed at the Second Baylor College of Medicine & DNAnexus hackathon. These tools successfully cover relevant topics in the SV field and certainly will be appreciated by the scientific community. As other reviewers pointed out, my primary concerns are that the text still needs some work to improve readability and fix inconsistencies (e.g., American vs. British spelling). Also, a table summarizing all tools described will be very welcome. There are also some issues specific to some tools that should be addressed. Response: We agree that the format of the manuscript is somewhat cumbersome to read, however this is a pre-requisite determined by the journal for manuscripts associated with hackathons. Comment 2: For the Developer of NibbleSV: The tool seems great, performs efficiently, and the results are impressive. I just have a few comments that would be interesting to see. First, the authors could add more details about the tests using the HG002. If I understood correctly, the GiaB tier 1 v0.6 was used as a candidate for genotyping using the Illumina reads (250bp), is that correct? Also, how was the evaluation done? Second, if possible, it would be interesting to see how NibbleSV compares with other tools (e.g., paragraph). Finally, it would be nice to see how it performs in more complicated regions (e.g., segmental duplications). I wonder if NibbleSV could help filter artifact SVs found by misalignment in those regions. Response: Yes, the tests were done using GIAB Tier 1 v0.6 truth SV set and alignment file of illumina 2x250 bp dataset for HG002 sample. The true positive count is the number of genotyped SVs that are not parental SVs i.e. HG2count > 0 and the FP count is the parental SVs i.e. HG2count=0. The parental exclusive SVs that are not genotyped are counted as TNs and the HG002 SVs that are not genotyped by nibSV are counted as FN. The following metrics are used to evaluate performance of nibSV: Recall = TP/ (TP+FN); Precision = TP/(TP+FP); Accuracy = (TP+TN)/(TP+FP+FN+TN); False discovery rate = FP/(TP+FP). The performance of nibSV was compared with SVTyper. SVTyper can genotype only non-insertion (ie. here deletions) type SVs, so we compared nibSV with SVtyper only for deletion type of SVs. nibSv was run with parameters k=23 and m=0. Tool,TP,FP,FN,TN,Recall,Precision,Accuracy,FDR nibSV,12152,2055,17957,5248,0.4,0.86,0.47,0.14 SVTyper,5873,212,24236,7091,0.20,0.97,0.35,0.03 The high recall score of nibSV shows that it outperformed SVTyper for genotyping the non-insertion type SVs. The high precision rate and low false discovery rate of SVTyper is due to the very low number of total genotyped SVs. The Paragraph tools required to add the padding bases to the SVs in the truth set. We could not successfully run Paragraph without making any changes to the truth set. Therefore, we have not included that tool in this result. Comment 3: For the CNV2SV Developers: The motivation and the tool description must be improved in the manuscript. Also, the results are not well described and discussed, being restricted to the legends of Figures 11 and 12. Minor:In the methods, CNV2SV circularlize should be circlize to refer to the R package.Missing description of letter C in figure 11 legends. Response: Thank you for your assessment. We have restructured the respective sections in the manuscript in order to clarify the tool motivation and description of operation. We have also corrected the figure accordingly. Comment 4: For the CoronaSV Developers: The method proposes a Snakemake pipeline for SV discovery in SARS-CoV-2 genomes. It integrates short and long reads SV discovery tools, as well as assembly-based methods. CoronaSV also handles downloading sequencing data from SRA for variant calling. As a use case, the pipeline was applied to over 200 genomes, and a basic report of the results was shown. I’m not familiar with viral genomes, but I’m wondering what is the actual gain of applying such a complex pipeline instead of performing de novo assembly and getting the SVs from it instead. Response: The reviewer makes a good point with respect to de novo assembly from short reads, which would accurately capture small structural variants. However, given SARS-CoV-2 is sequenced from an intrahost population, which often is from metatranscriptomes (RNA-sequencing of a microbiome sample) containing subgenomic RNAs, SVs reflect the transcriptional landscape of SARS-CoV-2. Thus we feel it is of use to capture the concordance across short reads, long reads, and assembly for structural variants calling. Comment 5: For the CleanSV Developers: The tool proposes a systematic way for filtering false-positive somatic SVs in cancer genomics. The approach uses germline SVs identified in normal tissue samples to find the best filtering thresholds for specific SV callers. There is no description of how to run the tool, and an example dataset could be added to the GitHub page. Response: Thank you to the reviewer for the response. As mentioned in the previous reviews, our contribution to the hackathon was a proof of concept. Releasing the filters for general use would require more work specifically investigating tumors of a given sequencing depth and tumor content. The panel of normals used for the paper are accessible, as cited in the paper. Comment 6: For the Sniphles Developers: More details could be added to the diagram of the pipeline, the calling and merging steps are oversimplified. Is there a reason why Sniffles need Mosdepth to estimate its parameters? It would be great to see how it compares with the “first'' approach of phasing mentioned by the authors, using tagged reads to phase SVs. Response: We would like to thank the reviewer for the comments and questions. We agree with the reviewer regarding the merging step, while this is a prototype of the idea, we will be working on enhancing the merging step. Additionally, we stated that in the manuscript. Comment 7: For the Sniphles Developers: “Sniffles need Mosdepth to estimate its parameters''. Response: Sniffles use a minimum of 10 reads to call an SV, we suggest to use mosdopth to calculate the coverage for the region we call SVs in, so it could adapt to low and high coverage as well as technology used for sequencing (PacBio or Oxford Nanopore Technology). Comment 8: For the Sniphles Developers: ‘’It would be great to see how it compares with the “first'' approach of phasing mentioned by the authors, using tagged reads to phase SVs.”. Response: We will be working on that, as the second approach still needs more tuning. Comment 9: For the Swagg Developers: The motivation and methods are not very clear in the manuscript. It seems to me that the protein-graph is basically capturing small-variants. Where do SVs fit in this context? The example shown in Figure 15 needs a more detailed explanation (e.g What does the color mean? Is there any SV affecting this protein?). Also, some phrases are repeated in the introduction and methods sections. Response: We would like to thank the reviewer for their comments and questions regarding the manuscript. In response to their questions, the different colors are associated with different sequences used to build the graph, with each sequence taking a certain path in the graph, which yields the colors. Comment 10: For the PanOriginSV Developers: I’m unfamiliar with the topic addressed by this tool. For the little information I could get, the proposal seems very relevant, and the results look promising. In the introduction, the authors discuss the drawbacks of using machine learning approaches and highlight PlasmidHawk advantages, but in the end, propose another machine learning method? What is different in this method compared to existing ones? I’m wondering if extending that tool to work non-linear pangenomes would be possible. Also, it would be nice to see the same benchmarking against PlasmidHawk. Response: We’d first like to thank the reviewer for their feedback. While PanOriginSV does use machine learning, it has the advantage that random forests are much easier to inspect, train, and interpret than other ML models. In addition, the step of constructing the pangenome already constructs features of the sequence. The results of PlasmidHawk are shown as the “linear” model in Table 1 as opposed to PanOriginSV, the graph model. Comment 11: For the GeneVar Developers: The proposal of GeneVar seems interesting and novel. However, not all features described in the manuscript seemed to be implemented. For instance, the authors state that a rare-variant burden test is performed but, I could not find that on the demo website. Also, the annotations are still very basic, the presentation of the overlap is not user-friendly. I would suggest improving how information is shown, with more summarized information about the overlap. Response: Thank you reviewer, for your thoughts and assessment. Indeed, GeneVar is a work in progress and what you see now is the result of only 3 days of work. The developers agree that to make this a public tool, additional time and effort is needed. Comment 12: For the SVTeaser Developers: SVTeaser is a framework for benchmarking SVs using simulations. Simulations are performed using SURVIVOR. Overall, the method seems well developed, and the contribution is relevant for the field. Response: We appreciate the reviewer's careful and detailed assessment of our work, as well as his complimentary remarks. We believe that our tool will be useful in genetic research on SV predictions. Comment 13: For the XSVLen Developers: The methods sound truly relevant and novel. I’m very interested in applying this method in the future. I’m wondering if a more refined report could be implemented. It would be interesting to see results summarized for each haplotype separately. In the manuscript, the results table is hard to understand. For example, the first row shows 14942 INS >=50, while the second row shows a higher number when I would expect just a subset based on the description. Response: Many thanks to the reviewer for pointing this out and for the interest in the method, we have updated the main table for including the right numbers and also to help comprehension of categories. This was due to a bug in the annotation script that has been fixed. We did not perform a detailed exploration of haplotype-overlapping calls or the generation of a more detailed report as this was a proof-of-concept of the method but we agree it would be interesting if future work is performed. We would like to thank the reviewer for their kind comments and feedback and hope that they have addressed all questions or concerns posed."
}
]
},
{
"id": "82807",
"date": "07 Jun 2021",
"name": "Loren L. Flynn",
"expertise": [
"Reviewer Expertise Genetic therapies",
"functional 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\nMcCartney and colleagues describe a compelling and comprehensive account of the outcomes of an international hackathon to develop new tools for the discovery and analysis of structural variants (SVs). The authors describe 10 novel software tools to overcome gaps in the available tools to more accurately identify, genotype and map SVs, as well as provide predictive functional effects of the variants to gene expression. The identification of new and accurate tools to identify SVs is of critical importance for understanding the genetic underpinnings of complex disease with no monogenic pattern of disease inheritance. This manuscript is the product of a virtual international hackathon, describing newly developed tools as a foundation for future discussion and development, and the links to the already available online tools provide additional and necessary information for understanding the software applications and outputs. I recommend this manuscript for indexing following amendments. From a functional genetics perspective, I provide the following comments and suggestions:\n1. The manuscript does not provide full detail about the code, methods and analysis of the individual tools, however, the purpose of the manuscript is to describe the hackathon and the resultant projects, with the intention for future development of these tools. This could be made clearer in the text with the development status and future requirements for each tool discussed.\n2. A summary table of the main applications, benefits, and stage of development for each of the tools and the future direction would be helpful for readers. In particular, more information on the specific applications of each of the tools would be helpful for those reading the manuscript without a bioinformatics background.\n3. The manuscript is written with an introduction to each tool, the operation for each and finishing with use cases or results for each. As a suggestion, describing each tool separately under its own heading and incorporating each of these sections would improve the flow of the manuscript.\n4. The current tools for accurate SV calling and genotyping from GWAS data are limited for poly-nucleotide variations. Do any of the described tools address this limitation?\n\n5. The Swagg software describes a tool for SV calling and mapping at both the gene and protein level. However, the advantage of SV calling and mapping at the protein level is not clear given that many SVs are found in non-coding regions. The protein function is not further described in the methods and the interpretation of the figure in the results section was not clear. It would be useful to provide more information for the protein mapping. Can this software show predictive changes to mRNA or protein structures induced by SVs in non-coding regions?\n6. The GenVar tool offers a clinically relevant analysis with predictions to SV effects on regulation of gene expression. Does the tool identify SV regions based only on the reference sequence or is it able to further compare a patient sequence to the RefSeq and provide information as to the carriage of potential risk variants/variants known to effect gene expression?\n7. There is no figure displaying the result output for the phase sequencing analysis Sniphles tool, this would help in explaining the data analysis and output.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-246
|
https://f1000research.com/articles/10-885/v1
|
03 Sep 21
|
{
"type": "Review",
"title": "Horticultural therapy, nutrition and post-traumatic stress disorder in post-military veterans: developing non-pharmaceutical interventions to complement existing therapeutic approaches",
"authors": [
"Richard Mottershead",
"Marjorie Ghisoni",
"Marjorie Ghisoni"
],
"abstract": "Non-pharmaceutical interventions for veterans living with post-traumatic stress disorder are becoming a more popular way to address some of the social and personal needs identified by this group. Horticultural therapy or growing and eating food together provides several ways to increase mood, improve nutritional status, reduce loneliness and reduce the physical health impacts of mental illnesses such as post-traumatic stress disorder. In this paper we will discuss some of the issues people living with post-traumatic stress disorder might face. We will also provide an overview of the therapeutic effects of these approaches and how they will be applied in a locally identified group.",
"keywords": [
"Post-Traumatic Stress Disorder",
"Veteran’s Mental Health",
"Horticultural Therapy",
"Nutrition",
"Psychosocial Interventions."
],
"content": "Introduction\n\nAt present, in the United Kingdom (UK), there are former service-personnel leaving the military with no physical injuries but with underlying mental health problems. These may surface on return to the family unit, or at times of stress triggered by alcohol or homelessness. It was highlighted in a recent PhD thesis by one of the authors (Mottershead, 2019) that the post military veterans interviewed feared for their sanity, suffered flashbacks, night terrors and experienced struggles with employment and families, reporting concerns for their partners or family. This is supported by Hossain et al. (2020) who in a review of the literature following a major crisis or trauma, revealed that there is a higher prevalence of mental health problems including anxiety, depression, substance misuse, suicidal ideation and post-traumatic stress disorder (PTSD) within the local population.\n\nThis is not a new concept for post military veterans, as similar problems have been reported as a result of the nations’ involvement in armed conflict since the commencement of the 21st century. Harold Bridger (1985) suggested that the concept of non-pharmaceutical interventions arose in the autumn of 1942 at Northfield military Hospital in Birmingham, where a move to improve the return of neurotic casualties to military duty was tried out as a new form of treatment. The therapeutic community only lasted six weeks due to the chaos it created, but in that very short time it had given a glimpse of the success that could be achieved, and had been achieved previously in the Peckham experiment in the 1930s, with the creation of an” unintentional therapeutic community” (Bridger, 1985. p.8.). In the following review of the literature, we will discuss how the non-pharmacological interventions of horticultural and nutrition therapy, can minimise, or reduce the physical and mental health effects of PTSD.\n\n\nDiscussion\n\nMilitary personnel exposed to war-zone stress are at significant risk of developing PTSD. Post-traumatic stress disorder (PTSD) has been studied in military personnel for more than 30 years, and PTSD may develop after an individual experiences or witnesses to a traumatic event, such as natural disasters or violent personal assault, life-threatening events such as terrorist attacks, violent crime and abuse, military combat, serious accidents or extended combat, exposure to certain environmental toxin (Iribarren et al., 2005).\n\nIn 2015, a joint report by Help for Heroes and Kings Centre for Military Health Research (KCMHR), suggested that at least 10% of veterans who served over the last 20 years present mental health conditions that need treatment. The same report estimated that at least 61,300 out of 601,000 veterans who served as Regulars in the UK Armed Forces between 1991 and 2014 might suffer from mental health problems, and that this would require professional intervention (Help for Heroes & KCMHR, 2015). Amongst these mental health problems was post-traumatic stress disorder (PTSD). This is a psychiatric disorder that results from the experience or witnessing of traumatic or life-threatening events which thereby impairs the person’s daily life and can be life threatening (Reisman, 2016). Moreover, Reisman (2016) explains that PTSD can cause significant disruption and interfere with personal and social performance, which subsequently leads to social withdrawal, anger, and aggression. Fear et al. (2010) demonstrated that PTSD in military personnel has a broad impact on military preparedness, and achievement of military objectives. However, data that identified a significant increase in PTSD symptoms at 3-year and 6-year follow up reviews on UK military veterans may be more worrying. Sareen (2014) resonates with this concern in highlighting scientific evidence and empirical research that suggests that military personnel with PTSD are at greater risk for more physical health problems, poorer health status, and higher medical service usage. Hence, much more research is needed on this perspective. Depression is the most common comorbidity of PTSD among military personnel (Kessler et al., 1995). A meta-analysis of 57 studies, conducted among both military and civilian samples, found a major depressive disorder and PTSD comorbidity rate of 52% (Rytwinski et al., 2013). Other prevalent psychiatric comorbidities of PTSD exhibited among military veterans include anxiety and substance abuse or dependence (Hoge et al., 2006).\n\nResearchers have proposed several theories to explain the development of PTSD, including psychological theories, cognitive theories, emotional processing theory. Pan et al. (2018), suggests that the contemporary PTSD research aims to better understand the disease-related risk factor. They go on to suggest that there is convincing evidence of the relationship between abnormal levels of catecholamines, or stress hormones, in people living with PTSD, including the hormone norepinephrine as a result of facing fear and stress.\n\nFurthermore, studies of risk factors of PTSD show that not everyone who experiences a traumatic event will develop PTSD, and therefore that there is role of individual factors in contributing to the development of PTSD (Reisman, 2016). They also suggest that associated and identified individual and social risk factors include young age at the time of trauma, low socio-economic status and lack of support. More recently in a review by Herringa (2017) it was found that brain development in children can be affected by trauma in early life which increase the significance of psychological support and good nutrition for brain health in adulthood. The use of complementary and alternative medicine (CAM), such as horticultural therapy or nutrition advice, has been found to be on the increase in Sweden, as a way of developing coping skills in managing personal mental health needs (Wemrell et al., 2020). The management of nutrition and its effects on mental health is therefore a simple and easy way, alongside other complementary interventions, to improve resilience within the mind and body, and reduce the effects of living with long-term stress.\n\nWhile horticultural therapy is not considered a first-line treatment for people living with PTSD, there are many studies that demonstrate improvement in overall health in the wider literature (Detweiler et al., 2015). In a pilot study on physical health and PTSD in veterans, Hall et al. (2020) found that being more active could improve the health outcomes for people living with PTSD, by reducing obesity and improving their mood. Similarly, Detweiler et al. (2015) found that horticultural therapy is an active, non-pharmaceutical intervention that can help people to improve their mood, reduce obesity and increase social interactions, often caused by isolation in veterans. Furthermore, they found that there was a notable improvement in scores on outcome measures such as quality of life and alcohol craving questionnaires. They go on to suggest that horticultural therapy as an extension of occupational therapy, has been found to have beneficial effects on both physical and mental health recovery. More recently, Wemrell et al. (2020) found in a review of complementary and alternative medicine (CAM) for people with mental illness in Sweden, that 14% of respondents were using horticultural therapy as an addition to their prescribed treatments.\n\nThe evidence above supports the findings of Cipriani et al. (2017), within their systematic review of the effects of horticultural therapy on persons with mental health conditions. This research revealed that horticulture can provide physical, neurological, and psychological rehabilitation, whilst improving motor skills as well as strength and endurance. They go on to suggest that being outside in the natural environment has been found to reduced stress and improve concentration and cognitive function. This has been known for some time in helping military personnel to return to civilian life. Wang (2010 p.4) cites Franklin Roosevelt in 1944, who in writing to the then secretary of war argued that,\n\n“No overseas casualty should be discharged from the armed forces until he has received the maximum benefit of hospitalisation and convalescent facilities, which must include physical and psychological rehabilitation, vocational guidance, pre-vocational training and re-socialisation”.\n\nOne of the results of this was the application of a rehabilitation model by Dr Howard Rusk (cited in Blum & Fee, 2008), that was so successful that it was adopted by the military. Patients were not allowed to stay in bed, instead they were urged to get up and begin a re-conditioning program to develop residual capabilities. The flaw in the system was that while the goal was to make possible the integration of personnel with disabilities into society, the commitment ended at the hospital door. Once the doctors and therapists had done all they could, patients and families were on their own, and had to come to terms with society individually. Reisman (2016) argues that as the number of people with PTSD increases, there is still a need to develop a range of therapeutic approaches to help people living with PTSD, including complementary alternative medicine (CAM) in the community.\n\nIn recent years, there has been more research on how the microbiome, or gut health, influence overall health, including the brain. Wang et al. (2018), in a review of the literature on systemic inflammation and neuroinflammation, found that consuming foods that contain phytochemicals that can cross the blood brain barrier (BBB), has been shown to reduce oxidative damage in the brain. Similarly, Bandyopadhyay (2021), in a review of neurodegeneration in the brain, found that there are certain influences upon brain health that can improve neurofunction by improving the function of the BBB and associated pathways. Poor brain health due to poor nutrition can cause damage to nerve cells within the body and the central nervous system (CNS), and to the part of the brain that can produce more nerve cells, the hippocampus (Firth et al., 2020). This can lead to negative effects on memory, mood and overall cognitive functioning. Kerage et al. (2019) in a review of the literature on the interaction between neurotransmitters and lymphocytes, found that there is direct communication between the two in response to threat, demonstrating that the brain can influence, and can be influenced, by the immune system. An overactive immune system together with overactive or damaged nerve cells can therefore lead to long term inflammation within the brain. People who experience chronic stress such as PTSD, may experience these symptoms as a sign of poor brain health (McCarty & DiNicolantonio, 2016). This is caused by the brain becoming overexcited in response to stress hormones being produced in response to fear, and the oxidative stress damage caused by free radicals on the nerve cells (Wang et al., 2018). This is a natural response to stress via the vagus nerve which is part of the CNS, and the main communication channel between the brain and the other major organs in the body (LaChance & Ramsey, 2018). An overactive stress response, as can be experienced by people with PTSD can therefore lead to widespread inflammatory damage around the body and within the brain (Parker et al., 2020). Good brain health is therefore highly dependent upon good nutrition and the absorption of nutrients in the body that can cross the BBB, together with a reduction of exposure to stressful environments. Growing and eating nutritious food can therefore aid in developing awareness of the importance of good nutrition for both physical and mental health (Tanagra et al., 2013).\n\nA whole food diet that is rich in nutrients can improve mental health and wellbeing in many ways, including improving brain health, improving digestive health, increasing the absorption and transport of nutrients around the body and eliminating toxins quickly and effectively (Solovyev et al., 2021). Whole foods include food that has been grown naturally and retains their beneficial phytochemicals and nutrients, which are either not present or removed in processed or refined foods. LaChance & Ramsey (2018), in a systematic review of the literature on a nutrient profiling system for depression, found that people who were deficient in Omega 3, Zinc, Magnesium, B vitamins, Vitamin C and A, and Selenium and Potassium were more likely to experience mental health problems. Horticultural therapy offers the opportunity to grow fresh, nutrient-rich food, and to control the amount of chemicals added, while at the same time develop individual knowledge about nutrition (Tanagra et al., 2013). In addition, fresh, home-grown food will contain more nutrients than food that has spent a long time in transportation. The gut is where the human body processes the food it ingests, an activity which is dependent upon millions of “friendly” bacteria (Firth et al., 2020). Feeding the friendly bacteria in the gut with whole food will also enable it to function better, and filter out toxins or absorb more nutrients, which in turn can improve mood and brain health. Solovyev et al. (2021) found in a review of the effectiveness of neural barriers, that the gut microbiome is important in breaking down nutrients for transportation to the brain and to prevent toxins reaching the BBB, where they can cause further damage. The also brain requires a lot of energy and hydration from food to function properly, so it is dependent upon a healthy gut that can process food efficiently and transport nutrients to the brain (Bandyopadhyay, 2021). Most plant-based foods contain phytonutrients that are needed for a healthy nervous system and to remove toxins from the body (Firth et al., 2020). The brain also causes oxidative stress as it metabolises nutrients in nerve cells, which can cause inflammation if not removed quickly (Li et al., 2019). Anti-inflammatory and antioxidant foods that can be grown locally such as vegetables and fruit, are therefore essential for good brain health and can improve the functioning of the brain. The gut and the brain also produce the neurotransmitter serotonin, which in turn improves mood (Bandyopadhyay, 2021). This synergetic process of digestion, cell production and repair and resilience, is essential all around the body including the gut and the brain (Lin et al., 2019). As a consequence of improving nutrient intake, the body will be able to fight off infection, reduce inflammation, improve mood and functions of all the major organs in the body, including the brain. Horticultural therapy alongside nutrition education can therefore become a very effective, non-pharmaceutical psychosocial intervention for people living with PTSD.\n\nThis overview of the literature will inform the development of opportunities to take part in horticultural therapy with nutrition advice, for the well-being and rehabilitation of military veterans, reservists, emergency service personnel and their families in North Wales, UK (Firth et al., 2020). Instead of working in confined environments, the participants will be invited to join a small farm, Ty Gwalia, in the open countryside with gardens and greenhouses, and will aid in improving the re-integration and development of relationships through the execution of horticultural tasks, cooking together and other outdoor activities (Detweiler et al., 2015; Reisman, 2016). For those veterans making the transition to a civilian identity, the combination of directed physical work and the need to work as a team with others, provide a route back into civilian life and improve confidence, self-esteem and personalised wellbeing (Hall et al., 2020; Tanagra et al., 2013). In addition, providing nutrition advice will also improve outcomes in physical and mental wellbeing, and help veterans to reduce the effects of stress and physical health problems (Detweiler et al., 2015).\n\nThe Ty Gwalia project would aim to look at the problems encountered by people living with PTSD who have passed through the “hospital door”, and how a horticultural or land-based setting alleviates the problems encountered through involvement with new environmental and social situations (Wemrell et al., 2020). The project will be carried out by the registered UK charities Woody’s Lodge and Wintergreen UK - CIC. Both organisations offer complementary interventions, free of charge to local people with lived experience of PTSD including emergency workers, to support their recovery, and provide local mental health services. This has been found to have beneficial effects for people who want to personalise their recovery without needing further access to increased medical or other interventions (Cipriani et al., 2017).\n\n\nConclusions\n\nThis review has highlighted an awareness of the benefits of horticultural and nutritional therapy, as a therapeutic treatment for mental health and mental disorders. However, in traditional health practice, there still exists a persistence to align the health needs of military veterans with a medical model. The authors advocate a broader, holistic framework, evident within the suggested care pathway, that acknowledges personal health needs, relationships and social conditions, using a more integrative medical model that combines medical prescribing practices with psychological and psychoeducational practice.\n\nThis paper describes the use of holistic, non-medical interventions to improve the mental health and wellbeing of military veterans. A regional project has been identified that will support improved access to both psychological treatments and interventions addressing the wider determinants of mental health. The authors acknowledge the strength of the veteran identity and entrenched social identity assimilated through military service. Through the proposed use of veteran peer-support, the Ty Gwalia project will be coproduced in collaboration with local veteran voluntary organisations, as an empowering lead within the suggested therapeutic framework. Ty Gwalia has the potential to become fully integrated as a pathway for primary care and social prescribing practices, and will strengthen the links between healthcare providers and community, voluntary and statutory services. The project is of importance in seeking to meet what is likely to be an upsurge of mental health issues for military veterans as they deal with the visual reporting of the withdraw from Afghanistan.\n\nThis review acknowledges the role that medication has within a treatment plan, but advocates the use of psychosocial interventions to provide a further opportunity to respond effectively, and at an early stage, to symptoms of mental distress in people living with PTSD, as well as to initiate a more proactive approach to mental health promotion for military veterans. The proposed intervention of horticultural therapy with nutrition advice for military veterans will provide a gateway to community-based resources, improved access to psychological treatments, as well as to services and interventions addressing the wider determinants of mental health.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "References\n\nBandyopadhyay S: Role of Neuron and Glia in Alzheimer’s Disease and Associated Vascular Dysfunction. Front Aging Neurosci. 2021; 13: 653334. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlum N, Fee E: Howard A. Rusk (1901–1989) From Military Medicine to Comprehensive Rehabilitation. Am J Public Health. 2008; 98(2): 256–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBridger H: The Discovery of the Therapeutic Community. 1985. Last accessed 20th Oct 2011. Reference Source\n\nCipriani, J, Benz A, Holgren A, et al.: A Systematic Review of the Effects of Horticultural Therapy on Persons with Mental Health Conditions. Occupational Therapy in Mental Health. 2017; 33(1): 47–69. Publisher Full Text\n\nDetweiler MB, Self JA, Lane S, et al.: Horticultural therapy: A pilot study on modulating cortisol levels and indices of substance craving, posttraumatic stress disorder, depression, and quality of life in veterans. Altern Ther Health Med. 2015; 21(4): 36–41. PubMed Abstract\n\nFear NT, Jones M, Murphy D: What are the consequences of deployment to Iraq and Afghanistan on the mental health of the UK armed forces? A cohort study. Lancet. 2010; 375(9728): 1783–97. PubMed Abstract | Publisher Full Text\n\nFirth J, Gangwisch JE, Borisini A, et al.: Food and mood: how do diet and nutrition affect mental wellbeing? BMJ. 2020; 371: m4269. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHall KS, Morey CM, Beckham JC, et al.: Warrior Wellness: A Randomized Controlled Pilot Trial of the Effects of Exercise on Physical Function and Clinical Health Risk Factors in Older Military Veterans With PTSD. J Gerontol A Biol Sci Med Sci. 2020; 75(11): 2130–2138. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHelp for Heroes and King’s Centre for Military Health Research: Counting the Costs. King’s College London. 2015; 3–4. Reference Source\n\nHerringa RJ: Trauma, PTSD, and the Developing Brain. Curr Psychiatry Rep. 2017; 19(10): 69. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoge CW, Auchterlonie JL, Milliken CS: Mental health problems, use of mental health services, and attrition from military service after returning from deployment to Iraq or Afghanistan. JAMA. 2006; 295(9): 1023–1032. PubMed Abstract | Publisher Full Text\n\nHossain MM, Tasnim S, Sultana A, et al.: Epidemiology of mental health problems in COVID-19: a review [version 1; peer review: approved]. F1000Res. 2020; 9: 636. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIribarren J, Prolo P, Neagos N, et al.: Post-Traumatic Stress Disorder: Evidence-Based Research for the Third Millennium. Evid Based Complement Alternat Med. 2005; 2(4): 503–512. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKerage D, Sloan EK, Mattarollo SR, et al.: Interaction of neurotransmitters and neurochemicals with lymphocytes. J Neuroimmunol. 2019; 332: 99–111. PubMed Abstract | Publisher Full Text\n\nKessler RC, Sonnega A, Bromet E, et al.: Posttraumatic stress disorder in the National Comorbidity Survey. Arch Gen Psychiatry. 1995; 52(12): 1048–1060. PubMed Abstract | Publisher Full Text\n\nLaChance LR, Ramsey D: Antidepressant foods: An evidence-based nutrient profiling system for depression. World J Psychiatry. 2018; 8(3): 97–104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi X, Chu S, Liu Y, et al.: Neuroprotective Effects of Anthraquinones from Rhubarb in Central Nervous System Diseases. Evid Based Complement Alternat Med. 2019; 2019: 3790728. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLin S, Lee IH, Tsai HC, et al.: The association between plasma cholesterol and the effect of tryptophan depletion on heart rate variability. Kaohsiung J Med Sci. 2019; 35(7): 440–445. PubMed Abstract | Publisher Full Text\n\nMcCarty MF, DiNicolantonio JJ: Lauric acid-rich medium-chain triglycerides can substitute for other oils in cooking applications and may have limited pathogenicity. Open Heart. 2016; 3(2): e000467. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMottershead R: British Military Veterans and the Criminal Justice System in the United Kingdom: Situating the Self in Veteran Research. (Unpublished doctoral dissertation). University of Chester, Chester, UK. 2019. Reference Source\n\nPan X, Kaminga AC, Wen SW, et al.: Catecholamines in Post-traumatic Stress Disorder: A Systematic Review and Meta-Analysis. Front Mol Neurosci. 2018; 11: 450. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParker A, Fonseca S, Carding SR: Gut microbes and metabolites as modulators of blood-brain barrier integrity and brain health. Gut Microbes. 2020; 11(2): 135–157. PubMed Abstract | Publisher Full Text | Free Full Text\n\nReisman M: PTSD Treatment for Veterans: What’s Working, What’s New, and What’s Next. P T. 2016; 41(10): 623–634. PubMed Abstract | Free Full Text\n\nRytwinski NK, Scur MD, Feeny NC, et al.: The co-occurrence of major depressive disorder among individuals with posttraumatic stress disorder: a meta-analysis. J Trauma Stress. 2013; 26(3): 299–309. PubMed Abstract | Publisher Full Text\n\nSareen J: Posttraumatic stress disorder in adults: impact, comorbidity, risk factors, and treatment. Can J Psychiatry. 2014; 59(9): 460–467. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSolovyev N, Drobyshev E, Blume B, et al.: Selenium at the Neural Barriers: A Review. Front Neurosci. 2021; 15: 630016. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTanagra D, Panidis D, Tountas Y, et al.: Implementation of a worksite educational program focused on promoting healthy eating habits [version 2; peer review: 2 approved]. F1000Res. 2013; 2: 201. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang S: What's Work Got To Do With It? Policy Highlights. 2010; 1930–1970. Reference Source\n\nWang J, Song Y, Chen Z, et al.: Connection between Systemic Inflammation and Neuroinflammation Underlies Neuroprotective Mechanism of Several Phytochemicals in Neurodegenerative Diseases. Oxid Med Cell Longev. 2018; 2018: 1972714. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWemrell M, Olsson A, Landgren K: The Use of Complementary and Alternative Medicine (CAM) in Psychiatric Units in Sweden. Issues Ment Health Nurs. 2020; 41(10): 946–957. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "93381",
"date": "08 Sep 2021",
"name": "Alun Charles Jones",
"expertise": [
"Reviewer Expertise I am a qualified researcher and mental health specialist with experience of working with military personnel experiencing complex PTSD"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 asking me to review this paper. I have read the discussion with care and have the following comments to make:\nThis is a generally well-composed paper, which will be of interest to all healthcare practitioners working with trauma, regardless of the origins. The authors are both respected and experienced research academics and have both made long-standing contributions to the research literature and clinical practice for military veterans, experiencing mental and physical ill-health. The paper proposes an ecological or horticultural model of care that is respectful of dignity, non-pharmaceutical, outside of formal psychiatric treatment settings and so is likely to be effective in reducing stigma and shame - both self-to-self and other-to-self. It is an approach to care that is also likely to promote a sense of purpose and meaning to participants along with social inclusion, and so facilitate the safe transition from military to civilian life.\nMoreover, the method proposed, also reduces the likelihood of military personnel embarking on a psychiatric career pathway with the disadvantages that this would entail. I do, however, think the paper may have a greater impact with the inclusion of a brief discussion of any proposed selection criteria and possible ethical concerns regarding the recruitment of participants - along with some brief thoughts given over to complex PTSD. A paragraph or two would be sufficient and the authors can decide if they consider it appropriate and how best to structure this aspect of their discussion.\nThe paper will undoubtedly be followed up by others, at some future date, discussing the benefits gained by participants in the project and, if so, might usefully include those involved with the organisation of treatment and care.\nI wish both authors well with this and future work, which can only provide long-term benefits to the health and well-being of military personnel, their families, and friends.\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": "7476",
"date": "22 Nov 2021",
"name": "Dr. Richard Mottershead",
"role": "Author Response",
"response": "I would like to thank you Dr. Alun Jones for his insightful and supportive comments which both myself and my co-author have reviewed and assimilated. His considerable expertise as a researcher and mental health practitioner who supports military veterans has meant that the paper has benefited from his review and will guide our future research. In response to his guidance that - \"the paper may have a greater impact with the inclusion of a brief discussion of any proposed selection criteria and possible ethical concerns regarding the recruitment of participants - along with some brief thoughts given over to complex PTSD\". Once the co-author and myself progress to undertaking data collection within the next stage of our research on the experiences of participants utilisation of the charities supporting services then we will undoubtfully seek to include sections on recruitment and ethical concerns. Both myself and the co-author sincerely thank Dr. Alun Jones for his time and consideration of our work."
}
]
},
{
"id": "94279",
"date": "21 Sep 2021",
"name": "Andrew Williams",
"expertise": [
"Reviewer Expertise Social prescribing and ecotherpaies/green therapies linked to physical literacy and social integration. Insider knowledge of military service and the specific issues (including PTSD) facing military veterans."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAn interesting article that is highly topical given the emergence of alternative therapeutic modalities in recent years that is becoming focused under the umbrella term 'social prescribing'. Horticultural therapies are part of an emerging strand of social prescribing known as 'green prescribing' and this paper identifies military veterans with PTSD and continuing/debilitating psychological and mental health concerns as an identifiable study group who can benefit from this alternative approach. The paper is what I would call an 'advocacy paper' recognising the need for research to explore alternative approaches to supporting military veterans with PTSD that can be delivered using horticulture therapy and outlines a future intervention that has been put in place to provide empirical data to inform future 3rd sector and green prescribing commissioning.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
},
{
"id": "93600",
"date": "22 Sep 2021",
"name": "Nicholas G Procter",
"expertise": [
"Reviewer Expertise Trauma Responses and Trauma Informed Practice"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is great to see this paper. What I think is most helpful and beneficial is that as a discursive paper, the descriptive information takes the reader, in a scholarly way, through both the history and thought surrounding non-pharmacological ways of responding to PTSD. The level of detail is good and aligns with the descriptive information provided. The section on neurobiological processes including the interaction between neurotransmitters and lymphocytes is helpful. The work undertaken in nutritional mental health/ psychiatry is progressive in this regard. There is an important body of work helping us to pinpoint and understand the way in which the immune system is involved and implicated in threat detection and threat responses. The information presented is also current- right up to the recent troop withdrawal from Afghanistan.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-885
|
https://f1000research.com/articles/9-1386/v1
|
01 Dec 20
|
{
"type": "Study Protocol",
"title": "Using citation tracking for systematic literature searching - study protocol for a scoping review of methodological studies and an expert survey",
"authors": [
"Julian Hirt",
"Thomas Nordhausen",
"Christian Appenzeller-Herzog",
"Hannah Ewald",
"Julian Hirt",
"Thomas Nordhausen",
"Christian Appenzeller-Herzog"
],
"abstract": "Background: Up-to-date guidance on comprehensive study identification for systematic reviews is crucial. According to current recommendations, systematic searching should combine electronic database searching with supplementary search methods. One such supplementary search method is citation tracking. It aims at collecting directly and/or indirectly cited and citing references from \"seed references”. Tailored and evidence-guided recommendations concerning the use of citation tracking are strongly needed.\nObjective: We intend to develop recommendations for the use of citation tracking in health-related systematic literature searching. Our study will be guided by the following research questions: What are the benefits of citation tracking for health-related systematic literature searching? Which perspectives and experiences do experts in the field of literature retrieval methods have with regard to citation tracking in health-related systematic literature searching?\nMethods: Our study will have two parts: a scoping review and an expert survey. The scoping review aims at identifying methodological studies on benefits or problems of citation tracking in health-related systematic literature searching with no restrictions on study design, language, and publication date. We will perform database searching in MEDLINE, The Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science Core Collection, two information science databases, and free web searching. Two reviewers will independently assess full texts of selected abstracts. We will conduct direct backward and forward citation tracking on included articles. The results of the scoping review will inform our expert survey through which we aim to learn about experts΄ perspectives and experiences. We will narratively synthesize the results and derive recommendations for performing health-related systematic reviews.",
"keywords": [
"Citation Tracking",
"Literature Search",
"Supplementary Search",
"Methods",
"Scoping Review",
"Research Methodology",
"Survey",
"Systematic Review"
],
"content": "Introduction\n\nSystematic reviews are considered to be of high clinical and methodological importance as they help to derive recommendations for health care practice and future research1–3. A comprehensive literature search aiming to identify the available evidence as completely as possible is the foundation of every systematic review4–6. Due to an ever-growing research volume, lack of universal taxonomy and indexation, as well as extensive time requirements for identifying studies in a systematic way, effective search approaches are required5,7,8. According to current recommendations, systematic search approaches should include both electronic database searching and one or several supplementary search methods9. Potential supplementary search methods include citation tracking, contacting study authors or experts, handsearching, trial register searching, and web searching10. In this study, we focus on citation tracking.\n\nCitation tracking is an umbrella term for multiple methods which directly or indirectly collect related references from so called \"seed references\". These references are usually eligible for inclusion into the review and known at the start of the citation search10–12. In the workflow of a systematic review, seed references for citation tracking often are records derived from screening bibliographic database search results. The taxonomy used to describe the principles of citation tracking is non-uniform and heterogeneous13–16. Citation tracking methods are sub-categorized into direct and indirect citation tracking (Figure 1a). For direct citation tracking, the words \"backward\" and \"forward\" denote the directionality of tracking13,17,18. Backward citation tracking is the oldest form of citation tracking. It aims at identifying references cited by a seed reference - which can easily be achieved by checking the reference list. Terms like \"footnote chasing\" or \"reference list searching\" are synonyms6,13. In contrast, forward citation tracking or chaining aims at identifying citing references, i.e. references that cite a seed reference19. Indirect citation tracking describes the identification of (i) co-cited references or co-citations (i.e. other references cited by citing literature of a seed reference) and of (ii) co-citing references (i.e. references sharing references with a seed reference)11,20. Direct and indirect citation relationships of references based on a seed reference are illustrated in Figure 1b. Both direct and indirect citation tracking may contain one or more layers of iteration. To this end, researchers may use newly retrieved references as new seed references.\n\n1a: Hierarchical illustration of different citation tracking methods; 1b: Direct and indirect citation relationships of references based on a seed reference. A → B denotes A cites B.\n\nDirect backward citation tracking of cited references is currently the most common citation tracking method. However, recent guidance suggests that combining several citation tracking methods (e.g. screening cited, citing, co-cited and co-citing references) may be the most effective way to use citation tracking for systematic reviewing. It is quite possible that the added value of any form of citation tracking is not the same for all systematic reviews. It rather depends on a variety of factors. For instance, citation tracking may be especially beneficial in case of (i) complex searches (e.g. for reviews on public health topics), (ii) searching for health outcome measurement instruments, or (iii) research areas without consistent taxonomy, with vocabulary overlaps with other fields, or with a lack of index terms in databases (e.g. methodological topics)10,20,21. Hence, tailored and evidence-guided recommendations on the use of citation tracking are strongly needed. However, none of the current topical reviews has in fact systematically identified available evidence on the use and benefits of citation tracking in the context of systematic literature searching10.\n\nTherefore, the aim of our study is to develop recommendations for the use of citation tracking in health-related systematic literature searching and to identify research gaps. Our study will be guided by the following two research questions:\n\n- What are the benefits of citation tracking for health-related systematic literature searching?\n\n- Which perspectives and experiences do experts have with regard to citation tracking in health-related systematic literature searching?\n\n\nProtocol\n\nThis protocol is reported according to the “Preferred Reporting Items for Systematic review and Meta-Analysis Protocols” (PRISMA-P) checklist22. Details on the structure of our manuscript reporting related to PRISMA-P are provided elsewhere23. Our study will have two parts: a scoping review and an expert survey. The scoping review has the objective to map the benefits or problems of citation tracking or, if that is not sufficiently informative, possible gaps in related research. The objective of the expert survey is to identify the perspectives, experiences and perceptions of experts in the field of literature retrieval methods with regard to citation tracking. Together, the scoping review and expert survey will serve as a basis to derive implications and recommendations for current practice and future research24–26. For the scoping review, we will use the framework by Arksey and O’Malley26,27 and the “Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews” (PRISMA-ScR)28. Since an expert survey can be part of a scoping review, and the scoping review and the expert survey serve the same overall aim, we will follow methodological recommendations for scoping reviews25,26 and the “Strengthening The Reporting of Observational Studies in Epidemiology” (STROBE) statement29.\n\nEligibility criteria. We will include any study with a focus on citation tracking as a means of evidence retrieval method which exhibits one of the following criteria: benefits/problems and/or effectiveness of (i) citation tracking in general; (ii) different methods of citation tracking (e.g. backward vs. forward, direct vs. indirect); or (iii) technical uses of citation tracking (e.g. comparing platforms and/or tools, e.g. Scopus vs. Web of Science, Oyster, Voyster). Eligible studies need to have a health-related context. Studies without an explicitly specified research context are also eligible. There will be no restrictions on study design, language, and publication date.\n\nWe will exclude studies solely using citation tracking for evidence retrieval, e.g. a systematic review applying citation tracking as a supplementary search technique, or studies focussing on citation tracking as a means to explore network or citation impact (i.e. bibliometric analysis). Additionally, we will exclude methodological guidelines only mentioning or recommending citation tracking without describing or assessing it. Furthermore, we will exclude editorials, commentaries, letters and abstract-only publications. Table 1 illustrates our inclusion and exclusion criteria per domain.\n\nInformation sources. We will search MEDLINE via Ovid, CINAHL (Cumulative Index to Nursing and Allied Health Literature), LLISFT (Library Literature & Information Science Full Text), LISTA (Library, Information Science & Technology Abstracts) via EBSCO, and the Web of Science Core Collection using database-specific search strategies. Additionally, we will perform free web searching via Google Scholar as well as direct forward and backward citation tracking of included studies. For citation tracking, we will use Scopus, as this database seems to cover the largest number of relevant citations for the purpose of our review30. We will also contact librarians in the field of health sciences and information specialists through several mailing lists (e.g. Netzwerk Fachbibliotheken Gesundheit, Canadian Medical Libraries, Expertsearching, MEDBIB-L/German-speaking medical librarians, and EAHIL-list) to ask for further studies.\n\nSearch strategy. Due to a lack of adequate index terms, our search strategy will be based on textwords only. To determine frequently occurring terms for inclusion into the search strategy, we analysed keywords in the titles and abstracts of potentially relevant publications retrieved from preliminary searches and similar articles identified via PubMed by using a text mining approach31. We restricted parts of our textwords to the title field in order to avoid retrieving systematic reviews using citation tracking.\n\nAll authors contributed to the development of search strategies. HE and CAH are information specialists with a professional background in research; JH and TN are researchers experienced in the development of search strategies. HE drafted the search strategy. To uncover potential flaws, JH peer-checked the drafted search strategy and discussed it with HE.\n\nBox 1 shows the final search strategy for MEDLINE in Ovid syntax. To use the strategy in other databases, we will translate it by means of Polyglot Search Translator32. CAH will conduct the searches and eliminate duplicates using the Bramer method33. We will perform free web searching in Google Scholar using search terms from our database search.\n\n(reference list OR reference lists OR ((reference OR references OR citation OR citations OR co-citation OR co-citations) ADJ3 (search OR searches OR searching OR searched OR screen OR screening OR chain OR chains OR chaining OR check OR checking OR checked OR chased OR chasing OR tracking OR tracked OR harvesting OR tool OR tools OR backward OR forward)) OR ((cited OR citing OR cocited OR cociting OR co-cited OR co-citing) ADJ3 (references OR reference)) OR citation discovery tool OR cocitation OR co-citation OR cocitations OR co-citations OR co-cited OR backward chaining OR forward chaining OR snowball sampling OR snowballing OR footnote chasing OR berry picking OR cross references OR cross referencing OR cross-references OR cross-referencing OR citation activity OR citation activities OR citation analysis OR citation analyses OR citation network OR citation networks OR citation relationship OR citation relationships).ti OR (((((strategy OR strategies OR method* OR literature OR evidence OR additional OR complementary OR supplementary) ADJ3 (find OR finding OR search* OR retriev*)) OR (database ADJ2 combin*)).ti) AND ((search OR searches OR searching OR searched).ab))\n\nData management. A bibliography management tool (e.g. Citavi, EndNote) will be used to manage the number of reference retrievals throughout the study selection process. Furthermore, we will use specific tools for study selection that we describe below.\n\nSelection of sources of evidence. After an initial calibration phase (TN, JH, HE), two authors (JH, TN) will independently screen titles, abstracts, and full texts using Rayyan34. They will solve disagreements by third author arbitration (HE). To screen the results of the citation tracking step, we will consider ASReview, particularly if the number of references exceeds 1000. ASReview combines machine (deep) learning models on a set of eligible studies with active learning on manual selections during title-abstract screening to generate a relevancy-ranked abstract list and to save screening time. Should the tool prove to be beneficial for reducing the screening load, we will consider conducting a more sensitive database search at a later stage and screen additional results with ASReview.\n\nData charting process. We will pilot a standardised data extraction sheet approved by consensus among the authors. We will extract bibliographic and geographic data, design- and study-specific data as well as results. We aim for an iterative data extraction process, but in the final publication, we will provide a detailed overview of extracted data items. The first author (JH) will extract data and the second author (TN) will peer-check the extraction. We will solve disagreements by third author arbitration (HE).\n\nSynthesis of results. One author (JH) will narratively summarise study characteristics and results based on the data extraction. Depending on the results, we will also chart them graphically.\n\nSetting. The results of the scoping review will inform our online expert survey (see below). We intend to collect data from international experts in the field of literature retrieval methods. To design and develop the survey, we will use SosciSurvey35. The survey language will be English.\n\nRecruitment. Recruitment will be based on a triple approach. First, we will contact authors of pertinent articles identified during the literature search as well as experts from our professional networks. This \"person-based\" approach will help us to identify experts who authored papers, books, comments, and reviews in the field of citation tracking. We will ask the contacted persons to take part in the survey and to forward the invitation36. Second, we will identify and contact relevant national and international networks as well as systematic review collaborations using institutional contacts (e.g. Cochrane, Joanna Briggs Institute, Campbell Collaboration, Institute of Medicine, expert information specialists, and Evidence Synthesis International). We will also use mailing lists (e.g. Netzwerk Fachbibliotheken Gesundheit, Canadian Medical Libraries, Expertsearching, MEDBIB-L/German-speaking medical librarians, and EAHIL-list). This \"network-based approach\" will allow us to reach experts in the field of literature retrieval methods who are potentially using citation tracking without necessarily being the authors of methodological studies (yet). Third, we will announce the expert survey on our project page on ResearchGate, aiming to recruit further experts missed by our person- and network-based approaches. By using this triple approach, we intend to recruit between 60 and 150 participants. The authors of this study will not participate in the survey.\n\nData collection. We will iteratively develop the survey questions during the scoping review process based on our findings. Broadly speaking, our survey will contain questions on the use of citation tracking, preferred taxonomy, experiences with citation tracking, as well as recommendations for future practice and research. We will collect participantsʼ sociodemographic data, e.g. professional education and background, current field of work, years of experience in literature searching and citation tracking. We will schedule approximately five weeks for participation. Table 2 illustrates our reminder strategy to reach as many experts as possible.\n\nNote: Person-based approach: contacting national and international networks and systematic review collaborations using mailing lists.\n\nData analysis. To analyse the survey data, we will apply descriptive statistics based on frequencies, percentages, and cross tables. We will thematically categorise free text answers37.\n\nEthical concerns. The online expert survey will contain introductory information on our aims, the survey itself, data management and security. Since we do not expect vulnerability on the part of participants, we will not apply for ethical approval of the expert survey. Taking part in the survey will indicate consent to participate.\n\n\nDissemination of results\n\nOur dissemination strategy uses multiple ways to share our study results with academic stakeholders. The final review and expert survey will be published in an international open access journal relevant in the field of information retrieval. Additionally, we will discuss our results with experts at national and international conferences (e.g. conference of the German Network for Evidence-based Medicine (EbM-Netzwerk), conference of the European Association for Health Information and Libraries (EAHIL). To inform about our study results and publications, we will use Twitter, ResearchGate, and mailing lists from relevant stakeholders such as Netzwerk Fachbibliotheken Gesundheit, Canadian Medical Libraries, Expertsearching, MEDBIB-L/German-speaking medical librarians, and EAHIL-list.\n\n\nStudy status\n\nWe intend to start our search in November 2020 and expect to complete the study in April 2022.\n\nCurrent study status: preliminary searches: yes; piloting of the study selection process: yes; formal screening of search results against eligibility criteria: no; data extraction: no; data analysis: no.\n\n\nConclusions\n\nDepending on the available study landscape, missing pertinent evidence might have an impact on the validity of systematic reviews and, consequently, on the quality of clinical care38–41. Therefore, authors of systematic reviews should conduct high quality literature searches aiming to detect all relevant evidence. Citation tracking may be a good way to complement electronic database searches and to broaden the scope of possible findings. Therefore, our study intends to provide literature- and expert-based recommendations on the use of citation tracking for systematic literature searching. Specifically, we will provide guidance on; (i) situations in which citation tracking is likely to be particularly effective, (ii) situations in which a particular method of citation tracking is specifically indicated, and on (iii) technical/methodological aspects and pitfalls. We will also point out (iv) areas requiring more research in order to provide recommendations. It is possible that the recommendations developed during this project in a health-related context may prove relevant also for other academic fields such as social or environmental sciences9,42. Finally, tailored and evidence-based recommendations concerning the use of citation tracking for systematic literature searching may guide future steps in semi-automated and automated literature retrieval methods43,44.\n\n\nData availability\n\nNo underlying data are associated with this article.\n\nOpen Science Framework (OSF): PRISMA-P checklist for ‘Using citation tracking for systematic literature searching: study protocol for a scoping review of methodological studies and an expert survey’, https://doi.org/10.17605/OSF.IO/7ETYD23.\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\nIoannidis JPA: The Mass Production of Redundant, Misleading, and Conflicted Systematic Reviews and Meta-analyses. Milbank Q. 2016; 94(3): 485–514. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbbas Z, Raza S, Ejaz K: Systematic reviews and their role in evidence-informed health care. J Pak Med Assoc. 2008; 58(10): 561–67. PubMed Abstract\n\nGough D, Davies P, Jamtvedt G, et al.: Evidence Synthesis International (ESI): Position Statement. Syst Rev. 2020; 9(1): 155. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSutton A, Clowes M, Preston L, et al.: Meeting the review family: exploring review types and associated information retrieval requirements. Health Info Libr J. 2019; 36(3): 202–22. PubMed Abstract | Publisher Full Text\n\nGusenbauer M, Haddaway NR: Which academic search systems are suitable for systematic reviews or meta-analyses? Evaluating retrieval qualities of Google Scholar, PubMed, and 26 other resources. Res Synth Methods. 2020; 11(2): 181–217. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLefebvre C, Glanville J, Briscoe S, et al.: Searching for and selecting studies. In: Higgins JPT, Thomas J, eds. Cochrane Handbook for Systematic Reviews of Interventions: Version 6, 2nd edn. Hoboken: Wiley Online Library. 2019; 67–108. Publisher Full Text\n\nMcGowan J, Sampson M: Systematic reviews need systematic searchers. J Med Libr Assoc. 2005; 93(1): 74–80. PubMed Abstract | Free Full Text\n\nde Souza Leão L, Eyal G: The rise of randomized controlled trials (RCTs) in international development in historical perspective. Theor Soc. 2019; 48(3): 383–418. Publisher Full Text\n\nCooper C, Booth A, Varley-Campbell J, et al.: Defining the process to literature searching in systematic reviews: a literature review of guidance and supporting studies. BMC Med Res Methodol. 2018; 18(1): 85. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCooper C, Booth A, Britten N, et al.: A comparison of results of empirical studies of supplementary search techniques and recommendations in review methodology handbooks: a methodological review. Syst Rev. 2017; 6(1): 234. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBelter CW: Citation analysis as a literature search method for systematic reviews. Journal of the Association for Information Science and Technology. 2016; 67(11): 2766–77. Publisher Full Text\n\nHu X, Rousseau R, Chen J: On the definition of forward and backward citation generations. Journal of Informetrics. 2011; 5(1): 27–36. Publisher Full Text\n\nBooth A: Unpacking your literature search toolbox: on search styles and tactics. Health Info Libr J. 2008; 25(4): 313–17. PubMed Abstract | Publisher Full Text\n\nSaimbert MK, Fowler SA, Pierce J, et al.: Search Resources and Techniques to Maximize Search Efforts. In: Holly C, Salmond SW, Saimbert MK, eds. Comprehensive Systematic Review for Advanced Nursing Practice. New York: Springer Publishing Company 2016; 139–72.\n\nChoong MK, Tsafnat G: Role of citation tracking in updating of systematic reviews. AMIA Jt Summits Transl Sci Proc. 2014; 2014: 18. PubMed Abstract | Free Full Text\n\nLowe J, Peters J, Shields B, et al.: Methods to update systematic literature searches: full update searching vs. forward citation chasing: A case study from a systematic review of diagnostic test accuracy. Exeter o J. Reference Source\n\nBooth A: Innovative approaches to systematic reviewing. In: Levay P, Craven J, eds. Systematic Searching: Practical ideas for improving results. London: Facet Publishing. 2019; 25–50.\n\nLefebvre C, Glanville J, Briscoe S, et al.: Chapter 4: Searching for and selecting studies. Draft version (13 September 2018) 2018. Reference Source\n\nCribbin T: Augmenting Citation Chain Aggregation with Article Maps. CEUR Workshop Proceedings. 2014; 1311, (accessed 18 Aug 2020). Reference Source\n\nJanssens ACJW, Gwinn M: Novel citation-based search method for scientific literature: application to meta-analyses. BMC Med Res Methodol. 2015; 15: 84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLinder SK, Kamath GR, Pratt GF, et al.: Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments. J Clin Epidemiol. 2015; 68(4): 412–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShamseer L, Moher D, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015: elaboration and explanation. BMJ. 2015; 350: g7647. PubMed Abstract | Publisher Full Text\n\nHirt J: Using citation tracking for systematic literature searching (supplementary material). 2020,. http://www.doi.org/10.17605/OSF.IO/7ETYD\n\nRuiz-Perez I, Petrova D: Scoping reviews. Another way of literature review. Med Clin (Barc). 2019; 153(4): 165–68. PubMed Abstract | Publisher Full Text\n\nLevac D, Colquhoun H, O'Brien KK: Scoping studies: advancing the methodology. Implement Sci. 2010; 5: 69. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArksey H, O'Malley L: Scoping studies: towards a methodological framework. Int J Soc. 2005; 8(1): 19–32. Publisher Full Text\n\nMunn Z, Peters MDJ, Stern C, et al.: Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Med Res Methodol. 2018; 18(1): 143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA Extension for Scoping Reviews (PRISMA-ScR): Checklist and Explanation. Ann Intern Med. 2018; 169(7): 467–73. PubMed Abstract | Publisher Full Text\n\nvon Elm E, Altman DG, Egger M, et al.: Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. BMJ. 2007; 335(7624): 806–08. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi J, Burnham JF, Lemley T, et al.: Citation analysis: Comparison of Web of Science®, Scopus™, SciFinder®, and Google Scholar. J Med Libr Assoc. 2010; 7(3): 196–217. Publisher Full Text\n\nGlanville J: Text mining for information specialists. Levay P Craven J eds. Systematic Searching: Practical ideas for improving results. London: Facet Publishing, 2019: 147–70. Reference Source\n\nClark JM, Sanders S, Carter M, et al.: Improving the translation of search strategies using the Polyglot Search Translator: a randomized controlled trial. JMLA. 2020; 108(2): 195–207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBramer WM, Giustini D, de Jonge GB, et al.: De-duplication of database search results for systematic reviews in EndNote. J Med Libr Assoc. 2016; 104(3): 240–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan-a web and mobile app for systematic reviews. Syst Rev. 2016; 5: 210. Reference Source\n\nSoSci Survey GmbH: SoSci Survey 2020. Accessed August 14, 2020. Reference Source\n\nCooper C, Garside R, Varley-Campbell J, et al.: \"it has no meaning to me\". How do researchers understand the effectiveness of literature searches? A qualitative analysis and preliminary typology of understandings. Res Syn Meth. 2020; 11(5): 627–640. Publisher Full Text\n\nSaldaña J: The Coding Manual for Qualitative Researchers, 2nd edn. London: SAGE Publications, 2013. Reference Source\n\nSampson M, McGowan J: Errors in search strategies were identified by type and frequency. J Clin Epidemiol. 2006; 59(10): 1057–1063. PubMed Abstract | Publisher Full Text\n\nSalvador-Oliván JA, Marco-Cuenca G, Arquero-Avilés R: Errors in search strategies used in systematic reviews and their effects on information retrieval. J Med Libr Assoc. 2019; 107(2): 210–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNussbaumer-Streit B, Klerings I, Wagner G, et al.: Abbreviated literature searches were viable alternatives to comprehensive searches: a meta-epidemiological study. J Clin Epidemiol. 2018; 102: 1–11. PubMed Abstract | Publisher Full Text\n\nEwald H, Klerings I, Wagner G, et al.: Abbreviated and comprehensive literature searches led to identical or very similar effect estimates: meta-epidemiological study. J Clin Epidemiol. 2020; 128: 1–12. PubMed Abstract | Publisher Full Text\n\nJames KL, Randall NP, Haddaway NR: A methodology for systematic mapping in environmental sciences. Environ Evid. 2016; 5: 7. Publisher Full Text\n\nO'Connor AM, Glasziou P, Taylor M, et al.: A focus on cross-purpose tools, automated recognition of study design in multiple disciplines, and evaluation of automation tools: a summary of significant discussions at the fourth meeting of the International Collaboration for Automation of Systematic Reviews (ICASR). Syst Rev. 2020; 9(1): 100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKohl C, McIntosh EJ, Unger S, et al.: Online tools supporting the conduct and reporting of systematic reviews and systematic maps: A case study on CADIMA and review of existing tools. Environ Evid. 2018; 7(1): 2420. Publisher Full Text"
}
|
[
{
"id": "76282",
"date": "05 Jan 2021",
"name": "Julie Glanville",
"expertise": [
"Reviewer Expertise Information retrieval for evidence identification for systematic reviews."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 to conduct a scoping review of the use of citation tracking techniques to identify research evidence to inform systematic reviews and also to survey experts on their use of citation tracking.\n\nMy suggestions for action on the proposal are as follows:\nIntroduction: 'These references are usually eligible for inclusion into the review and known at the start of the citation search10–12.' I think this could be reworded for clarity along the following lines: 'These references are usually eligible for inclusion into the review and some may be known at the beginning of the review and others may emerge as eligible records following the main database searches10–12.' Then perhaps you may not need the sentence that follows the one I am commenting on.\n\nIntroduction: 'The taxonomy used to describe the…'. I think it might be better to use a word such as 'terminology' rather than 'taxonomy'.\n\nFigure 1. The figure would be more helpful if it could show the relationships of the indirect citation tracking in the Figure 1b perhaps by colour coding. Please check diagrams in the following references which incorporate chronology into the citation picture as well as showing the indirect citation tracking clearly. Belter CW. A relevance ranking method for citation-based search results. Scientometrics. 2017;112(2):731-46.1 Janssens A, Gwinn M, Brockman JE, Powell K, Goodman M. Novel citation-based search method for scientific literature: a validation study. BMC Med Res Methodol. 2020;20(1):25.2\n\nIntroduction: 'However, recent guidance suggests that combining several citation tracking methods (e.g. screening cited, citing, co-cited and co-citing references) may be the most effective way to use citation tracking for systematic reviewing. ' Please cite the guidance.\n\nIntroduction: ' It rather depends on a variety of factors. For instance, citation tracking may be especially beneficial in case of (i) complex searches (e.g. for reviews on public health topics), (ii) searching for health outcome measurement instruments, or (iii) research areas without consistent taxonomy, with vocabulary overlaps with other fields, or with a lack of index terms in databases (e.g. methodological topics)'. These are all important issues and each deserves a bit more description so that readers can understand the differences. Again I think the word 'taxonomy' should be replaced with 'terminology'.\n\nIntroduction: current 'topical reviews' - suggest replacing with 'recent reviews on this topic'. Then please add in more citations so that 'reviews' can be supported with more than one reference.\n\nIntroduction: 'health-related systematic literature searching'. This occurs three times and for each occurrence I suggest rewording as follows for clarity: 'literature searching for systematic reviews of health and health-related topics'.\n\nEligibility criteria. 'evidence retrieval method'. Suggest that 'method' is not needed as the sentence has 'means'.\n\n'Eligible studies need to have a health-related context. Studies without an explicitly specified research context are also eligible. ' This seems contradictory. Why are studies in education topics for example not useful if they are looking at the methods rather than the topic? Just including papers where the topic is not clear seems arbitrary when there may be much to learn from a paper even if it has an engineering topic, say. Perhaps reword along the lines of 'although studies undertaken in the context of health-related topics are the main focus, studies of citation tracking in other literatures will also be eligible where the focus is on exploring the methods rather than the subject topic'.\n\nTable 1. Publication Type cannot be 'Any' when there are publication types listed as ineligible. The authors should list eligible study types or use some sort of exception wording.\n\nInformation sources. I am not sure 'free web searching via Google Scholar' is a helpful description, perhaps just say 'searches of Google Scholar' here and further down where it is mentioned again.\n\n'For citation tracking, we will use Scopus, as this database seems to cover the largest number of relevant citations for the purpose of our review30. ' There is quite a lot of research that reports that other resources such as Google Scholar or Microsoft Academic provide wider coverage - the authors may wish to consider searching some of the free resources as well (since Scopus alone is not going to find the largest number of results) or finding other reasons for the use of a Scopus only approach.\n\n'MEDBIB-L' - I think there may be a typo here and it is MEDLIB-L? I think it may also need to be corrected in the Dissemination section.\n\nMy understanding of the purpose of a protocol is that it should list what will happen and therefore the resources to be searched should be listed and there should be no examples which imply that other things may be added. So there should be no' e.g.'.\n\n'text mining approach' - the chapter describes many approaches - which one was used in this case?\n\n'parts of our textwords' - suggest 'some of our textwords'?\n\nBox 1 - there is harmless redundancy in the search. For example co-citation is searched alone and in combination with other terms - it only needs to be searched alone.\n\nBox 1 - with the focus on searching in the titles, the use of such close adjacency does not seem warranted - it would be more sensitive to use AND for title searching.\n\nBox 1 - it might be helpful in the absence of subject headings and the focus on searching mainly in titles to also search the author keywords field.\n\nData charting process: I realise it is difficult to know what will happen but the authors description is not very clear about their plans 'We aim for an iterative data extraction process, but in the final publication, we will provide a detailed overview of extracted data items.' What is an 'iterative data extraction process' - what might it look like and what does it involve?\n\nData collection 'preferred taxonomy' - again, I suggest the word you mean is 'terminology' not 'taxonomy'.\n\nData analysis. 'To analyse the survey data, we will apply descriptive statistics based on frequencies, percentages, and cross tables.' I think it may be 'cross tabulations' rather than 'cross tables'?\n\nDissemination of results - it might be useful to also to try to present results at conferences of systematic review experts - Cochrane Colloquium and the Health Technology Assessment International (HTAi) conferences. These organisations also have active information retrieval special interest groups.\n\nConclusions: 'Depending on the available study landscape' - this seems rather vague to me - it would help the reader if the authors could be more explicit about what they mean.\n\n'consequently, on the quality of clinical care' - I think it might not only be clinical care that could be impacted - it might be any aspect of health care depending on what is being reviewed e.g. a service, a policy, a new method of organising staff etc.\n\n'in a health-related context may prove relevant also for other academic fields such as social or environmental sciences' - I think that much of what you find may be generalisable to other disciplines, so I suggest that you state this earlier as a possibility.\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": "6897",
"date": "04 Aug 2021",
"name": "Julian Hirt",
"role": "Author Response",
"response": "Dear Julie Glanville We are grateful for your reviewer report and, in particular, for your helpful suggestions for improvement of our scoping review protocol. Below, we provide a detailed point-by-point response with changes that we implemented in version 2 of our manuscript. Please note that in response to the comments by reviewer 2 (David Moher), we replaced the planned survey with a planned Delphi study to address the original objective. This change also entails the reformulation of our research questions and the intent to publish the final scoping review and the results of the Delphi study separately. We hope our revisions now fully meet your concerns. Sincerely yours, Julian Hirt, Thomas Nordhausen, Christian Appenzeller-Herzog, and Hannah Ewald Reviewer comment: Introduction: 'These references are usually eligible for inclusion into the review and known at the start of the citation search10–12.' I think this could be reworded for clarity along the following lines: 'These references are usually eligible for inclusion into the review and some may be known at the beginning of the review and others may emerge as eligible records following the main database searches10–12.' Then perhaps you may not need the sentence that follows the one I am commenting on. Authors’ response: We adapted this sentence and the subsequent one according to your suggestion. Reviewer comment: Introduction: 'The taxonomy used to describe the…'. I think it might be better to use a word such as 'terminology' rather than 'taxonomy'. Authors’ response: Thank you. We now use terminology instead of taxonomy throughout the manuscript. Reviewer comment: Figure 1. The figure would be more helpful if it could show the relationships of the indirect citation tracking in the Figure 1b perhaps by colour coding. Please check diagrams in the following references which incorporate chronology into the citation picture as well as showing the indirect citation tracking clearly. Belter CW. A relevance ranking method for citation-based search results. Scientometrics. 2017;112(2):731-46.1 Janssens A, Gwinn M, Brockman JE, Powell K, Goodman M. Novel citation-based search method for scientific literature: a validation study. BMC Med Res Methodol. 2020;20(1):25.2 Authors’ response: We have colour coded the 4 citation tracking techniques as suggested. We had already consulted the citation tracking figures of Belter et al. and Janssens. et al. amongst others. Furthermore, we have added text to the figure caption. We feel that our figure is now clearer with respect to chronology. Reviewer comment: Introduction: 'However, recent guidance suggests that combining several citation tracking methods (e.g. screening cited, citing, co-cited and co-citing references) may be the most effective way to use citation tracking for systematic reviewing.' Please cite the guidance. Authors’ response: We added a reference. Reviewer comment: Introduction: ' It rather depends on a variety of factors. For instance, citation tracking may be especially beneficial in case of (i) complex searches (e.g. for reviews on public health topics), (ii) searching for health outcome measurement instruments, or (iii) research areas without consistent taxonomy, with vocabulary overlaps with other fields, or with a lack of index terms in databases (e.g. methodological topics)'. These are all important issues and each deserves a bit more description so that readers can understand the differences. Again I think the word 'taxonomy' should be replaced with 'terminology'. Authors’ response: Thank you for this point! We have revised and elaborated this section. Reviewer comment: Introduction: current 'topical reviews' - suggest replacing with 'recent reviews on this topic'. Then please add in more citations so that 'reviews' can be supported with more than one reference. Authors’ response: We adapted the sentence according to your suggestion, thank you. Reviewer comment: Introduction: 'health-related systematic literature searching'. This occurs three times and for each occurrence I suggest rewording as follows for clarity: 'literature searching for systematic reviews of health and health-related topics'. Authors’ response: Thank you for your proposition. We now use “systematic literature searching for health-related topics“. Reviewer comment: Eligibility criteria. 'evidence retrieval method'. Suggest that 'method' is not needed as the sentence has 'means'. Authors’ response: We deleted the word ‘method’. Reviewer comment: 'Eligible studies need to have a health-related context. Studies without an explicitly specified research context are also eligible.' This seems contradictory. Why are studies in education topics for example not useful if they are looking at the methods rather than the topic? Just including papers where the topic is not clear seems arbitrary when there may be much to learn from a paper even if it has an engineering topic, say. Perhaps reword along the lines of 'although studies undertaken in the context of health-related topics are the main focus, studies of citation tracking in other literatures will also be eligible where the focus is on exploring the methods rather than the subject topic'. Authors’ response: We agree that it is interesting to learn about citation tracking from other disciplines. However, we have decided to focus on studies in a health-related context because this enables us to (i) consider the context in which the studies were conducted and to (ii) specifically direct our conclusions and recommendations to the health context. Furthermore, we concentrate on health-related studies for practical reasons facing the high number of references that need screening. We deleted the sentence ‘Studies without an explicitly specified research context are also eligible’ to avoid misunderstandings. On that note we also improved our exclusion criteria by adding this criterion: ‘any study only assessing the benefit of combined search methods (whereas the isolated benefit of citation tracking cannot be extracted)’. Reviewer comment: Table 1. Publication Type cannot be 'Any' when there are publication types listed as ineligible. The authors should list eligible study types or use some sort of exception wording. Authors’ response: We now use ‘Any reports of empirical studies’. Reviewer comment: Information sources. I am not sure 'free web searching via Google Scholar' is a helpful description, perhaps just say 'searches of Google Scholar' here and further down where it is mentioned again. Authors’ response: We now use ‘web searching’ instead of ‘free web searching’ throughout the manuscript. Reviewer comment: 'For citation tracking, we will use Scopus, as this database seems to cover the largest number of relevant citations for the purpose of our review30.' There is quite a lot of research that reports that other resources such as Google Scholar or Microsoft Academic provide wider coverage - the authors may wish to consider searching some of the free resources as well (since Scopus alone is not going to find the largest number of results) or finding other reasons for the use of a Scopus only approach. Authors’ response: We agree and now plan forward citation tracking using a triple approach: Scopus, Web of Science, and Google Scholar. We will iteratively repeat citation tracking on newly identified records to include until no further eligible references will be identified. We now describe this new approach in the methods. Reviewer comment: 'MEDBIB-L' - I think there may be a typo here and it is MEDLIB-L? I think it may also need to be corrected in the Dissemination section. Authors’ response: The correct name is MEDIBIB-L (the “I” was missing), a mailing list specific to libraries of medicine in the German-speaking area (library = Bibliothek; https://lists.uni-due.de/mailman/listinfo/medbib-l). Reviewer comment: My understanding of the purpose of a protocol is that it should list what will happen and therefore the resources to be searched should be listed and there should be no examples which imply that other things may be added. So there should be no' e.g.'. Authors’ response: We deleted ‘e.g.’ Reviewer comment: 'text mining approach' - the chapter describes many approaches - which one was used in this case? Authors’ response: We used several tools that were used to improve our search. We now list all the tools that we used during search drafting phase in our manuscript and here: PubMed PubReMiner: https://hgserver2.amc.nl/cgi-bin/miner/miner2.cgi AntConc 3.5.7 (Windows), developed by Laurence Anthony, Faculty of Science and Engineering, Waseda University, Japan Yale MeSH Analyzer: http://mesh.med.yale.edu/ TerMine: http://www.nactem.ac.uk/software/termine/ Text Analyzer: https://www.online-utility.org/text/analyzer.jsp Voyant: https://voyant-tools.org/ VOSviewer: https://www.vosviewer.comrt Reviewer comment: 'parts of our textwords' - suggest 'some of our textwords'? Authors’ response: We agree, thank you. Reviewer comment: Box 1 - there is harmless redundancy in the search. For example co-citation is searched alone and in combination with other terms - it only needs to be searched alone. Authors’ response: Yes, these are remnants of a previously more specific search and indeed now redundant. Since we already ran the searches by now, we would prefer to leave the search string exactly as we ran it for precise documentation. However, we noted this in our search files in case of a later update. Reviewer comment: Box 1 - with the focus on searching in the titles, the use of such close adjacency does not seem warranted - it would be more sensitive to use AND for title searching. Authors’ response: Again, this is very good input which we noted in our search files in case of a later update. Unfortunately, we already ran the searches by now and are done screening. We are, however, confident that any article that we missed due to the close adjacency will be retrieved through our extensive citation tracking, web searches or expert contacting. Reviewer comment: Box 1 - it might be helpful in the absence of subject headings and the focus on searching mainly in titles to also search the author keywords field. Authors’ response: Thank you for the sensible suggestion which we also noted in our search files in case of a later update. Reviewer comment: Data charting process: I realise it is difficult to know what will happen but the authors description is not very clear about their plans 'We aim for an iterative data extraction process, but in the final publication, we will provide a detailed overview of extracted data items.' What is an 'iterative data extraction process' - what might it look like and what does it involve? Authors’ response: We revised this paragraph and provide more details: ‘Since we expect heterogeneous studies in terms of aim, design, and methods, we aim for an iterative data extraction process. This allows a flexible and study-specific data extraction process, e.g. by adding previously neglected data extraction items that might contribute to the overall body of knowledge to the data extraction form.’ Reviewer comment: Data collection 'preferred taxonomy' - again, I suggest the word you mean is 'terminology' not 'taxonomy'. Authors’ response: Indeed, thank you. Reviewer comment: Data analysis. 'To analyse the survey data, we will apply descriptive statistics based on frequencies, percentages, and cross tables.' I think it may be 'cross tabulations' rather than 'cross tables'? Authors’ response: We revised this paragraph to address a suitable type of analysis for our data retrieved in Delphi rounds. For free text answers and statements of experts, we will use thematic categorisation. For votes whose results are available or can be converted into numbers, we will use descriptive statistics. Reviewer comment: Dissemination of results - it might be useful to also to try to present results at conferences of systematic review experts - Cochrane Colloquium and the Health Technology Assessment International (HTAi) conferences. These organisations also have active information retrieval special interest groups. Authors’ response: Thank you, we added these conferences to our list of potential conferences. Reviewer comment: Conclusions: 'Depending on the available study landscape' - this seems rather vague to me - it would help the reader if the authors could be more explicit about what they mean. Authors’ response: We deleted ‘Depending on the available study landscape’ to be more precise. Reviewer comment: 'consequently, on the quality of clinical care' - I think it might not only be clinical care that could be impacted - it might be any aspect of health care depending on what is being reviewed e.g. a service, a policy, a new method of organising staff etc. Authors’ response: We agree and revised the sentence to ‘health care’ instead of ‘clinical care’. Reviewer comment: 'in a health-related context may prove relevant also for other academic fields such as social or environmental sciences' - I think that much of what you find may be generalisable to other disciplines, so I suggest that you state this earlier as a possibility. Authors’ response: We agree that our results may indeed prove relevant to other disciplines. However, we decided to narrow our research efforts to the health-related fields, so we think this should be rather a part of the discussion/outlook than earlier in the manuscript. We changed the sentence to underline that aspect: “Although we solely focus on a health-related context, it is possible that some of the recommendations developed during this project may prove relevant also for other academic fields such as social or environmental sciences”."
}
]
},
{
"id": "81307",
"date": "07 Apr 2021",
"name": "David Moher",
"expertise": [
"Reviewer Expertise Systematic reviews",
"open science",
"reporting guidelines."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 a new guidance on citation tracking. They will achieve this by completing a scoping review and subsequently a survey. The authors propose using appropriate methods (and reporting) for conducting the scoping review. I found the methods for the survey less clear and hope my comments/questions, below, are helpful in revised the protocol.\nQuestions/comments:\nA more conceptual question is to what degree this initiative overlaps and differs from PRISMA-S (Rethlefsen ML, Kirtley S, Waffenschmidt S, Ayala AP, Moher D, Page MJ, Koffel JB; PRISMA-S Group. PRISMA-S: an extension to the PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Syst Rev. 2021 Jan 26;10(1):39. doi: 10.1186/s13643-020-01542-z)1.\n\nFor example, item 5 of PRIMSA-S – Citation searching - states “Citation searching 5 Indicate whether cited references or citing references were examined, and describe any methods used for locating cited/citing references (e.g., browsing reference lists, using a citation index, setting up email alerts for references citing included studies).” I think this is important so as not to potentially confuse readers. Indeed, should the current initiative be seen as an implementation of PRISMA-S?\n\nI had more difficulty understanding the proposed survey. For me, much of the methods were missing. I understand the recruitment (well reported). I would recommend the authors include the PRISMA-S group unless there is a lot of overlap between PRISMA-S and the other groups mentioned.\n\nIt was not clear to me how long the authors will make completing the survey– 15 minutes of 45 minutes? Similarly, will the respondents receive an incentive for completing the survey?\n\nWhy ‘simply’ a survey rather than a Delphi (or modified) approach? Will the survey (or Delphi) be pilot tested for question and response option clarity and language?\n\nThe data analysis describes cross tables. I assume the authors mean cross tabulations which can be more than descriptive. Will the authors be conducting Chi-square analysis or other analytical approaches of the cross tabulations (e.g., p values)?\n\nThe ethical concerns section is likely jurisdiction specific. In my setting ethics would be required. Can the authors explicitly indicate whether ethics is required or not. The section is currently vague on this critical issue.\n\nFor the survey, do the authors have an estimated sample size they are aiming for. Similarly, do the authors have an estimated response rate they are aiming for?\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": "6898",
"date": "04 Aug 2021",
"name": "Julian Hirt",
"role": "Author Response",
"response": "Dear David Moher We are grateful for your reviewer report and, in particular, for your helpful suggestions to derive evidence-based recommendations from our study. Below, we provide a detailed point-by-point response with changes that we implemented in version 2 of our manuscript. You will see that in response to your comments, we replaced the planned survey with a planned Delphi study to address the original objective. This change also entails the reformulation of our research questions and the intent to publish the final scoping review and the results of the Delphi study separately. We hope that these changes fully meet your concerns. Sincerely yours, Julian Hirt, Thomas Nordhausen, Christian Appenzeller-Herzog, and Hannah Ewald Reviewer comment: A more conceptual question is to what degree this initiative overlaps and differs from PRISMA-S (Rethlefsen ML, Kirtley S, Waffenschmidt S, Ayala AP, Moher D, Page MJ, Koffel JB; PRISMA-S Group. PRISMA-S: an extension to the PRISMA Statement for Reporting Literature Searches in Systematic Reviews. Syst Rev. 2021 Jan 26;10(1):39. doi: 10.1186/s13643-020-01542-z). Authors’ response: PRISMA-S is a reporting guideline for systematic literature searches. However, it is lacking on precise recommendations how to report citation tracking methods and results. By conducting a Delphi study with selected experts in the field (see our answer below for details), we aim at developing more detailed recommendations on adequately reporting citation tracking methods as part of systematic literature searching. This may complement recommendations on reporting given by the PRISMA-S group or could even be integrated in future versions. For the Delphi, we will invite the PRISMA-S group to best use synergies and experiences. Reviewer comment: For example, item 5 of PRIMSA-S – Citation searching - states “Citation searching 5 Indicate whether cited references or citing references were examined, and describe any methods used for locating cited/citing references (e.g., browsing reference lists, using a citation index, setting up email alerts for references citing included studies).” I think this is important so as not to potentially confuse readers. Indeed, should the current initiative be seen as an implementation of PRISMA-S? Authors’ response: See answer above. An important detail for the reporting of our study: since we will use citation tracking as part of our information retrieval, we will use PRISMA-S to guide our reporting of the scoping review. In the revised version, we reference it accordingly: “We will document our search strategy according to PRISMA-S”. Reviewer comment: I had more difficulty understanding the proposed survey. For me, much of the methods were missing. I understand the recruitment (well reported). I would recommend the authors include the PRISMA-S group unless there is a lot of overlap between PRISMA-S and the other groups mentioned. Authors’ response: As detailed further below, the survey will be replaced by a Delphi study. So, we replaced the survey methods with more detailed methods for the Delphi study. Concerning PRISMA-S, we agree with the reviewer and will ask the PRISMA-S working group to participate in our Delphi study (see below). Reviewer comment: It was not clear to me how long the authors will make completing the survey– 15 minutes of 45 minutes? Similarly, will the respondents receive an incentive for completing the survey? Authors’ response: Following your recommendation below, we now plan to conduct an expert Delphi study containing multiple Delphi rounds. We expect that experts will invest around 30 to 90 minutes per Delphi round depending on the underpinning aim of the Delphi round as well as experts’ familiarity and experiences with the topic. Participants will not receive an incentive for participation. Reviewer comment: Why ‘simply’ a survey rather than a Delphi (or modified) approach? Will the survey (or Delphi) be pilot tested for question and response option clarity and language? Authors’ response: This is an important point and we thank the reviewer for raising it. We agree that a Delphi study containing several Delphi rounds is suitable to collect the perspectives of international experts on citation tracking, promote discussions on the topic as well as to derive consensus recommendations for future practice and research on the use of citation tracking in systematic literature searching for health-related topics. We subjected our protocol to a major revision based on this point and now outline the methods for the Delphi. As stated in the revised text, we will pilot test and discuss our Delphi items with a person experienced in literature searching but who is not an author and not involved in the Delphi study. Reviewer comment: The data analysis describes cross tables. I assume the authors mean cross tabulations which can be more than descriptive. Will the authors be conducting Chi-square analysis or other analytical approaches of the cross tabulations (e.g., p values)? Authors’ response: We revised the corresponding section to address a suitable type of analysis for our data retrieved in Delphi rounds. For free text answers and statements of experts, we will use thematic categorisation. For votes whose results are available or can be converted into numbers, we will use descriptive statistics. Reviewer comment: The ethical concerns section is likely jurisdiction specific. In my setting ethics would be required. Can the authors explicitly indicate whether ethics is required or not. The section is currently vague on this critical issue. Authors’ response: We added details to the ethical concerns section. With regard to the Swiss Human Research Act, our research does not concern human diseases and the structure and function of the human body. We will therefore not apply for ethical approval of the expert Delphi study. Reviewer comment: For the survey, do the authors have an estimated sample size they are aiming for. Similarly, do the authors have an estimated response rate they are aiming for? Authors’ response: This answer concerns the recruitment of experts for the Delphi study, not the survey. We intend to recruit at least 15 participants by using our stepwise approach for recruitment, the person-based approach (contacting authors of pertinent articles identified during the literature search as well as experts from authors’ professional networks) and the organisation-based approach (contacting national and international organisations and systematic review collaborations)."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1386
|
https://f1000research.com/articles/10-286/v1
|
13 Apr 21
|
{
"type": "Research Article",
"title": "A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes",
"authors": [
"Granger Sutton",
"Gary B. Fogel",
"Bradley Abramson",
"Lauren Brinkac",
"Todd Michael",
"Enoch S. Liu",
"Sterling Thomas",
"Gary B. Fogel",
"Bradley Abramson",
"Lauren Brinkac",
"Todd Michael",
"Enoch S. Liu",
"Sterling Thomas"
],
"abstract": "Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.",
"keywords": [
"pan-genome",
"pan-genome graph",
"core genes",
"essential genes"
],
"content": "Introduction\n\nOver the last decade, considerable interest has been directed towards the determination of a minimal bacterial cell, making use of a short genome consisting of only essential genes for viability. The Mycoplasma mycoides JCVI-syn3.0 is a case example of synthetic engineering to design and build a genome that contains a streamlined gene set essential for cell viability and cell replication.1 Multiple genome reduction projects have been undertaken.2–4 More targeted genomic deletions of genomic loci have been performed to characterize essential genes, but generally targeted approaches are too laborious to perform on a whole genome.5,6 However, the identification of “essential” genes - those genes that are critical for cell viability and replication - takes considerable time and effort in a laboratory setting and is usually determined with respect to one reference genome under one set of specific growth conditions. For instance, Kobayashi et al.7 and Koo et al.8 experimentally and computationally determined the minimal gene set in the gram-positive bacterium Bacillus subtilis. Koo et al.8 used a strictly experimental approach but Kobayashi et al.7 used three forms of evidence for their essential genes as given in their Table 4: RB: previous experimental work in B. subtilis; RO: previous experimental work in other bacteria; and TW: their experimental work. The RO evidence used is a mix of experimental and computational as the determination of orthologs is computational and essentiality of those orthologs was not experimentally confirmed: “Through predictions we propose that 79 other genes are essential, whereas 106 are not (Table 3)”.7 Of the ~4,100 genes of the type strain, a total of 271 genes for Kobayashi et al.7 and 257 genes for Koo et al.8 were shown to be essential. These essential genes were further categorized in terms of cell metabolism and enzymatic capability. Additionally, for the ~4400 genes in the gram-negative bacterium Escherichia coli, Goodall et al.,9 Baba et al.,10 and Yamazaki et al.,11 it was determined that 414 genes were essential to strain K-12.\n\nReuß et al.3 completed extensive further experimental and computational work to determine a minimal B. subtilis genome they call MiniBacillus. They present a list of 523 protein coding and 119 RNA genes necessary for a minimal B. subtilis cell growing in complex medium at 37°C. While many of these genes are not essential under single deletion experimental conditions, they are required for survival because a cell needs certain essential functions which may be carried out independently by more than one gene. As noted by Reuß et al.,3 the choice of which functionally isologous genes to choose for a minimal cell depends upon minimization goals and gene choices for different functions are not independent of one another. One criterion used by Reuß et al.3 is the conservation of the gene: “More strongly conserved genes were preferred over less conserved genes. In this respect, gene conservation and essentiality in genome-reduced Mycoplasma and other mollicutes species and the inclusion of genes in the genome of M. mycoides JCVI-syn3.0 had a high priority”. Reuß et al.3 do not explicitly use gene conservation at the species/subspecies pan-genome level but this seems in spirit with their criteria.\n\nReuß et al.3 extended their computational prediction of MiniBacillus by building on previous work to generate B. subtilis strains with large genome reductions.2 They started by constructing the delta 6 strain12 (~8% genome reduction). This reduction removed: “two prophages (SPβ, PBSX), three prophage-like regions, and the largest operon of B. subtilis (pks).” The phage/prophage regions were identified in part by GC content and codon usage as a method to identify probable horizontally transferred regions. Pan-genome analysis was not used. Next, strain IIG-Bs20 was constructed from delta 613 by removing “all nine prophages, seven antibiotic biosynthesis gene clusters and two sigma factors for sporulation” in part to have a strain that would “not produce spores, antibiotics or bacteriocins”. A direct descendant of IIG-Bs20, strain IIG-Bs27-47-24 (~31% genome reduction), was then used to generate more reductions in two independent strains, PG10 (~35% genome reduction) and PS38 (~36% genome reduction)2 with the goal of removing genes “not necessary for the survival of the cell (e.g., sporulation, antibiotic production, motility, metabolism of secondary carbon sources, and genes of unknown functions)”. For the strains IIG-Bs27-47-24, PG10, and PS-38, pan-genome analysis was not explicitly used but one of several criteria for deleting genes was a lack of conservation across broader taxonomic groups.\n\nFor E. coli, Kolisnychenko et al.5 generated an initial reduced genome in order to “serve both as a better model organism and as a more useful technological tool for genome science” by “deleting the largest K-islands of E. coli, identified by comparative genomics as recent horizontal acquisitions”. K-islands are regions unique to the K-12 strain MG1655 compared with the O157:H7 strain Sakai, and the uroseptic E. coli strain CFT073. This comparative analysis with a limited set of genomes is an obvious precursor to pan-genome analysis with a much larger set of genomes. Umenhoffer et al.14 generated the reduced E. coli strain MDS42 to be “free of mutation-generating IS elements”. This approach does not rely on comparison to other strains, just the ability to identify IS elements. Csorgo et al.15 further reduced the MDS42 strain by “constructing low-mutation-rate variants … to lack most genes irrelevant for laboratory/industrial applications.” They targeted genes likely to be core and necessary for the species to adapt to the environment but detrimental in an industrial setting where strain stability is important.\n\nExperimental studies to determine such essential genes are time consuming and often restricted to a single environmental condition using a single strain of the species. In addition, these approaches also knock out one gene at a time. As such, genes with multiple copies with redundant functions are often not considered as essential following knockout, as their additional copy is able to maintain cellular function. In other words, a viable organism would not result from deleting all but the experimentally determined essential genes from the genome. Another peculiarity of the single knockout essential genes is that pairs or cassettes of genes which can be removed and still have a viable organism are labeled essential because removal of just one gene is lethal. For example, removing the methylation gene(s) without removing the restriction digestion enzyme genes from the restriction mechanism results in cell death but the cell survives if the entire system is removed. This is likewise true for toxin/antitoxin systems.\n\nWhile it is possible to define “essential” genes relative to viability, another larger question remains; which genes define a species? While specific phenotypes can vary across strains, in general a species seems to require some minimal set of genes to not only survive in the laboratory but to thrive in its natural environment. In contrast, some strains may have retained or acquired some genes which improve survival for specific niches. Comparing the genes from multiple diverse strains of a species can help answer these questions. We define the pan-genome for a species/subspecies to be the set of predicted orthologous gene clusters (OGC) across that set of strains. Others have allowed paralogs to be included in these gene clusters16–18 but here we do not. This constraint forces there to be at most one gene per genome in an OGC.\n\nWe further define a pan-genome graph (PGG) to be a graph with the pan-genome OGCs as nodes where an edge exists between two nodes if the respective genes for any genome from the two OGCs are adjacent in that genome. More precisely, an OGC node is represented as a dipole with 5′ and 3′ ends and the edges go between an end of one node (5′ or 3′) to an end of another node depending on the orientation of the genes which are adjacent. The edges primarily represent the order and orientation of OGCs in the pan-genome genomes. Secondarily, the edges also represent the interstitial DNA sequences between the genes. A PGG edge has a weight equal to the number of genomes which contain the indicated adjacent gene ends. Core OGCs are defined to be those OGCs present in some large percentage of the strains in the pan-genome (≥95% in this work). Core edges are defined similarly. Core regions are defined to be the coordinates in a genome for each set of adjacent core genes in that genome provided the edges between the core genes are also core edges.\n\nCore OGCs should determine the baseline phenotype (capabilities and traits) of a species. Previous pan-genome studies19 have shown that species tend to only tolerate the placement of noncore genes between core regions and not within those core regions. The reason an organism might constrain a core region rather than just core OGCs is that the region may include regulatory mechanisms such as operons, which allows for co-expression of multiple functionally associated genes, or regulons which would be disrupted with the insertion of other genes. We believe that conservation of core regions in species indicates resistance to insertion or deletion of genes in these regions through evolution or through human-mediated genetic engineering.\n\nHere we present a pan-genome based calculation of core regions for B. subtilis ssp. subtilis and for E. coli. These core regions are compared with previous experimentally determined essential genes from the literature. These core regions are not a replacement for experimentally determined essential genes, but rather provide complementary information about a much larger portion of the genome. We expect that all truly essential genes for the species/subspecies would be a subset of the core OGCs/regions, since core OGCs would encompass genes responsible for providing a fitness advantage in environmental conditions as well as being essential for viability. This approach automates computational prediction of core OGCs/regions which can be used to help guide the removal of genome regions not needed for species fitness and indicate which genome regions are amenable to engineered insertions. This approach is an incremental improvement over previous computational methods to aid genome engineering. Ortholog prediction17,18,20 and determination of genes essential for most bacteria has a long history.21,22 Computational prediction of nonessential genes via predicting prophage regions or other horizontal transfer events is also well established.23–25 Pan-genome tools, most of which at some level predict core genes, are also not new.26,27 Our method builds directly upon our previous pan-genome work28–30 and includes several improvements: 1) being able to use only complete high-quality genomes; 2) checking for including the correct species/subspecies using average nucleotide identity (ANI); 3) reannotating gene features using homology and gene context; and 4) generating a PGG for a rigorous definition of a core region. Figure 1 shows the high-level view of our method with details provided in the Methods section.\n\n\nMethods\n\nFor B. subtilis ssp. subtilis and E. coli, we selected strains with complete genomes in RefSeq.31 We restricted our analysis to complete genomes to ensure that missing genes due to incomplete genome sequencing/assembly did not affect the approach or results. We limited our choice to RefSeq for two reasons: RefSeq performs a series of quality checks to remove dubious genome assemblies, and the initial pan-genome construction depends upon reasonably consistent annotation which RefSeq provides. We extracted the genomes based on organism name: Bacillus subtilis (we did not specify subspecies, since for many RefSeq genomes a subspecies is not given) and Escherichia coli (we also specified Shigella since all Shigella species are actually considered to be the same species as Escherichia coli).32,33 For each pan-genome, we then compared the genomes using a fast Average Nucleotide Identity (ANI) estimate generated using MASH.34 We used type strains and ANI to determine which of these genomes were the desired organism. We also used ANI to remove very closely related strains to reduce oversampling bias (for example for the B. subtilis type strain, 168, has at least eight genomes in RefSeq). We used GGRaSP28 to choose a single medoid sequence from any complete linkage ANI cluster with a threshold of 0.01% or 1/10,000 base pair difference. The strain 168 medoid genome is the Entrez reference genome for the B. subtilis type strain (GenBank sequence AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1/GCA_000009045.1) which can be used to map the Kobayashi et al.7 and Koo et al.8 results.\n\nUsing this approach, for B. subtilis, 143 genomes were downloaded from RefSeq. Of these, 132 genomes were determined to be B. subtilis ssp. subtilis based on type strains and ANI. The minimum ANI between any pair of the 132 B. subtilis ssp. subtilis genomes was 97.28% whereas the maximum ANI of any of the 11 other genomes to the 132 genomes was 95.73%, providing good separation between the other subspecies. The 132 genomes were reduced to 109 genomes after removing redundant strains. Finally, we removed strain delta6 (BioSample SAMN05150066) because it is known to have been engineered to remove multiple genes. Thus, we were left with 108 B. subtilis genomes. For E. coli (and Shigella) we downloaded 1097 complete genomes from RefSeq. Of these, 1096 were determined using ANI to be E. coli. The non-E. coli genome was clearly mislabeled as its maximum ANI to any other genome was 82.27%. The minimum pairwise ANI of any of the 1096 genomes was 95.53% which is not as tight as for B. subtilis ssp. subtilis which is to be expected given that E. coli is a species grouping not a subspecies grouping. One could arbitrarily try to choose a tighter grouping around the K-12 reference genome but the pairwise ANI values of the other genomes compared with the K-12 reference genome vary continuously from 96.22% to 100% with no punctate break in the values. After removing redundancy, 969 E. coli genomes remained. We added back in two redundant genomes: The K-12 Entrez E. coli reference strain MG1655 (BioSample SAMN02604091) and the K-12 strain BW25113 (GenBank sequence accession CP009273.1, GenBank Assembly accession ASM75055v1/GCA_000750555.1, GenBank BioSample accession SAMN03013572) used by Goodall. By using a 95% threshold for the number of genomes an OGC must be in to be considered core, some small number of the 971 genomes could be engineered to remove what are normally core OGCs and not affect the assignment of core OGCs.\n\nFor B. subtilis ssp. subtilis and E. coli, initial pan-genomes were based on the RefSeq annotation of these genomes. The pan-genome was generated using the pan-genome pipeline at the J. Craig Venter Institute (JCVI) at the nucleotide level using default parameters with the exception that a minimum of 90% identity and 90% length for pairwise Blast matches were used to prevent possible clustering of non-orthologous genes.29 This produced OGCs using gene context30 as well as a PGG.19 The PGG has two main components: nodes representing OGCs, and edges representing the sequence between OGCs and the order and orientation of the OGCs in the genomes. We updated the code repository for the JCVI pan-genome pipeline with a script: iterate_pgg_graph.pl, which calls pgg_annotate.pl for the genomes in the existing PGG in order to ensure consistent annotation of the genomes and iterates until the PGG stabilizes. The script pgg_annotate.pl uses an existing PGG to assign regions of a genome to nodes of the graph. This is done by blasting the medoid sequence for the OGC the node represents against the genome and then uses Needleman – Wunsch35 to extend the alignment if needed. If there are conflicting blast matches, then the matches are resolved based on which matches are consistent with the structure of the PGG which encapsulates gene context across the entire pan-genome. Once the nodes of the PGG are mapped to each of the genomes in the pan-genome a new version of the PGG is intrinsic and then explicitly extracted. This process is iterated to stability. This ensures that each genome is consistently annotated so that genes missing from the original annotation of some genomes will be consistently annotated across all genomes. A user manual for this new functionality is available at https://github.com/JCVenterInstitute/PanGenomePipeline.\n\nCore regions were determined based on the PGG. Nodes in the PGG were OGCs. Edges in the PGG represented adjacency of genes (contained in the OGCs) in the underlying genomes. The definition of which OGCs were or were not considered “core” was determined relative to a threshold criterion. We used a criterion for core such that 95% or more of the underlying genome had to contain the OGC or edge. Considering that we used only complete genomes it might have been possible to use a 100% threshold. However, we opted for a 95% threshold based on prior experience and an abundance of caution to not under call core OGCs/edges. Each core region began with a core OGC followed by a core edge (if possible, otherwise the core region comprises a single OGC) to another core OGC and so on until a core edge cannot be found to continue the core region. A core region is just a path in the PGG which was then mapped onto each genome to determine the core region coordinates. When the core threshold was below 100% any genome may be missing an OGC (gene) or edge along this path which results in the path being broken into its remaining constituent parts.\n\nIn order to compare core regions to experimentally determined essential genes we needed a common base of reference. For each of the experimental studies, the genes are specified based on a reference strain that was used for the experiments and has a complete genome in RefSeq. For Kobayashi et al.,7 only gene symbols/names were given which we mapped to Entrez GeneIDs using Entrez search. GeneIDs with no matches were manually curated to estimate the best matching gene symbol listed in the literature. For Koo et al.,8 locus IDs were provided giving direct access to the gene coordinates for RefSeq accession NC_000964.3 (BioSample SAMEA3138188, Assembly GCF_000009045.1). For Goodall, we used the data from three studies in Table S2 from Goodall et al.9 Gene symbols/names again were all that was available but these were consistent with the GenBank annotation downloadable in gff format for the K-12 BW25113 reference genome (GenBank accession CP009273.1) used by Goodall et al.9 (BioSample SAMN03013572). This gave us coordinates for all essential genes on RefSeq genomes which were annotated with a PGG which produces a file with coordinates for OGCs and edges mapped to the genome. These coordinates allow us to affiliate essential genes to OGCs.\n\n\nResults\n\nThe original and refined PGG statistics for B. subtilis and E. coli are provided in Table 1. The major goal of refining the PGG using reannotation and iteration until stabilization was to achieve consistent annotation across all genomes in the PGG leading to a more comprehensive and cohesive PGG. While the RefSeq annotations of these genomes tends to be highly consistent, many small genes are often arbitrarily called from genome to genome and even some common longer genes can occasionally be missed. There are three obvious points of improvement in the refined PGG for both the OGC and edge stats: the number of size 1 OGCs/edges significantly decreased due to some dubious RefSeq gene calls being eliminated and some becoming shared with other genomes; the number of core OGCs/edges significantly increased showing an improvement in the consistency of annotation across all genomes; and the number of genes/edge instances in OGCs/edges greatly increased again indicating a much more consistent annotation.\n\nThe B. subtilis ssp. subtilis refined PGG annotates 4654 OGCs for the reference genome (GenBank sequence AL009126.3, BioSample SAMEA3138188, Assembly ASM904v1/GCA_000009045.1) (Supplementary Table 1): 876 (18.8% of OGCs) noncore (<95% of genomes 102 or less), 359 (7.71%) core but not present in all genomes (≥95% and <100% of genomes 103–107), and 3419 (73.5%) core and present in all 108 genomes. For the union of the Koo et al.8 and Kobayashi et al.7 essential gene data sets there are 305 genes (Supplementary Table 2): 16 (5.25%) noncore (≤102 genomes), 2 (0.656%) core but not all (103–107 genomes), and 287 (94.1%) core all (108 genomes). This shows that most essential genes in B. subtilis ssp. subtilis are encompassed by core OGCs/regions. There are 258 core regions for B. subtilis (Supplementary Table 3). The 289 essential genes which are core OGCs are contained in only 63 of these regions. These 289 essential genes are not evenly distributed in these 63 regions (e.g. 46 are in core region 3). Similarly, the 16 essential genes in non-core regions (the regions between core regions) are contained in only seven non-core regions with eight genes in the non-core region between core regions 206 and 207 (Figure 2). A table of all B. subtilis genes mapped to the reference genome is provided in Supplementary Table 1.\n\nGoing from the outside to the inside: track 1) core regions, 2) Minibacillus genes, 3) Koo et al.8 essential genes, 4) Kobayashi et al.7 essential genes, 5) deleted genes in strain delta 6, 6) deleted genes in strain IIG-Bs27-47-24, 7) deleted genes in strain PG10, and 8) deleted genes in strain PS38.\n\nThe Reuß et al.3 data set for MiniBacillus has 523 protein coding and 119 RNA genes predicted to be necessary for a minimal B. subtilis. For the 523 protein coding genes: 18 are noncore (≤102 genomes), 16 are core but not in all genomes (one in 105, one in 106, 14 in 107 genomes), and 489 are in all 108 genomes (Supplementary Table 1). They include all 30 rRNA and 86 tRNA genes from the reference genome as well as three “misc” RNA genes in MiniBacillus. The three misc RNA genes are present in all 108 genomes. In all likelihood, the 10 copies of the 16S-23S-5S RNA operon are not required but it is safer for robust growth not to delete any of them. Likewise, for the tRNA genes where many are redundant. For the 30 rRNA genes: six are noncore (92–102 genomes), 16 are core but not in all genomes (103–107), and eight are in all 108 genomes. It is clearly possible that some of these strains are dispensing with some of the RNA operons but at most this is happening rarely reinforcing the decision not to remove any from MiniBacillus. In addition, some of the missing RNA operon genes may be due to incorrect assembly of the two sets of tandem RNA operons (one a two-unit tandem and one a three-unit tandem) as large tandem repeats can be problematic for assemblers. All the rRNA genes in fewer than 106 genomes are in the tandem rRNA operons (Supplementary Table 4). Of course, the tandem rRNA operons are the most likely to be deleted via recombination as well. For the 86 tRNA genes: 13 are noncore (100–102 genomes), 18 are core but not in all genomes (103–107), and 55 are in all 108 genomes. Retaining all the tRNA genes in MiniBacillus also seems to be the correct decision as strains rarely dispose of the tRNA genes.\n\nBoth the experimentally determined essential genes and the predicted core OGCs/regions are important data for genome engineering. They both indicate regions that should not be deleted without careful consideration. The noncore regions also indicate where the bacterium is more likely to tolerate engineered insertions. As a validation of our method and how to interpret the results our method produces it is important to understand why 16 essential genes are in noncore regions.\n\nFor B. subtilis, both Kobayashi et al.7 and Koo et al.8 used similar single knockout methods to determine “essential” protein-coding genes when grown in LB at 37°C. Koo et al.8 identified 257 essential genes while Kobayashi et al.7 identified 271 essential genes. The union of these two sets results in 305 essential genes (Supplementary Table 2). The Koo et al.8 data set has 257 genes. The Kobayashi et al.7 data set has 271 genes. There are 223 genes in common between the two data sets. 48 genes are only in the Kobayashi et al.7 data set. 34 genes are only in the Koo et al.8 data set. The Kobayashi et al.7 data set has been refined with time:36 “Of the original 271 genes, 31 were shown to be non-essential in recent studies. Moreover, 21 new genes (19 protein-coding genes and two RNA-coding genes) were added to the list. Thus, 261 genes encoding 259 proteins and two RNAs are regarded as being essential today”. This list of 259 protein-coding genes is more consistent with the more recent Koo et al.8 data set. The 305 genes found in either data set were mapped to the PGG OGCs using the RefSeq genome NC_000964.3 (BioSample SAMEA3138188). Interestingly through this mapping, 16 of the essential genes were not identified as core OGCs (two more essential genes were core OGCs but not present in all 108 genomes). For the 18 essential genes not present in all 108 genomes (Supplementary Table 5), 12 are in both data sets and six are only in the Koo et al.8 data set. We believe only 11 of the 18 genes are truly essential. Gene wapI/yxxG (OGC 4769 present in 39 of 108 genomes) is an antitoxin for the wapA toxin gene which is adjacent to it (present in 85 of 108 genomes).37 Gene rttF/yqcF (OGC 4590 present in 46 of 108 genomes) and gene rtbE/yxxD (OGC 4772 present in 53 of 108 genomes) are also the antitoxin of a cognate toxin-antitoxin pair.38 Gene yezG (OGC 4411 present in 43 of 108 genomes) is also the toxin for a cognate toxin–antitoxin pair.39 Gene sknR/yqaE (OGC 4643 present in 34 of 108 genomes) is part of a phage-like region which, if removed would still allow B. subtilis to remain viable12 possibly because it is another antitoxin or similar mechanism. Genes bsuMA/ydiO (OGC 4838 present in 24 of 108 genomes) and bsuMB/ydiP (OGC 4839 present in 24 of 108 genomes) are part of a prophage region of about 15 genes in 48 genomes which includes ydiR and ydiS which are type-2 restriction enzymes. These are not essential genes, but they are essential if the restriction enzymes are present.40 We are not the first to notice these issues with experimentally determined essential genes indicated by our references above. In their review, Commichau et al.36 referred to these as \"protective essential genes.\" In fact, Koo et al.8 also addressed this in their paper: “Of the 257 genes essential in LB medium, 30 are not essential in some other growth condition or genomic context...LB may have an insufficient amount of particular compounds; e.g., the ylaN mutant requires a higher amount of iron than that present in LB … or may lack a compound that could bypass the need for that gene product; e.g., eno, pgm, gapA, and alrA … Some gene products are essential only at high growth rates typical of LB at 37°C (smc and scpA …), and these may not be essential in the natural soil environment where B. subtilis grows slower. Finally, some genes are non-essential in specific genetic backgrounds, e.g., antitoxins can be deleted in strains lacking their cognate toxin gene”.\n\nAnother eight essential non-core genes are involved in wall teichoic acid (WTA) biosynthesis: Genes tuaB (OGC 4729 present in 85 of 108 genomes), mnaA/yvyH (OGC 4735 present in 84 of 108 genomes), tagH (OGC 4744 present in 84 of 108 genomes), tagG (OGC 4745 present in 35 of 108 genomes), tagF (OGC 4746 present in 35 of 108 genomes), tagD (OGC 4748 present in 35 of 108 genomes), tagA (OGC 4749 present in 35 of 108 genomes) and tagB (OGC 4750 present in 35 of 108 genomes). The WTA genes are involved in production of anionic glycopolymers required for consistent cell shape and division.41 The WTA genes are part of a 31 gene region which has been shown to be dispensable42 but results in malformed cells with poor growth properties. Gene rodA (OGC 3994 present in 97 of 108 genomes) appears to be the exception as it is asserted to be essential for maintaining a rod shape and preventing spherical cells which lyse.43 Kobayashi et al.7 stated: “Ten essential genes are involved in cell shape and division. Septum formation requires seven (ftsA, L, W, and Z, divIB and C, and pbpB …), whereas cell shape requires three (rodA, and mreB and C).” Interestingly, genes ftsZ (OGC 1675 present in 105 of 108 genomes) and pbpB (OGC 1662 present in 107 of 108 genomes) while considered core, using our 95% of genomes definition are the only core OGCs not present in all 108 genomes. We investigated these 11 genes further to understand why essential genes did not appear to be core OGCs. By examining the PGG we discovered that alternate OGCs with homology to the essential genes had replaced the essential genes. Gene pbpB (OGC 1662 in 107 genomes) is replaced in the one remaining genome by OGC 7120 which is also annotated as pbpB. Gene ftsZ (OGC 1675 in 105 genomes) is replaced in three genomes by a four gene insertion of OGCs 8068, 8300, 8069, and 8070 where both 8068 and 8070 are annotated as ftsZ. Gene rodA (OGC 3994 in 97 genomes) is replaced by either: OGC 8718 (two genomes) or OGCs 10492, 6436, and 6437 (one genome) or OGCs 6436 and 6437 (eight genomes) where 8718 and 6436 are annotated as rodA. As an illustrative example for rodA, Figure 3 shows how this is represented in the PGG. The medoid sequences for OGCs 6436 (A4A60_RS20560), and 8718 (C7M30_RS12210) have full length homology to the medoid sequence for rodA (OGC 3994, ETA10_RS20040) with 66% nucleotide /65% peptide and 83% nucleotide/85% peptide identity respectively. For B. subtilis ssp. spizizenii strain W23, poly (ribitol phosphate) is the main teichoic acid44 and this was thought to distinguish ssp. spizizenii from ssp. subtilis whose type strain 168 has poly (glycerol phosphate) as the main teichoic acid. Further study found that the ribitol/glycerol distinction does not distinguish between spizizenii and subtilis subspecies45 but rather either subspecies can contain one or the other. Our PGG confirms this and in fact finds six distinct variants of the WTA region. For example the tagD gene (OGC 4748 in 35 genomes) has been replaced by multiple orthologs with the same annotation: OGC 3746 (23 genomes), OGC 5431 (43 genomes), OGC 6915 (two genomes), OGC 7624 (three genomes), and OGC 8731 (one genome). The variation of the WTA region in B. subtilis will be the focus of a future paper.46\n\nOGC 3994 (red) contains the rodA gene from the reference strain. The medoid sequences of OGCs 6436 and 8718 (green) have RefSeq annotations of rodA and full-length homology below our 90% threshold to the medoid sequence for OGC 3994. The arrow boxes represent OGCs with gene directionality indicated by the 5′ end being flat and the 3′ end being pointed. Numbers above boxes and edges are the number of genomes the OGC or edge are in.\n\nFor the 34 protein coding genes from MiniBacillus3 which were not in all 108 genomes, 10 were already discussed above as to why they were essential but not core. The seven essential genes previously shown to be protective essential genes are as expected not in the MiniBacillus data set. The noncore tuaB gene was essential in both data sets but not included in MiniBacillus. This leaves 24 MiniBacillus protein coding genes which are noncore and unexplained. The tagU and gtaB genes are part of the WTA cassette discussed above. The four fecC-F (also called yfmC-F) genes form a cassette and are in 98 genomes. From Reuß et al.:3 “For iron uptake, the minimal cell should possess the EfeUO system for elemental iron uptake and the iron-citrate ABC transporter YhfQ-YfmCDEF (136, 137).” (yhfQ is present in all 108 genomes) but no alternate mechanism is specified. The seven purEKBCSQL genes form a cassette and are in 107 genomes. These genes are involved in purine biosynthesis (see Figure 5 in Reuß et al.3) and it is not clear what alternative could be used. The guaA gene is involved in nucleotide biosynthesis downstream of purine biosynthesis (see Figure 5 in Reub et al.3) present in 107 genomes. The mntH gene is a manganese transporter (see Figure 2 in Reuß et al.3) present in 106 genomes. The rlmCD gene is an rRNA methyltransferase present in 107 genomes. The lytE, and ponA genes are in 107 genomes. The pbpB gene was essential as discussed above and in 107 genomes. The pbpA gene is in 50 genomes. From Reuß et al.:3 “For the minimal cell, we have selected penicillin-binding proteins 1 (PonA), 2B (PbpB), and 2A (PbpA) and the autolysins LytE and LytF. As outlined above, this selection was made according to their expression profiles and the dependence on other proteins. As an example, there is a functional paralog of LytE, CwlO. For the activity of CwlO, B. subtilis also needs the ABC transporter FtsEX and the small protein Mbl. Thus, the choice of LytE allowed a smaller number of genes.”. Interestingly, genes cwlO, ftsE, ftsX, and mbl are in all 108 genomes. The yitI gene is in 107 genomes. From Reuß et al.:3 “Moreover, based on our own experimental data and those of colleagues, YitI, YitW, and YqhY are important for viability (P. Dos Santos, personal communication; our unpublished results).”. The yoaE gene is a formate dehydrogenase present in 89 genomes. The thyB gene is thymidylate synthase B present in 70 genomes. The rpoE gene is in 107 genomes. From Reub et al.:3 “Moreover, we have included the RNA polymerase-interacting protein HelD and the nonessential delta subunit (RpoE). HelD binding stimulates transcription in an RpoE-dependent manner, suggesting that these two accessory proteins are important to allow rapid growth (59, 60).”. The hutM gene is a histidine permease present in 90 genomes. MiniBacillus does not include the adjacent hutPHUIG genes which are in 88-91 genomes probably indicating a cassette of genes which interact.\n\nWe looked at how our OGGs intersected with the gene deletions from B. subtilis strains delta 6, IIG-Bs27-47-24, PG10, and PS38 from Reuß et al.’s3 Supplemental Table S1. Strains PG10 and PS38 were derived from strain IIG-Bs27-47-24 which in turn was derived from strain delta 6. This means all deletions in delta 6 are present in the other strains, and all deletions in IIG-Bs27-47-24 are present in PG10 and PS38. For delta 6, most of the deleted genes are noncore which would be expected since most of the deleted regions were phage/prophage regions (Table 2). For additional deletions to IIG-Bs27-47-24, almost a quarter of the deleted genes are noncore which would again be expected as more prophage and horizontally transferred regions were intentionally targeted but now more core genes were deleted based on core functionality deemed not to be essential for laboratory growth such as sporulation (Table 2). For additional deletions to PG10 and PS38, most deleted genes were core as most of the obviously horizontally transferred regions had already been deleted (Table 2). While pan-genome analysis was not used to select the deleted regions, we believe it could have provided strong evidence to support the deletion of the noncore genes/regions which were deleted. In addition, it could be used to suggest further deletions. There are nine noncore regions which contain seven or more noncore genes which have not yet been deleted in any of these strains (Table 3). The largest of these regions contains the WTA genes cassette we discussed above and is not a good candidate for deletion. By examining the refined PGG at these regions it is straightforward to determine if there are alternate OGC choices for the region that in sum designate the region as likely to be core as we showed in Figure 3.\n\nTo show that our method produces significantly different results than previous methods we compared our pan-genome analysis to the very recent work on a B. subtilis pan-genome by Wu et al.47 While the focus of Wu et al.47 was on determining which genomes should be excluded from a species/subspecies pan-genome based on “incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains”, their analysis focused on how this affected the determination of core OGCs. We compared our core OGC set to theirs for the reference genome. Wu et al.47 discussed two pan-genome data sets: “old (89 strains) and new (153 strains)”. We compared to the new data set which is more recent and more comparable to our pan-genome of 108 strains (Supplementary Table 5). After removing “confounding” strains the new data set had 128 strains. From their Table 1 compared to our Table 1, Wu et al.47 have many fewer core OGCs whether defined at 95%, 99%, or 100% both for our original and refined PGGs. We compared their methods to ours to attempt to account for the difference. They also apparently restricted genomes to those available from RefSeq since they mention a RefSeq ID. They did not require the genomes to be considered complete by RefSeq as we did but instead used these criteria: “Among these B. subtilis strains, we removed strains whose N base content was greater than 1% of the genomic size (FB6-3,GS 188, SR1), and we removed the chimeric genome BEST7613 with a genome size of 7.6 Mb.”. We used the RefSeq annotation which is generated by a consistent NCBI annotation pipeline. They also tried to ensure consistent annotation: to “ensure the consistency and reliability of the annotation and gene prediction of the genome, we used the program Prokaryotic Genome Annotation System (Prokka)”. We doubt the different annotations from these two established pipelines accounts for many differences in core OGCs. Both methods used a whole genome ANI method to discard outlier genomes. There are multiple differences in our pan-genome approach. First, we used PanOCT and they used Roary. Second, we used all annotated gene features: gene (protein coding), pseudogene, miscRNA, rRNA, and tRNA, whereas they used only protein-coding genes. Finally, and we think most importantly, we iterated over annotating the genomes and PGG refinement to ensure consistent annotation and they did not. To see what impact our choice of all gene features versus just protein-coding genes had we looked at the annotation of core OGCs on the reference genome (Supplementary Table 1). Luckily all 3778 core (95% threshold) OGCs are present in the reference genome. Of these, 3473, 3334, and 3189 are protein coding OGCs at thresholds 95%, 99%, and 100% respectively. All these numbers are still much higher than those reported by Wu et al.47 We should note that even though we did not count the 25 core OGCs annotated as pseudogenes in the reference genome, some of the core protein-coding OGCs in the reference genome might be annotated as pseudogenes in other genomes which could impact the Wu et al.47 numbers. Roary tends to require near full length gene matches which is why we required PanOCT to only use 90% or longer length matches. The authors chose to limit Roary to 95% identity or higher matches which we think is much too high since the species ANI threshold is 95% and even subspecies ANI threshold of 98% is too close to this threshold given that some genes are more rapidly evolving than others so we used a threshold of 90% or higher identity for matches. Even with our 90% identity threshold some genes such as rodA, discussed above, drop below this threshold generating possibly unnecessary branching in the PGG. Of the 128 strain pan-genome from Wu et al.47 that we compared to our 108 strain pan-genome, 92 strains were in common with 16 being exclusive to our pan-genome and 36 being exclusive to theirs. Of the 36 strains exclusive to theirs 23 were removed as being redundant at the ANI level by us, 9 were in RefSeq but not complete genomes, and 4 either were never in RefSeq (they do not have RefSeq IDs in their Supplementary Table 3) or no longer are. Interestingly, while 15 of the 16 genomes exclusive to ours are just more recent strains to RefSeq, one strain, D12-5, was used by us but discarded by them. They discarded D12-5 because “BS155 and D12-5 possess the largest proportion of pseudogenes (37.96% and 11.32%) among the B. subtilis strains” and for D12-5 they indicated this was due to a large number of frameshifts. Pseudogenes due to frameshifts are often an indication of lower quality assembly consensus sequence from using only long reads at lower coverage. Our pan-genome method is resilient to this kind of error profile in the genome due to reannotation of the genomes and PGG refinement whereas other pan-genome methods are not. We believe our higher counts for core protein coding OGCs is correct. To validate this, we compared how many of the 305 essential B. subtilis genes are core for both methods. For the 18 genes we discussed above that are essential but not in all 108 genomes of our PGG, 2 are core at 95% and 1 is core at 99%; whereas, for Wu et al.47 2 are core at 95%, 2 are core at 99%, and 1 is core at 100%. The only significant difference for these 18 genes is that ftsZ is in 95% (105) of our pan-genome and 100% of theirs. The Wu et al.47 pan-genome misses many additional essential genes which ours does not: 28, 39, and 47 for 95%, 99%, and 100% thresholds respectively.\n\nFor E. coli, Goodall et al.9 determined E. coli essential genes using an analysis of transposon insertion events (TraDIS). The results of their study and two other studies, the Keio collection10 and the Profiling of the E. coli Chromosome (PEC)11 were captured in Table S2 of Goodall et al.9 Of the 414 genes with overlap between these studies, the 248 essential genes in common for all three studies are all core OGCs (Figure 4 and Supplementary Table 6). This set of 248 essential genes should be the highest quality predictions as determined by all three studies and confirms our assertion that essential genes should almost always be core OGCs. The next highest quality set of essential gene predictions is the 45 essential genes where two of the three studies agree which 41 are core OGCs: for Keio–PEC, 15 of 16 are core OGCs; for TraDIS–Keio, eight of 11 are core OGCs; and for TraDIS–PEC, 18 of 18 are core OGCs (Supplementary Table 6). The lowest quality set of essential gene predictions is the 121 essential genes where only one study agrees which 89 are core OGCs: for Keio only, 12 of 22 are core OGCs; for PEC only, 18 of 18 are core OGCs; and for TraDIS only, 59 of 81 are core OGCs (Supplementary Table 6). One of the noncore essential genes present in two studies (TraDIS–Keio), racR, is probably a toxin suppressor which is not essential in the absence of the toxins. Bindal et al.48 noted, “We further show that both YdaS and YdaT can act independently as toxins and that RacR serves to counteract the toxicity by tightly downregulating the expression of these toxins”. The racR gene is found in only 106 of the 971 genomes in the E. coli PGG, whereas ydaS and ydaT are found in 106 and 150 genomes respectively, perhaps arguing that ydaS is the key toxin gene. This recapitulates the pattern we observed in B. subtilis where toxin suppressor genes are only essential in the presence of toxin genes. Similarly, the dicA gene (TraDIS–Keio) can be deleted if the dicB gene is also deleted. Kato et al.49 noted: “The dicA gene encoding a repressor of a cell division inhibitor was deleted in our study with the dicB, the inhibitor gene”. There are 521 core regions for E. coli (Supplementary Table 7). The 378 essential genes which are core OGCs are contained in only 133 of these regions. These 378 essential genes are not evenly distributed in these 133 regions (e.g., 27 are in core region 362). Similarly, the 36 essential genes in non-core regions (the regions between core regions) are contained in only 23 non-core regions with four in the non-core region between core regions 152 and 153. A table of all E. coli genes mapped to the reference is provided in Supplementary Table 8.\n\nGoing from the outside to the inside: track 1) core regions, 2) TraDis essential genes, 3) Keoi essential genes, and 4) PEC essential genes.\n\nYang et al.50 presented a similar pan-genome analysis for 491 E. coli strains. There were 420 strains in common between the Yang et al.50 491 strain pan-genome and our 971 strain pan-genome (Supplementary Table 9). Our pan-genome included Shigella species (see Methods) which Yang et al.50 did not. This added diversity of our pan-genome should reduce the number of core OGCs. Likewise, the much larger number of strains in our pan-genome should reduce the number of core OGCs. Yang et al.50 report 867 core protein-coding genes presumably at a 100% threshold although this is not explicitly stated. For our refined PGG, we had 1501 core OGCs at the 100% threshold. We include all genes in our OGCs but 1234 of the 1501 core OGCs are protein coding at the 100% threshold. Yang et al.50 did not provide a table of their core genes for sake of comparison, however we expect for the same reasons as for our more detailed analysis of the B. subtilis pan-genome that our set of core OGCs is more complete. Yang et al.50 reported that their core genes included 243 essential genes from the DEG database51 which contains essential genes from many studies but did not provide a table of these genes. Yang et al.50 also reference two essential gene studies one by Gerdes et al.52 and one by Baba et al.10 which was one of the three studies we used (Keio). In the DEG database the Gerdes et al.52 study has 609 essential genes, and the Baba et al.10 study has 296 essential genes. Our version of the Baba et al.10 study we called Keio had 297 essential genes of which 218 were core OGCs at the 100% threshold. For the union of the three studies we compared against, we had 289 essential genes out of 414 which were core OGCs at the 100% threshold. It is unclear whether the 243 core essential genes Yang et al.50 reported were from the Baba et al.10 study, the Gerdes et al.52 study, or the union of the two studies. Given the much lower number of core genes for the Yang et al.50 core genes compared with our core OGCs, we believe that Yang et al.50 used the union of essential genes from the Baba et al.10 and Gerdes et al.52 studies.\n\n\nDiscussion\n\nFor the purpose of biological engineering, determining the set of core regions for a given species is critical as changes to these regions should be expected to reduce fitness or be lethal. Core regions indicate parts of the genome that are conserved across evolution within a species. These regions are not necessarily required for survival but presumably confer a fitness advantage and define the characteristic core genotype which produces the core phenotype (lifestyle). Since most essential gene studies are carried out under specific static laboratory growth conditions, genes which would normally be essential for a species across a diverse set of dynamic environmental conditions might not be discovered (e.g., necessary for fluctuating temperatures). Correspondingly, genes required to out compete rival organisms through increased fitness or to evade immune responses might not be found under laboratory conditions are considered facultative essential.31 Core regions, therefore, should be a superset of essential genes in most cases but exceptions might occur for genes which are not needed in a species’ natural niche but are required in a laboratory setting. Another exception would be for genes which are essential for a particular strain but not for other strains due to the presence of compensating non-core genes.\n\nNoncore OGCs/regions which are determined by pan-genome analysis are often horizontally transferred elements, such as phage, prophage, or mobile elements. For industrial applications these regions are dispensable and can even be sources of genome instability.3,12–14,53 While there are other methods for identifying these regions, pan-genome analysis is a reliable complimentary tool. Pan-genome analysis can also reveal enzymatic and other systems/pathways that are present in some strains but not others53 which indicates they can likely be removed. When choosing between retaining alternate systems for essential functions, biological engineers have looked at conservation of those systems across broad taxonomic levels3 as an indication of utility and we believe conservation across the pan-genome should also be considered. When specific genes/systems of known function are being targeted for removal pan-genome analysis is less useful but still good information to have. For instance, Reuß et al.2 tried to delete region BSU07710-07820 from B. subtilis which was lethal. In this region, six of the 11 OGCs are core but the five noncore genes are adjacent so perhaps region BSU07750-07790 could have been successfully deleted.\n\nGiven that we believe pan-genome analysis is a useful complimentary tool for biological engineers, it is important that the pan-genome analysis used be as accurate and helpful as possible. We showed by comparing with other recent pan-genome studies for B. subtilis and E. coli that our method is more accurate for determining core OGCs/regions as validated by coverage of essential genes. Further, we believe that the PGG is valuable for confirming when noncore OGCs may be compensated for with alternate homologous OGCs at the same relative genomic location performing the same function as we showed in Figure 3. The function of these noncore OGCs may be essential and should be considered appropriately.\n\nPan-genome studies often capture the diversity of sequenced species but fail to compare gene lists to experimentally validated essential genes lists or the results are confusing. Interestingly in Mycoplasma, fewer essential genes were determined with the pan-genome method compared with the laboratory experimental approach.54 In Pseudomonas, only one-third of the pan-genome single copy genes had overlap with the essential genes from experimentally reduced genomic studies.55 We showed that the core OGCs/regions from our refined PGG encompass 91% and 95% of the E. coli and B. subtilis experimentally determined essential gene lists, respectively. Both model bacterial species E. coli and B. subtilis have had many genome reduction studies performed and reviewed elsewhere.56\n\nExperimental verification of the essentiality of computationally predicted core OGCs or regions requires that each strain of the pan-genome study be minimized. However, it is cost prohibitive to do knockout studies on all strains of a pan-genome. One must carefully choose a single genome as a representative of the entire pan-genome for the purpose of verifying the essentiality of core regions and/or the non-essentiality of noncore regions by experimental validation. However, given the diversity of most bacterial species it is unlikely that any one strain completely captures the capabilities of the species in all environmental conditions. Further, while there are clearly core OGCs/regions associated with viability for a species, other core regions probably contribute to a lesser degree to cell viability. For example, for the purpose of biological engineering, changes in these locations may reduce fitness by slowing cell growth.\n\nThe use of a PGG for identifying core regions of a bacterium is an automatable, low-cost, rapid, and effective way to evaluate both gram-negative and gram-positive bacteria. This method compliments and expands upon the experimental knockout approach by including environmental diversity as a measure of what regions and OGCs are conserved across the species. The approach also overcomes the limitations of knockout studies that are specific to the strains and growth conditions used.\n\nThe B. subtilis WTA region provides a cautionary note for relying entirely upon core regions to determine what is safe to remove. While most non-core regions involve cassettes of genes which are entirely absent from some strains such as phage regions, sometimes orthologous replacement possibly due to homologous recombination can have functionally equivalent genes appearing to be non-core. A closer examination of the PGG can determine if a region is simply missing from some strains versus being replaced in which case further study may be needed before removal of the region. Of course, in some cases the orthologous replacement does not need to occur at the same location in the genome but that was the case for all instances we examined in B. subtilis.",
"appendix": "Acknowledgements\n\nThe authors would like to thank IARPA for sponsoring this research and would like to thank Derren Barken for his assistance in table generation.\n\n\nData availability\n\nFigshare: Underlying data for ‘A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes’, https://doi.org/10.6084/m9.figshare.14132180.v1.57\n\nThis project contains the following underlying data:\n\n• Table 1. Pan-genome graph statistics for B. subtilis and E. coli.\n\n• Table 2. The number of deleted genes from B. subtilis reduced strains which are noncore versus core.\n\n• Table 3. Large noncore regions which have not been deleted from any of the strains delta 6, IIG-Bs27-47-24, or PG10, PS38.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC BY 4.0).\n\nFigshare: Extended data for ‘A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes’, https://doi.org/10.6084/m9.figshare.14132180.v1.57\n\nThis project contains the following extended data:\n\n• Supplementary Table 1\n\n• Supplementary Table 2\n\n• Supplementary Table 3\n\n• Supplementary Table 4\n\n• Supplementary Table 5\n\n• Supplementary Table 6\n\n• Supplementary Table 7\n\n• Supplementary Table 8\n\n• Supplementary Table 9\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC BY 4.0).\n\n\nReferences\n\nHutchison CA, Chuang RY, Noskov VN, et al.: Design and synthesis of a minimal bacterial genome. Science. 2016; 351: aad6253. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nYamazaki Y, Niki H, Kato J: Profiling of Escherichia coli Chromosome database. Methods Mol Biol. 2008; 416: 385–389. PubMed Abstract | Publisher Full Text\n\nWesters H, Dorenbos R, van Dijl JM, et al.: Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol. 2003; 20: 2076–2090. PubMed Abstract | Publisher Full Text\n\nWenzel M, Altenbuchner J: Development of a markerless gene deletion system for Bacillus subtilis based on the mannose phosphoenolpyruvate-dependent phosphotransferase system. Microbiology. 2015; 161(10): 1942–1949. PubMed Abstract | Publisher Full Text\n\nUmenhoffer K, Fehér T, Balikó G, et al.: Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications. Microb Cell Fact. 2010; 9: 38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCsörgo B, Fehér T, Tímár E, et al.: Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs. Microb Cell Fact. 2012; 1: 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTettelin H, Masignani V, Cieslewicz MJ, et al.: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome” Proc Natl Acad Sci U S A. 2005; 102(39): 13950–13955. [published correction appears in Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16530]. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRemm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 2001; 314(5): 1041–1052. PubMed Abstract | Publisher Full Text\n\nLi L, Stoeckert CJ Jr, Roos DS: OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9): 2178–2189. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan AP, Sutton G, DePew J, et al.: A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. Genome Biol. 2015; 16: 143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTatusov RL, Galperin MY, Natale DA, et al.: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000; 28(1): 33–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGil R, Silva FJ, Peretó J, et al.: Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev. 2004; 68(3): 518–537. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJordan IK, Rogozin IB, Wolf YI, et al.: Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 2002; 12(6): 962–968. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPodell S, Gaasterland T: DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 2007; 8(2): R16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol. 2001; 55: 709–742. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFouts DE: Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 2006; 34(20): 5839–5851. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPage AJ, Cummins CA, Hunt M, et al.: Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015; 31(22): 3691–3693. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVernikos GS: A Review of Pangenome Tools and Recent Studies. In: Tettelin H, Medini D, eds. The Pangenome: Diversity, Dynamics and Evolution of Genomes. Cham (CH): Springer; 2020: 89–112. PubMed Abstract | Publisher Full Text\n\nClarke TH, Brinkac LM, Sutton G, et al.: GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models. Bioinformatics. 2018; 34: 3032–3034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInman JM, Sutton GG, Beck E, et al.: Large-scale comparative analysis of microbial pan-genomes using PanOCT. Bioinformatics. 2019; 35: 1049–1050. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFouts DE, Brinkac L, Beck E, et al.: PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. Nucleic Acids Res. 2012; 40: e172. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO'Leary NA, Wright MW, Brister JR, et al.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016; 44: D733–45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLan R, Reeves PR: Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect. 2002; 4: 1125–1132. PubMed Abstract | Publisher Full Text\n\nMeier-Kolthoff JP, Hahnke RL, Petersen J, et al.: Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci. 2014; 8:9: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOndov BD, Treangen TJ, Melsted P, et al.: Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016; 17: 132. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNeedleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970; 48: 443–453. PubMed Abstract | Publisher Full Text\n\nCommichau FM, Pietack N, Stülke J: Essential genes in Bacillus subtilis: a re-evaluation after ten years. Mol Biosyst. 2013; 9(6): 1068–1075. PubMed Abstract | Publisher Full Text\n\nKoskiniemi S, Lamoureux JG, Nikolakakis KC, et al.: Rhs proteins from diverse bacteria mediate intercellular competition. Proc Natl Acad Sci U S A. 2013; 110: 7032–7037. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHolberger LE, Garza-Sánchez F, Lamoureux J, et al.: A novel family of toxin/antitoxin proteins in Bacillus species. FEBS Lett. 2012; 586(2): 132–136. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrantl S, Müller P: Toxin-Antitoxin Systems in Bacillus subtilis. Toxins. 2019; 11: pii: E262. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOhshima H, Matsuoka S, Asai K, et al.: Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg. J Bacteriol. 2002; 184: 381–389. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrown S, Santa Maria Jr JP, Walker S: Wall teichoic acids of gram-positive bacteria. Annu Rev Microbiol. 2013; 67: 313–336. PubMed Abstract | Publisher Full Text | Free Full Text\n\nD'Elia MA, Millar KE, Beveridge TJ, et al.: Wall teichoic acid polymers are dispensable for cell viability in Bacillus subtilis. J Bacteriol. 2006; 188: 8313–8316. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHenriques AO, Glaser P, Piggot PJ, et al.: Control of cell shape and elongation by the rodA gene in Bacillus subtilis. Mol Microbiol. 1998; 28: 235–247. PubMed Abstract | Publisher Full Text\n\nLazarevic V, Abellan F-X, Möller SB, et al.: Comparison of ribitol and glycerol teichoic acid genes in Bacillius subtilisW23 and 168: Identical function, similar divergent organization, but different regulation. Microbiology. 2002; 148: 815–824. PubMed Abstract | Publisher Full Text\n\nAhn S, Jun S, Ro H-J, et al.: Complete genome of Bacillus subtilis subsp. subtilis KCTC 3135T and variation in cell wall genes of B. subtilis strains. J Microbiol Biotechnol. 2018; 28: 1760–1768. PubMed Abstract | Publisher Full Text\n\nSutton G, Fogel G, Abramson B, et al.: Horizontal transfer and evolution of wall teichoic acid gene cassettes in Bacillus subtilis [version 1; peer review: awaiting peer review]. F1000Res. 2021. Publisher Full Text\n\nWu H, Wang D, Gao F: Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. Brief Bioinform. 2020; bbaa013. PubMed Abstract | Publisher Full Text\n\nBindal G, Krishnamurthi R, Seshasayee ASN, et al.: CRISPR-Cas-mediated gene silencing reveals RacR to be a negative regulator of YdaS and YdaT toxins in Escherichia coli K-12. mSphere. 2017; 2: e00483–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKato J, Hashimoto M: Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol. 2007; 3: 132. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang ZK, Luo H, Zhang Y, et al.: Pan-genomic analysis provides novel insights into the association of E. coli with human host and its minimal genome. Bioinformatics. 2019; 35(12): 1987–1991. PubMed Abstract | Publisher Full Text\n\nLuo H, Lin Y, Gao F, et al.: DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 2014; 42(Database issue): D574–D580. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGerdes SY, Scholle MD, Campbell JW, et al.: Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003; 185(19): 5673–5684. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChavda KD, Chen L, Fouts DE, et al.: Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. mBio. 2016; 7(6): e02093–16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu W, Fang L, Li M, et al.: Comparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome. PLoS One. 2012; 7(4): e35698. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoehorst JJ, van Dam JC, van Heck RG, et al.: Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data. Sci Rep. 2016; 6: 38699. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJuhas M, Reuß DR, Zhu B, et al.: Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology. 2014; 160(Pt 11): 2341–2351. PubMed Abstract | Publisher Full Text\n\nSutton G: PGG Core Genes - Tables F1000.xlsx. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "83244",
"date": "28 Apr 2021",
"name": "Kaleb Abram",
"expertise": [
"Reviewer Expertise Comparative genomics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction: The authors provide an adequate background literature detailing attempts by others in the field to produce minimal genomes. A variety of approaches are covered and drawbacks to these attempts are mentioned. The authors also provide sufficient explanation of the need for their approach in addition to experimental approaches. A good overview of their pan-genome graph approach is presented, along with the reasoning for their design choices for the graph.\nTowards end of first paragraph in Introduction - should be _G_ram-negative (name for the Danish microbiologist, Hans Christian Gram)\nLast sentence in last paragraph in Introduction - \"Our method builds directly upon our previous pan-genome work and includes several improvements: 1) being able to _automatically_ use only complete high-quality genomes...\" Surely the previous methods could also have used only complete high-quality genomes as input? My understanding is that the advantage of this new method is that it's now taking steps to ensure that 'bad genomes' are filtered out, and only the 'high-quality' ones are left....\nMethods: Figure 1, 2nd line: \"Compute genome ANI using Mash\". This doesn't make sense, as ANI and Mash are different approaches. Mash does not estimate ANI (as it is a distance). Unless the authors took the distance and subtracted it from 1 before multiplying by 100, they do not have an approximate ANI (see fastANI paper [PMID: 30504855]1 or the Mash paper [their ref. 34] where Mash and ANI methods are compared). Further, the authors state they use type strains and ANI (presumably using the Mash derived approximation which is not ANI) to remove very closely related strains but do not specify what criteria/value was used to determine very closely related strains. Since the authors chose to use a program (GGRaSP) that uses ANI matrixes as the input, it can be assumed that either ANI values were calculated by an unspecified method, or they used transformed Mash values to approximate ANI and need to specify this transformation earlier in the methods. Either way, this should be clearly stated in the methods section, and not leave the reviewer to guess how this might have been done.\n“The 132 genomes were reduced to 109 after removing…” – it is unclear what the condition for removal was. It would be helpful if this was explicitly stated (presumably an approximate ANI value between 95.73% and 97.28%). Also the authors state the minimum ANI between B. subtilis was 97.28% and the maximum ANI of any of the 11 other genomes to the 132 was 95.73%. The 11 genomes referenced here are unclear and the maximum ANI for the 132 is not provided. It is important to clearly bound their values, in order to enable comparison to other studies. For E. coli the parameters used to remove redundancy need to be explicitly stated and how the groups are collapsed (i.e. genomes A to genome B has 99% ANI value, which genomes is removed and which genome is retained?). The authors should explicitly state why they added 2 redundant genomes to the E. coli dataset but did not do similar additions for B. subtilis. While the PGG approach seems fairly good, the heavy reliance on RefSeq annotations could be problematic for other species.\nResults: The results shown in Table 1, and the bottom line is that for both B. subtilis and E. coli, the refined cores are a bit larger (and contain a larger fraction of 'essential genes' for the species). The E. coli core is about a third larger, going from 2200 to 3100. The latter number (3100) seems to be more consistent with what's expected for E. coli, based on many different experiments - historically, there has always been roughly 3000 E. coli genes. So from this perspective, 2218 genes seems a bit too small (and also some of the 'essential genes' were missing from the core.)\nI'm curious as to whether a non-RefSeq gene annotation tool (for example, Prokka) be utilized to improve the consistency of gene calls? The specific results with number breakdowns are very confusing to read on a first pass and require very careful reading to understand the somewhat odd notation being used. This should be cleaned up to enhance readability.\n\nFigure 2 should have a color key containing color to corresponding track to increase readability of this figure. (The same thing for Figure 4 for consistency.)\n\nDiscussion: The discussion surrounding the issue of lab conditions and core regions is a good. In addition, the discussion around noncore OGCs/regions also shows how the proposed pan-genome analysis could be used to identify noncore regions that could be removed that experimental results have been unable to identify. It might have been good to have a brief discussion of the phylogroup-specific cores in E. coli [see PMID: 335005522 - disclaimer - this is a recent publication from our group.]\nThe discussion section overall provides a good wrap up to the paper and summarizes how the PGG approach can be leveraged and the benefits from utilizing this approach.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7014",
"date": "02 Sep 2021",
"name": "Granger Sutton",
"role": "Author Response",
"response": "We thank the reviewers for their thoughtful comments and have attempted to address all of the suggestions in version 2 of our manuscript."
}
]
},
{
"id": "84280",
"date": "26 May 2021",
"name": "Christos Ouzounis",
"expertise": [
"Reviewer Expertise Computational Biology",
"Biological Computation",
"Systems Biomedicine",
"Bioinformatics",
"Protein Structure"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 extensive, complex report provides details about a new methodological approach for the detection of ‘core’ regions of Bacillus subtilis and Escherichia coli. Core regions are defined within the pan-genome context of conserved genomic loci for the two bacterial species, as a case study. An underlying assumption and implicit goal of the study is that the detected core regions largely correspond to ‘essential’ genes, as those have been determined by independent experimental methodology, with implications for synthetic engineering of bacteria. For both purposes, namely the detection of core regions and the correspondence of those to essential genes, this report is an important contribution, especially as it resolves the connection of core to essential genes. It brings to the forefront the use of pangenome analysis for synthetic biology – a factor that so far has been, to our amazement (!), ignored by biotechnologists. Solid work and a significant contribution to the field.\nMajor comments:\nA general stylistic observation is that the manuscript is dense, in particular the Introduction and Methods are quite extensive and discursive, the Introduction containing multiple quotes from previous works. While this is not necessarily a bad thing, some details (“in their table 4, etc.” and other quoted phrases from cited papers) could be avoided or better summarized. This level of detail is welcome for experts, but non-experts are at risk to miss the main point and the motivations for this study. A more standard style, perhaps for the first paragraph might be useful, in order to address a wider audience.\n\n“While it is possible to define “essential” genes”: the definition of ‘essential’ genes is problematic as it refers to the growth medium and general environmental conditions, as the authors correctly point out. Therefore, ‘essentiality’ is a functional definition. Core (conserved, species-defining) genes, on the other hand, do not rely on environmental factors but evolutionary history, therefore ‘conservation’ is a structural definition. Coupling those is always tricky, however as the authors state early on in their paper, the equivalence between core and essential genes is indeed their primary hypothesis (“We expect that all truly essential genes for the species/subspecies would be a subset of the core OGCs/regions”). This should be more explicitly stated, perhaps in the first paragraph of the Introduction.\n\nWhat advantage is provided by keeping the directionality of OGCs in the PGG? Is this purely a methodological checkpoint, i.e. improve the detection capability by reducing the number of false positive or negative hits, or is it further used in the analysis and interpretation of the results? Needs to be clarified, as it increases the complexity of the pan-genome turning a set into a graph. There is a passage “PGG refinement to ensure consistent annotation”, which alludes to the actual role of PGG.\n\nAnother general comment connected to the above, esp. major comment 2: the report serves a dual role as a software announcement (update) of JCVI’s pan-genome pipeline software suite, with additional elements and certain conceptual advances, as well as the comparison of the core-vs-essential sets for two of the best studied/sampled species pangenomes. This should be a bit more clearly explained perhaps. The correspondence of core to essential genes is a welcome contribution but may not be the main topic of the manuscript, just a conclusion drawn from the analysis.\n\nFollowing major comment 4: the method does well in identifying core regions and indeed makes a convincing case for an improvement over other methods. Yet, the comparison with essential genes is an addition, but not a comparison against other methods that define core regions. As the authors decided to take this direction, as they improve over their own previous methodology, this point should be qualified appropriately. In other words, the ‘improvement’ can be shown as an incremental step over a previous protocol and explicitly shown that it is validated against ‘essential’ gene sets. If this point is not emphasized, the analysis will be seen as lacking a comparison to another ‘gold-standard’ method (experts know that there is no such thing, yet). Pages 11-12 have some elements of a comparison to another approach, this could be extended by a couple of concluding sentences. A good spot where some concluding remarks can be made might be a short paragraph before the Discussion.\nMinor comments:\nIn Introduction: “We further define a pan-genome graph (PGG) to be a graph”, this should probably follow the paragraph starting “Here we present a pan-genome based calculation...” ?\n\n“For E. coli (and Shigella) we downloaded 1097 complete genomes”, start a new paragraph? Using subtitles for Methods might also be a good idea, to break down the dense text into digestible sections.\n\nFollowing minor comment 2: a mini table with three columns (filtering step, B. subtilis, E. coli) and as many rows as the filtering steps used with the number of genomes at each step might be helpful.\n\n“used by Goodall” (reference 9? missing).\n\n“This is done by blasting” - executing BLAST etc. / “conflicting blast” -> conflicting BLAST...\n\n“to not under call core OGCs/edges”, i.e. to reduce the number of potentialy false negatives. Or, increase coverage.\n\nfor B. subtilis: “3419 (73.5%) core and present in all 108 genomes”: this row in Table 1 should be somehow highlighted, perhaps by color or other means -- it is an important part of the study and a key result.\n\na word for missing genes in the context of potential gene loss and the possibility of including them in future steps (see PMID: 128400371); this is something we (and possibly others) have been trying to implement for pangenome data, without much success. Something to discuss as a partial explanation for ‘key’ (essential?) missing genes in certain lineages within the species pedigree, perhaps?\n\n“For the 34 protein coding genes”... good yet incredibly dense paragraph, a (supplementary) table might help here.\n\nWould the PGG implementation also help future studies in synteny analysis/conservation? Maybe a minor point that can be included in the discussion, with appropriate (1-2) references. A concluding short paragraph following the current one with the WTA region might be a good way to wrap up.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7015",
"date": "02 Sep 2021",
"name": "Granger Sutton",
"role": "Author Response",
"response": "We thank the reviewer for the thoughtful comments and have tried to respond to all of the suggestions including the new table and supplementary table in version two of our manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/10-286
|
https://f1000research.com/articles/10-677/v1
|
28 Jul 21
|
{
"type": "Opinion Article",
"title": "Conceptualizing an inquiry-based lingua-cultural learning through telecollaborative exchanges",
"authors": [
"Murod Ismailov"
],
"abstract": "In recent years, telecollaboration has been gaining popularity among scholars, teachers, and students engaged in foreign language education because it facilitates the use of Internet-mediated communication tools to connect language and culture learners in geographically distant locations. Telecollaboration, as currently viewed in academic and classroom settings, places greater emphasis on the development of learners’ intercultural communicative competence. The problem with this approach is that this process may not consider the possibility that learners engaged in online intercultural exchanges could have limited or no knowledge about certain aspects of their own lingua-culture. We argue that, for learners to effectively share lingua-cultural knowledge with their online peers abroad, there must be a framework that supports the construction of learners’ own intra-cultural knowledge to provide a solid foundation for intercultural learning and communication. In this paper, we develop an inquiry-based model of telecollaboration incorporating both inquiry and online exchange based on the inquiry cycle, which includes engagement, exploration, explanation, elaboration, and evaluation. This paper builds a case for the application of inquiry-based telecollaboration in a real classroom environment, which could not only help learners obtain and eventually share more authentic, deeper knowledge about their lingua-culture, but also promote informed intercultural exchange.",
"keywords": [
"telecollaboration",
"inquiry-based learning",
"intercultural communication",
"intra-cultural learning",
"online exchanges",
"opinion paper"
],
"content": "Introduction\n\nIn one of the early essays about the role of the Internet in foreign language instruction published in 1993, William J. Wyman pointed out that network technology would soon enable us ‘to do things differently, to learn in new ways, to see old things in new ways’ (Wyman 1993, 28). This was the time when, in Wyman’s own words, a group of foreign language teachers invited to his workshop were serious when asking him questions, such as ‘How much will it cost me (or my department) to send email to Russia?’ or ‘By the way, can I send email to Russia?’ (26). More than 25 years later, foreign language teachers and their students can not only send emails to any person in any country in the world, but also engage in discussions; exchange ideas; make presentations; practice their speaking, writing, reading, and listening skills; and instantly get feedback from their partners through real-time communication applications (Guth and Helm 2010).\n\nIn the academic literature, this form of interaction is known as telecollaboration, with some authors labelling it ‘an online intercultural exchange’ (O’Dowd 2007) or ‘Internet-mediated intercultural foreign language education’ (Belz and Thorne 2006). Telecollaboration is an important aspect of foreign language education because it highlights the importance of intercultural learning and communicative competence in the process of foreign language acquisition (Byram 1997; O’Dowd 2012). Telecollaboration allows instructors to engage students through synchronous and asynchronous communication with representatives of other cultures in geographically distant locations by using free and accessible communication tools such as email, Skype, Zoom, or Google Hangouts. Such projects, ideally facilitated by their respective institutions, provide learners the opportunity to learn about other cultures and their socio-linguistic norms and patterns through interactions with peers while staying within the supportive context of their foreign language classroom (O’Dowd 2012).\n\nThus, the main objective of such telecollaborative exchanges is not merely to provide a platform for language practice, but to promote the development of intercultural communicative competence among learners (Byram 1997) through interaction, exchange (Belz and Thorne 2006), and structured tasks (O’Dowd and Waire 2009). In other words, the aim of online exchanges and, more broadly, foreign language instruction, is no longer to produce near-native speakers but, in the words of Byram (1997, 12), intercultural speakers who can ‘see and manage the relationships between themselves and their own cultural beliefs, behaviours, and meanings [...] and those of their interlocutors’. Therefore, it is suggested that telecollaboration pieces together language and inter- and intra-cultural learning to help learners become more effective communicators (Belz and Thorne 2006).\n\nHowever, our examination of existing telecollaboration cases suggests that the intra-cultural learning aspect of online exchange is the least academically researched. In other words, while the foreign language and intercultural learning aspects of telecollaboration have been extensively studied by scholars and practitioners, intra-cultural learning has not been sufficiently addressed by field experts. Telecollaboration places greater emphasis on the development of intercultural communicative competence but, in the majority of the works reviewed, rarely takes into account the possibility that learners engaged in online intercultural exchanges may not have sufficient awareness of their own lingua-culture. Latest research in telecollaboration reveals that many teachers and facilitators continue to ‘teach the same thing in a different way’ (Kern, Ware, and Warschauer 2004), failing to help learners revisit the cultural precepts and phenomena within their own cultures.\n\nIn the telecollaboration context, we approach intra-cultural learning as a process of (re)discovering novel, sharable knowledge related to one’s own culture, language, and communicative patterns. It is an important constituent in evidence-based intercultural knowledge sharing between online exchange partners. The introduction of a functional framework for incorporating intra-cultural learning into telecollaborative projects could increase the effectiveness of online intercultural exchanges. We agree with Kern, Ware, and Warschauer (2004) that telecollaboration presents an opportunity for educators to use Internet-mediated tools not so much to teach the same thing in a different way, but to help learners carry out collaborative inquiry and acquire authentic knowledge by viewing their expanding identities and communication strategies as resources in the process.\n\nIn this study, we develop the notion of ‘inquiry-based telecollaboration’, as a practical framework for nurturing learners’ intercultural knowledge with the goal of developing their intercultural communication skills. Our study suggests that the practical application of inquiry-based telecollaboration could facilitate the development of foreign language learners’ essential skills of lingua-cultural inquiry and evidence-based knowledge sharing.\n\n\nLiterature review\n\nInformation and communications technology bring people of different cultures and nations closer together, especially through common media such as the Internet. High-speed Internet communications provide foreign language educators with multiple instruction tools and resources that enable cost-effective, time-efficient, and productive lingua-cultural exchange and learning (Kern, Ware, and Warschauer 2004; O’Dowd 2007; Guth and Helm 2010; Doolly 2017). Thorne (2010) points out that many of these new Internet-mediated learning practices that simultaneously incorporate multiple forms of media, such as text, voice, and video, used in both local and globally distributed settings, extend beyond traditional modes of information exchange dominated by print-based text.\n\nStudies over the past two decades have provided important information on the benefits of telecollaboration, including expanding L2 pragmatic competence among foreign language learners (Belz and Kinginger 2003), enhancing grammatical proficiency (Lee 2002), vocabulary (Dussias 2006), and spoken communication (Abrams 2003). Other studies have reported positive outcomes in enhancing students’ independent learning (Schwienhost 2000) and developing multiliteracies that include digital, organisational, and critical skills (Guth and Helm 2010).\n\nThe intercultural learning dimension of online exchanges is gaining prominence with culture and cultural knowledge playing a stronger role in the foreign language curriculum, and language learners being described as ‘cultural mediators’ and ‘intercultural speakers’ (Byram 1997). Telecollaboration also highlights the importance of differentiating between multilingual and intercultural communication (van der Kroon, Jauregi, and ten Thije 2015). Students learning a foreign language should not only develop grammatical competence, but also understand how language is used in a socially and culturally appropriate way. This awareness helps learners communicate and collaborate with speakers of other languages on equal terms, while simultaneously aware of their own identities and those of their exchange partners (Savignon 2004).\n\nCommunication and collaboration are facilitated through telecollaborative tasks. O’Dowd and Waire (2009, 176-177) identified three main categories of tasks to systematise telecollaborative exchange: (1) information exchange, (2) comparison/analysis, and (3) collaboration/product creation. Information exchange tasks involve authoring ‘cultural autobiographies’, conducting virtual interviews, engaging in informal discussions, and exchanging stories. Comparison/analysis tasks include comparing parallel texts and class questionnaires, analysing cultural products, and translating. Collaboration/product creation includes working together to create products, transforming text genres, conducting ‘closed outcome’ discussions, and making cultural translations/adaptations.\n\nThe introduction of the concept of intercultural communicative competence has led to a focus on raising learners’ awareness of how their own cultural background and assumptions may impact their attitudes towards and communication with people from other cultures (Alred, Byram, and Fleming 2003; Corbett 2003). A key characteristic of intercultural communicative competence is the fact that it prepares learners for exposure to all cultures, including their own (Mughan 1999, 64). This is where the notion of intra-cultural communication gains prominence; thus, at least in theory, it should emerge as a crucial component in online intercultural exchange projects.\n\nSamovar and Porter (2001) defined intra-cultural communication as communication that takes place between members of the same dominant culture, but with different values, as opposed to intercultural communication, which is the communication between two or more distinct cultures. According to Kecskes (2012, 68), this approach has led to a common but misinformed perception of inter-culturality as the main reason for miscommunication (House 2003; Kecskes 2008). Wray (2002) suggested that intra-cultural communication is dominated by preferred ways of saying things and, according to Kecskes (2008), of organising thoughts within a particular speech community. This occurs differently in intercultural communication because the development of ‘preferred ways’ requires time and conventionalisation within a speech community due to the flexibility of human languages (Kecskes 2012).\n\nIntra-cultural communication is intertwined with the notion of intra-cultural learning. All knowledge and information is formed or received by learners at a certain time via family, school, media, or broader societal exposure (Pinker 1999). This is especially true regarding learners’ own culture, native language, and norms of communication. This knowledge forms unwittingly through daily repetitive exposure, as evidenced by an average, healthy child less than six years who already can speak their native language without ever attending a language class (Chaney 2001). Typically, by early adolescence, this native lingua-cultural knowledge has already been formed to the extent that it allows the person to communicate with other members of the same community not only grammatically, but also in culturally appropriate ways. This process of native lingua-cultural knowledge development slows by early adulthood, but does not end completely (Crawford-Lange and Lange 1987).\n\nLearners acquire knowledge of their own language and culture dynamically, and the search for new knowledge stems from their motivation, expertise, and future career choices, especially among professional linguists, public speakers, and culturologists (Breen 1985). This is also true with regard to telecollaboration and online intercultural exchanges from which participants gain original insights of not only their peers’ language – manifested in the way they speak, pronounce words, and form expressions – but also their culture – the way they live, do things, articulate ideas, and understand concepts (Lamy and Goodfellow 2010). Many participants of online lingua-cultural exchanges share information about their language and culture based on their pre-existing, often limited, lingua-cultural knowledge.\n\nParadoxically, the abundance of highly specialised but easily searchable knowledge on the Internet (Jones and Kucker 2001) for anyone possessing a smartphone or computer may be the reason for Internet-mediated language exchanges eventually turning into a demotivating activity in which participants’ expectations of new cultural and linguistic knowledge are not met during telecollaborative interactions. Thus, online language and intercultural exchanges should be designed considering learners’ awareness of their own culture and language, its uniqueness and originality and, importantly, the level of knowledge credibility to be shared between online exchange partners.\n\nByram (1997, 53) proposed the concept of ‘critical cultural awareness’, defined as an ability to evaluate critically and on the basis of explicit criteria, perspective, practices and products in one’s own and other cultures and countries. Similarly, Risager (2007) suggested that intercultural competence comprises knowledge, skills, and attitudes at the interface between several cultural areas, including the students’ own culture and a target culture.\n\nOur review of the literature showed that telecollaboration to date has been extensively studied in relation to intercultural communication, but no major studies have been conducted to explore a systematic connection between online exchange and intra-cultural communication and learning. In the next section, we introduce the inquiry-based model of telecollaboration aimed at filling this gap, thus yielding both conceptual and practical implications for designing online intercultural exchanges.\n\n\nInquiry-based model of telecollaboration\n\nExisting telecollaboration cases reveal that online intercultural exchange necessitates the presence of two or more linguistically and culturally distinct groups of individuals whose goal is to learn about each other’s language and culture through various Internet-mediated activities, such as information exchange, comparison and analysis, and collaboration and product creation (see Figure 1).\n\nIn this conventional form, learners on both sides consider themselves representatives of their culture and native speakers of their language, viewing each other as possessors of authentic cultural and linguistic knowledge. We encounter four problems related to this approach. First, the cultural knowledge that a host member shares with a foreign member is often subjective, especially related to activities involving interpretation, contextualisation, comparison, and negotiation of meaning. However, online exchange may be less susceptible to subjectivity when partners engage in a rather technical language exchange, such as vocabulary learning, sentence construction, and practising correct pronunciation and grammar.\n\nThe second problem arises when the limited online interactions further augment learners’ stereotypical view of their partners’ culture. This impacts learners on both sides: foreign members solidify their stereotypes based on limited information gained through a short exercise, while host members remain convinced that these stereotypes concerning certain aspects of their lingua-culture are well-grounded because of insufficient intra-cultural knowledge. The third problem is related to foreign member generalising issues based on their interaction with a limited number of ‘host’ members.\n\nThe fourth and perhaps more salient problem is that the majority of telecollaborative tasks reported to date tend to initiate intercultural contacts without addressing the host members’ lack of knowledge about their own lingua-culture. This creates a learning environment in which foreign members may find it difficult to acquire authentic knowledge about the target culture, and host members might miss the opportunity to expand their knowledge reservoir of their own culture, which lies at the core of building intra-cultural competence. An integral part of becoming an intercultural speaker is intra-cultural learning; that is, learning about one’s own culture and developing the ability to reflect on the origin of one’s own beliefs and behaviours.\n\nThese combined problems present a challenge in the effective use of Internet-mediated tools for developing intercultural communicative competence. The modern multimedia-rich Internet offers enough terabytes of knowledge on any of the world’s cultures and languages to render the whole idea of online intercultural exchanges more burdensome to some learners, unless there is a framework that could help online exchanges pro-actively develop intercultural communicative competence. The question that we pose here, therefore, is: how could telecollaborative activity be re-designed to minimise the impact of these factors on the development of intercultural communicative competence aimed at online exchanges? Addressing this question brings us to intra-cultural communication and learning, or to be exact, their paucity in the design of most contemporary telecollaborative projects.\n\nOne important yet insufficiently explored area concerns the relationship between inquiry and the creation of a new lingua-cultural knowledge. In our proposed model, we closely examine inquiry-based learning because it represents a more systemic and scientific way of constructing new knowledge by following certain procedures, methods, and practices (Keselman 2003). Inquiry-based learning according to Pedaste et al. (2012) is a process of discovering new causal relations, with the learner formulating hypotheses and testing them by conducting experiments and/or making observations. Several studies support the effectiveness of inquiry-based learning as an instructional approach, suggesting that it can improve different skills, such as identifying problems, formulating questions, collecting and analysing authentic information, and presenting results and conclusions (Alfieri et al. 2011; Furtak et al. 2012).\n\nBecause our main concern about the effective implementation of telecollaboration as a medium of intercultural learning is the possible lack of host members’ knowledge of their own culture, the inquiry methods, especially those related to observation, identifying problems, formulating questions, and conducting experiments (interviews, surveys, etc.) provides a framework for the construction of intra-cultural knowledge aimed at elevating learners’ self-reflection and self-awareness. This telecollaboration model thus introduces an important new phase in the online exchange process that is designed to help host members discover authentic intra-cultural knowledge through inquiry within their own lingua-cultural environment (see Figure 2).\n\nAn inquiry-based model of online intercultural exchange can promote active learning because participants are expected to collect authentic knowledge by engaging members of their own community and then share the findings with their online exchange partners. Inquiry-based activity creates authentic contexts, and research in cognitive science highlights its role in effective learning (Greeno, Collins, and Resnick 1996). Edelson, Gordin, and Pea (1999) claim that authentic activities provide learners with the motivation to acquire new knowledge, an opportunity to incorporate it into their existing knowledge, and conditions in which to apply this knowledge in real life. While the transmission and reception of knowledge in conventional online intercultural exchange is passive, an inquiry-based model is active. As a practise aimed at discovering authentic perspectives within one’s own culture (stereotypes, perceptions, beliefs, norms of behaviour) and language (patterns of verbal and non-verbal communication, geographic peculiarities of language), inquiry-based telecollaboration also promotes informed intercultural communication.\n\nIt is important to mention that in our proposed telecollaboration model, the ‘inquiry phase’ and the ‘online exchange phase’ are not mutually independent processes; they are organically intertwined to provide a cohesive learning experience for online exchange partners. To understand this connection, one should recognise that inquiry itself is a process containing smaller, logically connected units (phases) that guide learners and draw attention to important features of scientific thinking. This set of connections represents an inquiry cycle (Pedaste et al. 2015).\n\nVarious academic studies of inquiry-based approaches to learning and teaching have attempted to propose different versions of an inquiry cycle. For example, in their meta-analysis of the strengths of over 30 inquiry-based learning frameworks, Pedaste et al. (2015) suggested five distinct general inquiry phases: orientation, conceptualisation, investigation, conclusion, and discussion. An inquiry cycle developed by White and Frederiksen (1998) also identified five inquiry phases, labelled question, predict, experiment, model, and apply.\n\nDespite the numerous variations in learning cycles, the one used in this study is the 5E Instructional Model (Bybee et al. 2006; Bybee 2009) in which each phase is highlighted using five words: engagement, exploration, explanation, elaboration, and evaluation. This approach is useful for inquiry-based telecollaboration design because it provides a format for online exchange that builds on what learners already know. Since the average host members already possess some knowledge of their lingua-culture, the 5E Instructional Model helps them revisit that knowledge from other angles and find new patterns and relationships. Moreover, the experience of undergoing all five phases enables online exchange participants to develop their understanding of a concept across time.\n\nThe 5E Instructional Model emphasises not only students’ hands-on knowledge acquisition and learning, but also the role of instructors in facilitating this process, which is why it is known as an instructional model. The role of teachers is reflected in a widely cited definition of telecollaboration as ‘institutionalised, electronically mediated intercultural communication under the guidance of a lingua-cultural expert (i.e. teacher) for the purposes of foreign language learning and the development of intercultural competence’ (Belz 2003).\n\nEven in the context of conventional telecollaborative projects in which a teacher's active involvement in conducting online tasks is not necessary because learners typically interact entirely with their distant partners (O’Dowd 2013), there is considerable need for instructors’ indirect participation and regular guidance. Right from the early stages of the project, teachers are responsible for designing tasks, choosing tools, and establishing the rules of engagement and a timeframe for self-reflection and group feedback in order to enable productive collaboration and communication between two or more socio-linguistically and culturally distinct groups of learners (Lewis, Chanier, and Youngs 2011). Because inquiry-based telecollaboration adds an additional layer to the design of an online exchange project, that is ‘intra-cultural inquiry’ phase, teachers’ guidance becomes even more significant.\n\nThe inquiry cycle contains multiple units that can be rolled out across both ‘inquiry’ and ‘online exchange’ phases (as shown in Figure 3), thereby creating a holistic framework that connects intra-cultural learning with the process of developing intercultural communicative competence. Below, we describe the five phases of inquiry-based telecollaboration that have been modified from the 5E Instructional Model. To illustrate the main points of our approach, we shall also use the hypothetical example of a telecollaborative project conducted between two groups of college students based in Japan and the US on the socio-cultural topic of ‘Parenting culture in Japan and the US: differences and similarities’. We assume that both groups have upper-intermediate knowledge of their exchange partners’ language, that is, Japanese and English, respectively. During this hypothetical project, participants virtually interviewed their partners, with the aim of practicing linguistic skills and acquiring deeper knowledge about their culture.\n\nIn this initial ‘inquiry’ phase, teachers work closely with their students to evaluate their prior knowledge and identify possible gaps in their current understanding of the topic. The key is that students at this phase are focussed on the knowledge and knowledge gaps relating to their own culture and society, not those of their online partners. Through visual demonstrations, questioning sessions, and graphic organisers, teachers help students clarify their thinking, make connections to prior knowledge and what is to be discovered, and stay mentally engaged in the new learning experience. One of the key responsibilities of the inquiry-based telecollaborative teacher is to stimulate interest and generate curiosity in their learners throughout the project. Thus, in our hypothetical telecollaborative project, the Japanese students may start brainstorming with an opening question ‘What do we already know about parenting in Japan?’. American students, on the other hand, ask ‘What do we already know about parenting in the US?’. One effective technique may involve the use of real KWL charts, wherein learners make a list of what they already Know, Want to know, and (eventually) have Learnt about the topic.\n\nThe students now proceed to the ‘core’ inquiry phase, involving an active exploration of the issue in the context of their own culture. In other words, they begin building essential intra-cultural knowledge by searching for authentic information. In terms of knowledge seeking, learners continue to stay within the boundaries of their own lingua-culture. This increased awareness about the specific aspect (topic) of their culture eventually helps both them and their online exchange partners to develop more effective intercultural understanding and communication. In this phase, students are encouraged to learn and apply core inquiry skills, such as observing, questioning, investigating, testing predictions, hypothesising, and eventually communicating with their online exchange partners.\n\nIn the context of our hypothetical telecollaborative project, both Japanese and American students (individually or in teams) will engage in real-life observations and collect and record data through face-to-face or online interviews, Facebook or Twitter polls, focus group interviews, and so forth. For example, one group of Japanese students may decide to conduct face-to-face interviews with their parents and grandparents in order to better understand the peculiarities of parenting culture in Japan, whereas another group may organise an opinion poll of younger and older generations of parents using a popular instant messaging application, LINE. In both cases, students will have to design structured, semi-structured, or open-ended questionnaires based on the work conducted during the ‘engagement phase’ (e.g. KWL charts).\n\nThe exploration phase of the project possibly incorporates the most critical inquiry-based experience aimed at developing students’ essential intra-cultural knowledge. This phase is unique because the students get a ‘hands-on’ experience collecting authentic intra-cultural insights based on real-world observations and explorations. Although they are encouraged to work in a co-operative learning environment without direct instruction from the teacher, teachers nonetheless actively guide students in their inquiry, regularly asking probing questions to enhance their students’ understanding.\n\nIn inquiry-based telecollaboration, the explanation phase signals the beginning of the ‘online exchange phase’, in which learners from project countries (cultures) connect with the aim of explaining the results of their intra-cultural inquiry. Students work together in pairs or small groups and verbalise their understanding of the information gathered in their respective countries during the exploration phase, seek and analyse patterns in their data, and describe what they observed. Teachers, on the other hand, begin playing more subtle roles, allowing students to actively interact with each other.\n\nDuring this phase, the Japanese and American participants of our hypothetical project connect with each other using Skype. The teachers previously created small groups and assigned two American and two Japanese students to each of the groups. The goal of this interaction is to conduct virtual interviews during which American students have the opportunity to share their observations and knowledge pertaining to parenting culture in their home country with their Japanese partners, and vice versa. The difference between conventional and inquiry-based telecollaborative environments is that the latter provides a stronger intra-cultural knowledge base, allowing for informed intercultural dialogue between the students. New insights and ideas are likely to be generated by the time participants complete the explanation phase.\n\nThe activities in this second ‘online exchange’ phase are designed to help exchange partners continue to collaborate in order to apply their new understanding of cultural concepts (similarities and differences in parenting cultures between two countries) shared by each country member. Students are encouraged to compare notes with their peers or formulate new observations of the concepts they have acquired. The goal of this phase is to help learners develop a deeper and broader understanding of each other’s cultural concepts. With this in mind, our hypothetical virtual groups of Japanese and American students conduct additional collaborative investigations (e.g., social media polls, surveys, mass media analyses, etc.) or activities such as reading articles and books, writing a blog post, creating web pages, or exploring related topics on the Internet through WebQuests. Teachers’ engagement remains minimal.\n\nThe evaluation phase may take different forms, it may continue as an ‘online exchange’ activity or students may return to their respective classrooms to assess the project’s achieved objectives. The aim is to encourage students to reflect on what they have learnt about their own and their partners' culture, pose questions, and illustrate their knowledge (understanding) and skills (abilities). For example, after completing online presentations, both American and Japanese students may return to their KWL charts and complete the ‘What I Have Learnt’ part. In this phase, teachers play an important role in evaluating the project’s success. The use of various forms of assessment – such as portfolios, concept maps, group presentations, and journal logs – may serve as important evidence of student learning. Students can also conduct self- or peer-assessments. This phase may also incorporate a summative assessment such as a quiz, test, or writing assignment. Teachers may conduct class surveys with the goal of understanding the problems students face during both intra-cultural learning and intercultural online exchange.\n\nThese five phases of inquiry-based telecollaboration represent a holistic framework that can practically help foreign language learners gain in-depth knowledge of their own lingua-culture in order to support more engaging intercultural communication with peers on a global level, and develop essential skills of inquiry and evidence-based knowledge sharing. The future development of this model could demystify the image of ‘inquiry-based learning’ as a method used mainly in science labs, instead promoting it as a practical and effective learning method in social sciences and humanities.\n\n\nConclusion\n\nSince its early emergence in the 1990s, telecollaboration has been gaining popularity among foreign language and culture learners mainly because of its broad use of communication technologies and the Internet to connect with lingua-cultures globally. With technological advancements, which began placing greater emphasis on user-generated content, ease of use, participatory culture, and interoperability for end users, as reflected in the phenomenon known as Web 2.0, it was inevitable that telecollaboration would soon follow suit. In 2010, a group of renowned experts joined forces and published a volume titled ‘Telecollaboration 2.0: Language, Literacies and Intercultural Learning in the 21st Century’ (Guth and Helm 2010), reflecting the prevailing role of communication technologies and the Internet in the design and effective execution of telecollaborative projects.\n\nOn the contrary, the broader aim of inquiry-based telecollaboration is to deemphasise the role of technology and the Internet in intercultural education, intending instead to accentuate the importance of acquiring authentic lingua-cultural knowledge and, in Byram’s words, develop ‘critical cultural awareness’ (1997, 35). Technology is only a medium, albeit an important one, whose underlying goal is to help learners access such lingua-cultural knowledge in a fast, engaging, and cost-effective way.\n\nDespite its relatively straightforward design, several questions still remain regarding the real-life implementation of the proposed model of telecollaboration. Therefore, future research on inquiry-based telecollaboration should address the issues that can be placed on four different levels, in accordance with the inventory of possible reasons for the breakdown of conventional telecollaborative exchanges (O’Dowd and Ritter 2006): the individual level (learners’ attitudes and motivation during ‘inquiry’ and ‘online exchange’ phases), the classroom level (how inquiries and exchanges were organised and implemented in both classes, and which telecollaborative tasks proved effective when incorporated within the inquiry model), the socio-institutional level (different levels of access to technology, challenges in designing inquiry and experiments, institutional attitudes toward online learning), and the interaction level (the quality and outcomes of intercultural communication that occurred between exchange partners). Answers to these questions may be found through continuous comprehensive studies that could potentially shed light on other crucial aspects of Internet-mediated intercultural exchanges.\n\n\nData availability\n\nNo data is associated with this study.",
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}
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[
{
"id": "90630",
"date": "02 Aug 2021",
"name": "Rustamjon Urinboyev",
"expertise": [
"Reviewer Expertise Social sciences"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author explores how intra-cultural language learning occurs through telecollaborative exchanges. He has rightly identified the gap in the literature, which is an understudied topic of the systematic connection between the online exchange and intra-cultural communication and learning. To fill this gap, the author proposes an inquiry-based model of telecollaboration, incorporating both inquiry and online exchange through macro- and micro- levels. One small comment would be to emphasize the argument in the section 'Conclusion'. I recommend this manuscript for indexing.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "90631",
"date": "17 Aug 2021",
"name": "Sherzod Muminov",
"expertise": [
"Reviewer Expertise Humanities",
"specifically history"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 innovative paper that draws attention to a gap in scholarship on the role of intra-cultural knowledge in building effective telecollaborations between learners from different cultures. The author rightly underlines the importance of intra-cultural knowledge and understanding, and not simply of intercultural differences, in establishing mutually beneficial telecollaborations in various educational settings. The paper then proposes a new inquiry-based model of intercultural communication. The model is well defined and explained through a five-phase process, with real-life examples and a lucid analysis of impacts and outcomes. As such, this paper contributes to current knowledge on telecollaborations and potentially in other fields, and should be recommended for indexing.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "91517",
"date": "25 Aug 2021",
"name": "Pramila Neupane",
"expertise": [
"Reviewer Expertise Comparative and International Education",
"Education Policy",
"Language 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 author examines the telecollaborative exchanges in foreign language education and emphasizes the importance of intra-/inter-cultural language learning for building intercultural communicative competence. Using the 5E Instructional Model suggested by Bybee et al. (2006), the author conceptualized an inquiry-based model of telecollaboration. This paper is a timely contribution by the author as telecollaboration is gaining popularity in teaching and learning in various fields in recent years.\n\nThe author's opinion and arguments would be stronger if the author could discuss how the model works in different teaching/ learning environments. I recommend this manuscript for indexing.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-677
|
https://f1000research.com/articles/10-293/v1
|
16 Apr 21
|
{
"type": "Research Article",
"title": "Sequence diversity and evolution of infectious bursal disease virus in Iraq",
"authors": [
"Ali Hadi Abbas",
"Haider Abas AL saegh",
"Furkan Sabbar ALaraji",
"Haider Abas AL saegh",
"Furkan Sabbar ALaraji"
],
"abstract": "Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools. Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq. Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.",
"keywords": [
"infectious bursal disease",
"VP1 gene",
"VP2 gene",
"hvVP2",
"poultry viral diseases",
"Gumboro",
"RNA viruses",
"very virulent vvIBDV."
],
"content": "Introduction\n\nInfectious Bursal Disease (IBD), or Gumboro, is a highly contagious disease of poultry, characterized by severe immune suppression (Van Den Berg, 2000). The birds surviving IBD suffer from poor feed conversion rate, poor growth, decreased egg production and quality, and reduced efficiency of vaccines. The economic losses due to IBD are not limited to the direct effect of the diseases, but also from decreasing the overall immune status of the flock leading it to be vulnerable to other diseases characterized by a high mortality rate such as Newcastle disease and Infectious Bronchitis. This immune suppression is a result of damage of Bursa of Fabricius, the target of IBDV, causing severe suppression to humoral and cellular immunity in the early stages of the bird’s life (Rautenschlein et al., 2002).\n\nThe causative agent of Infectious Bursal Disease (IBD) belongs to a viral family called Birnaviridae genus avibirnavirus, characterized by a double-stranded RNA viral genome consisting of two segments: the larger segment A and the smaller one B (Dobos et al., 1979). Segment A, known to contain the open reading frame (ORF), encodes for the capsid protein that comprises the epitope, which in turn interact with protective antibodies (By Kevin J. Fahey, 1989; von Einem et al., 2004; Coulibaly et al., 2005), while segment B hosts the ORF VP1, which is responsible for viral replication and, hence, pathogenicity of the virus (von Einem et al., 2004).\n\nThis virus is prone to frequent genomic recombination events, genetic reassortments of the RNA segments, and mutations that could allow changes in the virulence and most likely the antigenicity of the virus (Jackwood et al., 2008; Ibdv, Jackwood and Sommer-wagner, 2011).\n\nInfectious Bursal Disease Virus (IBDV) serotype1 is the most important serotype and it can be classified into three subgroups according to their virulence: sub-clinical (scIBDV), classical virulent (cvIBDV) and vey virulent (vvIBDV) (Berg et al., 2004). However, antigenic drift, shift and even a single nucleotide polymorphism (SNP) have shown to play a major role in creating antigenically different subtypes. These changes have been found to affect a specific region in the VP2 gene called hyper variable region (hvVP2) (Bayliss et al., 1990; Eterradossi et al., 1997, 1998; Brandt et al., 2001).\n\nDespite the vaccination programs that have been applied across the world, outbreaks in poultry flocks are still frequent, making IBD one of the most important diseases that hampers the poultry industry worldwide. In Iraq, although vaccination is practiced, the infection rate is high. Furthermore, studies on sequence diversity of the genes VP1 and VP2, as well as the link between the hvVP2 region of local strains with available vaccine strains, are limited. Here, we analysed the pathogenicity and the sequence diversity of the antigenic determinant (VP1 and hvVP2) of an isolated strain from Najaf city and all other sequences from Iraq isolated from other regions of the country available in GenBank. Furthermore, Iraqi sequences were compared to global and vaccine strains of IBDV.\n\n\nMethods\n\nThe study was conducted according to ethical guidelines approved by the committee of ethical approvals of Faculty of Veterinary Medicine, University of Kufa, BEC-20 in Jan_2019.\n\nA newly died bird from an outbreak of IBDV from a flock in An-Najaf province, was post-mortem examined and the enlarged Bursa of Fabricius was incised and examined.\n\nBursa contents was sampled on (FTA) card (Whatman® FTA® card technology) with four sample areas per card containing cell wall lytic enzymes, protein denaturing agents and inhibit the nucleases effects on nucleic acids (Ali et al., 2017).\n\nRNA samples on the FTA card were then sent to AniCon® Labor GmbH (Muehlenstraße 13a 49685 Hoeltinghausen, Germany), where the extraction of the IBDV RNA from FTA card was performed using Kylt® RNA/DNA Purification Kit according to the manufacturer’s protocol.\n\nReverse transcription, PCR amplification and Sanger sequencing of targeted regions of VP1 gene and hvVP2 were performed in AniCon® Laboratories. The partial VP1 and VP2 gene sequences performed in this study were deposited in the GenBank database under accessions MW020533 and MW020534, respectively.\n\nBLASTn search (Altschul et al., 1990) was performed against the NCBI database to show the closest matches to the sequenced ones in this study. NCBI BLASTn search results of partial VP1 and partial VP2 sequences and other sequences of vvIBDV from other countries were obtained from GenBank repositories (Extended Data: Table 1) (Abbas, 2021).\n\nA similar approach was used to get sequences for hvVP2. Sequences of the VP2 gene of known vaccine strains routinely used in the preparation of vaccines against IBDV worldwide, and available sequences of hvVP2 from Iraq, were also downloaded (Extended Data: Table 1).\n\nThe IBDV VP1 targeted region obtained in this study was aligned with other similar sequences downloaded from GenBank repositories using MUSCLE (Edgar and Edgar, 2004), alignments were manually edited, gaps removed and the percentage of pairwise sequence similarity matrices (Extended data: ABIC_andVentriVaccin_IraqV2_DNA_percentSimilrity_matrix.csv) (Abbas, 2021), were generated using the UGENE pipeline version 35.1 (Okonechnikov et al., 2012). This was also conducted for the hvVP2 nucleotide sequences.\n\nThe evolutionary history was obtained by the neighbour-joining (NJ) method (Saitou and Nei, 1987), with 1000 bootstrap replicates (Felsenstein, 1985), while the evolutionary pairwise distances (Extended data: IBVD_VP1_NCBI_Hits_OurVP1.txt), (Abbas, 2021), were calculated by Maximum Composite Likelihood Method (MCL) using Tamura-Nei model (Tamura and Nei, 1993).\n\nHeuristic search of initial tree was obtained automatically by applying Neighbour-Joining and BioNJ to a matrix of pairwise distances estimated by the MCL method, then the topology was selected with superior log likelihood value.\n\nFor hvVP2 sequences of Iraq and vaccine strains, a time-tree to the NJ phylogenetic tree was inferred using the RelTime method (Tamura et al., 2012; Tamura, Tao and Kumar, 2018). The time-tree was estimated using 31 correction restraints and all ambiguous positions were removed for each sequence to give a final dataset of 309 sites. Molecular phylogenetic analysis was also performed using the maximum-likelihood method based on the Tamura-Nei model (Tamura and Nei, 1993).\n\nAll DNA sequence analyses and evolutionary inferences were performed using MEGAx software version 10.1.8 (Kumar et al., 2018) and the plotting of datasheets to the phylogenetic tree was achieved by iTOL web application (Letunic and Bork, 2019) (Extended data: TextFileToShow_GRADIENT_iTol_VP2) (Abbas, 2021).\n\n\nResults\n\nUsing molecular methods, we analysed the sequences of the VP1 gene and hvVP2 sequenced in this study, and other sequences conducted in previous studies in order to assign the IBDV in Iraq to its pathogenic group and predict the best vaccine strain(s) that could be used to evoke the highest possible protection level against IBDV.\n\nA 544 bp targeted fragment (244-787 bp) of VP1 gene was sequenced. This sequence, along with other sequences that showed similarity by BLASTn search, were aligned and a phylogenetic tree was constructed using NJ method to reveal the relatedness of the isolated sequence to the existing genogroups/pathogroups of IBDV, regional and worldwide. The VP1 region sequenced in this study clustered in a monophyletic group with strains belonging to vvIBDV genogroup 3: a strain isolated from Kuwait, two strains from Iraq, and one from New York, USA (Figure 1). The analysis also showed that the most similar sequences from neighbouring countries other than Kuwait were isolated from Jordan.\n\nThe partial VP1 sequence achieved in this study was clustered in a branch with two sequences from Iraq, one sequence from Kuwait and one from New York, USA. Those sequences were sequenced in previous studies (shaded in green colour). The evolutionary history was inferred by using the Maximum Likelihood method and Tamura-Nei model (Tamura and Nei, 1993). The bootstrap consensus tree inferred from 1000 replicates (Felsenstein, 1985) is taken to represent the evolutionary history of the taxa analysed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura-Nei model (Tamura and Nei, 1993) and then selecting the topology with superior log likelihood value, the tree was drawn to scale. This analysis involved 145 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 528 positions in the final dataset. The phylogenetic data analyses were performed using MEGAx platform (Kumar et al., 2018) (Extended data: IBVD_VP1_NCBI_Hits_OurVP1.txt) (Abbas, 2021).\n\nA 522 bp segment of hvVP2 region between positions 673-1194 bp of VP2 was amplified and sequenced. BLASTn search against NCBI repositories revealed high similarity to sequences of the vvIBDV VP2 gene. Sequence alignment and phylogenetic clustering showed that our sequence paired in a monophyletic group with a sequence isolated from Iraq in 2017 (Figure 2, green shaded). On the other hand, a cluster of sequences from Kurdistan region in northern Iraq (blue shaded) were branched from our sequence (Figure 2). These sequences were isolated in previous studies in 2012. However, a sequence isolated from Iraq in 2017 (named 423) was clustered with others from China, and others isolated from Kurdistan (Figure 2, red shading) were clustered with sequences of vaccine strains (Figure 2). Such discrepancies shed light on possible genetic reassortments and mutations in the genome of vvIBDV, especially in an important region that acts as an epitope and therefore interacts with antibodies against the virus.\n\nOur sequence was clustered in a single branch with other Iraqi sequences collected in 2017 from previous study (green shaded), while other sequences were clustered in different branches. Remarkably, a group of sequences from the north of Iraq were clustered with vaccine strains (red shaded). The evolutionary history was predicted using the Maximum Likelihood method and Tamura-Nei algorithm (Tamura and Nei, 1993). The tree with the highest log likelihood (−11351.20) is shown. The tree was drawn to scale, with branch lengths measured in the number of substitutions per site. This analysis involved 122 nucleotide sequences and a total of 3,261 positions were evoked in the final dataset.\n\nThe putative sequence divergence proposed by previous analyses motivated us to challenge the possibility of the presence of sequence divergence in the VP2 gene within strains. NJ phylogenetic tree grouped our sequence with other sequences from Diyala in central Iraq isolated in 2018 and 2017 (Figure 3, green shaded), while other sequences from Kurdistan, sequenced in 2012 and 2018, were clustered separately (Figure 3, blue shaded). However, a group of sequences from Kurdistan isolated in 2012 clustered with a vaccine strain D78 Intervet (Figure 3, red shaded). Such clustering may indicate an origin of infection from a vaccine strain (Figure 3).\n\nThe molecular time tree was computed using 31 calibration constraints on a phylogenetic tree constructed using Neighbour-Joining method. This analysis involved 31 DNA sequences. All ambiguous sites were omitted for each sequence pair (pairwise deletion option). There are a total of 309 locations in the final dataset. Evolutionary analyses were performed using RelTime (Tamura et al., 2018) in MEGA X (Kumar et al., 2018). The tree was scaled to the molecular divergence time. In general sequences from central Iraq were clustered in a monophyletic group (shaded in green colour), while those of the Kurdistan region showed different grouping (blue and red colour shading).\n\nHence, it is worthwhile to predict the time these different groups diverged. The molecular clock analyses suggest that the divergence of the sequences from central Iraq and those of Kurdistan region occurred in 2008. Interestingly, sequences from Kurdistan which clustered with vaccine strains showed a divergence time similar to that of a live attenuated vaccine strain D78 Intervet (Figure 4).\n\nThe evolutionary history was inferred by means of the Neighbor-Joining method (Saitou and Nei, 1987). The optimal tree with the sum of branch length was 0.38665371 was generated. The replicate test of trees in which the associated sequences clustered together in the bootstrap test of 1,000 replicates are shown. Maximum Composite Likelihood method was used to infer the evolutionary distances and are in the units of the number of base substitutions per site. This analysis involved 31 nucleotide sequences. Ambiguous positions were removed for each pair of sequences. The final dataset contains 309 positions. A heatmap of sequence similarity matrices was plotted using web version of iTOL software (Letunic and Bork, 2019) (Extended data: TextFileToShow_GRADIENT_iTol_VP2), (Abbas, 2021). The heatmap demonstration of DNA sequence similarity plotted colour coded column next to the sequences names as red (the most similar) to blue colour (the least similar). The closest vaccine strains to Iraqi sequences are shaded in blue.\n\nIn order to assess which vaccine strain or strains have the most similar hvVP2 sequence to the Iraqi vvIBDV strains, a phylogenetic analysis and DNA sequence similarity analysis approach was conducted. We speculated that such an approach could predict the best vaccine strain that might be applied in control measures against IBDV.\n\nThis analysis determined that the highest sequence similarity to Iraqi hvVP2 was found in two vaccine strains named Ventry IBDV Plus and ABIC MB71. This showed by both phylogenetic analysis of NJ tree clustering (Figure 4) and the sequence similarity of more than 96% (Figure 5).\n\nSequences of VP2 of vaccine strains Ventri IBDV Plus and ABIC MB71 (blue shaded) showed =>96% sequence similarity (connection lines) to the most sequences from Iraq. Green lines indicating 96% of sequence similarity shown in, blue lines indicating 97% similarity and 98% (red lines) (Extended data: TextFileToShow_connection_iTol_VP2) (Abbas, 2021). iTOL web application (Letunic and Bork, 2019) was used to draw sequence similarity data matrix as radial connection lines (values of 96% and above are only shown) to a NJ phylogenetic tree.\n\n\nDiscussion\n\nIBD is a major hurdle in the poultry industry worldwide. Besides its huge direct economic impact, indirect losses are considerable as it reduces productivity and makes entire flocks vulnerable to a number of serious illnesses (Cosgrove, 1962; Van Den Berg, 2000; Eterradossi and Saif, 2017; Michel and Jackwood, 2017). The most effective way to control this disease is via vaccination. Although vaccination programs are applied, infection with IBDV is still frequent (Mahgoub, 2012). Iraq is no exception – despite vaccination programs, there continues to be a high infection rate in poultry. However, studies that involve sequencing of targeted regions of IBDV or comparison to the vaccine strains are limited. Therefore, we conducted sequencing of targeted regions of important IBDV genes related to the virulence of the virus (VP1 gene), as well as a comprehensive sequence analysis of hvVP2 region that encodes for the viral epitope that evokes immune response against the virus, using available Iraqi sequences and known vaccine strains.\n\nThe phylogenetic analysis of VP1 gene conducted in this study revealed that our sequence clustered with vvIBDV sequences from previous studies (Michel and Jackwood, 2017; Michel and Jackwood, 2019). This finding suggests that the IBDV strain sequenced in this study belongs to a vvIBDV based on molecular evidence (Islam et al., 2012).\n\nIn order to identify which genogroup this isolate belongs to, phylogenetic analyses of hvVP2 region were conducted. This analysis showed that our sequence grouped with other vvIBDV sequences belonging to genogroup 3. However, a sequence from Iraq is the only sequence that shared the same monophyletic group with our isolate, while the sequences from Kuwait and New York City seen in VP1 phylogenetic analysis did not show high similarity with our sequence in this genomic region, suggesting mutations are frequent in the hvVP2 region, as seen in previous studies (Michel, Kimber and Jackwood, 2019).\n\nThis result suggests a genetic reassortment. Such genetic modification is not uncommon: previous studies refer to similar genomic rearrangements in IBDV (Ibdv, Jackwood and Sommer-wagner, 2011; Michel and Jackwood, 2019). Other hvVP2 sequences from Iraq, especially those isolated from Kurdistan region (North of Iraq), showed a dispersal aggregation in the phylogenetic tree, suggesting genetic drift and possible mutations affected this protein coding region (Ali Khan et al., 2019). Despite this sequence variation between the results of the VP1 and hvVP2 phylogenetic analyses, both genic regions were clustered with vvIBDV isolates across the world, suggesting that our isolate is a vvIBDV strain.\n\nSequences of the hvVP2 region isolated from Iraq have shown a diverse clustering (Figure 3). While sequences from central Iraq clustered in the same clade, sequences from Kurdistan clustered in different clades indicating possible sequence divergence. Interestingly, a group of sequences from Kurdistan region were clustered with vaccine strains (Figure 3), especially vaccine strain D78 Intervet, which is used in the preparation of a live attenuated vaccine against Gumboro (Owoade et al., 2004; Arnold et al., 2012). It has been shown that the live attenuated vaccines may cause pathogenic and clinical manifestations in Bursa of Fabricius (Müller et al., 2012). This result might suggest either an infection of Bursa of Fabricius by the vaccine strain or it might propose a misdiagnosed infection of the flock, as sometimes live attenuated vaccines lead to clinical signs of infection with Bursa of Fabricius (Müller et al., 2012; Camilotti et al., 2016). The classification based on sequencing of viral strains is crucial to track the evolution and changes in virulence or antigenicity of such pathogens (Jackwood et al., 2008; Ibdv, Jackwood and Sommer-wagner, 2011).\n\nIdentifying the sequences of field strains and comparing them to the available vaccine strains is an important step in order to employ the most suitable vaccine strain in immunization programs against the circulating local virulent strains of IBDV. The analyses conducted in this study determined that the two vaccine strains (Ventri IBDV Plus and ABIC MB71) have the highest sequence similarity of viral epitope to the local virulent strains (Figure 4 and Figure 5). However, these vaccine strains have not yet been introduced in vaccination programs in Iraq. Sequence diversity of hvVP2 and lack of evidence of which vaccine strains show similarity to local circulating strains might explain why vaccination programs are failing in many parts of the country.\n\nIn this study we showed the diversity of the hyper variable region in the VP2 gene of vvIBDV and identified the potentially most suitable vaccine strains that could be used in vaccination programs to tackle this major issue in poultry industry in Iraq. However, a wider study involving the collection of many samples from outbreaks of IBDV across different parts of the country is needed in order to map the strains circulating in different regions and track possible sequence changes in the future.\n\n\nConclusion\n\nAlthough the vaccination program is routinely applied, poultry infection with IBDV is common. In this study we isolated and sequenced a very virulent strain of Gumboro, conducted an unprecedented comprehensive DNA sequence analyses of all available vvIBDV sequences from Iraq, and compared these sequences to vaccine strains.\n\nOur results indicated that sequences of vvIBDV from Iraq belong to genogroup 3 and the antigenic determinant of this virus is prone to genetic mutation, leading to sequence diversification. It is noteworthy that the vaccine strains that revealed the highest sequence similarity to the local virulent strains are not employed in the vaccination programs in Iraq, which might suggest why most vaccinations against IBDV in Iraq are not very effective. Indeed, a wider study involving isolation and sequencing of vvIBDV isolates from different regions across the country is crucial to draw a high-resolution map of the sequence diversity of this virus in Iraq.\n\n\nAuthors’ contributions\n\nSequence analyses, interpretation of the results and writing of all versions of the paper were performed by Abbas A.H. Forkan Al and Haider A, conducted the field trips and sample collection. All authors revised the final versions of the manuscript.\n\n\nData availability\n\nGenBank: Infectious bursal disease virus isolate IqKufa 01 VP2 gene, partial cds, Accession number MW020533.1: https://www.ncbi.nlm.nih.gov/nuccore/MW020533.1.\n\nGenBank: Infectious bursal disease virus isolate IqKufa 01 VP1 gene, partial cds, Accession number MW020534.1: https://www.ncbi.nlm.nih.gov/nuccore/MW020534.1.\n\nDryad: Supplementary Information for: Sequence diversity and evolution of Infectious Bursal Disease Virus IBDV in Iraq. https://doi.org/10.5061/dryad.s7h44j167 (Abbas, 2021).\n\nThis project contains the following underlying data:\n\n• Table 1_accesson_numbers_of_VP1_and_VP2_sequences_used_in_this_study. (GenBank accessions of VP1 and VP2 sequences used in this study.)\n\n• IBVD_VP1_NCBI_Hits_OurVP1.txt. (DNA sequences of all VP1 sequences used in this study.)\n\n• ABIC_andVentriVaccin_IraqV2_DNA_percentSimilrity_matrix.csv. (hvVP2 sequence similarity percentage of two vaccine strains compared to all Iraqi isolates.)\n\n• all_VP2_DNA_sequencesUsed.txt. (DNA sequences of all VP2 sequences used in this study.)\n\nDryad: Supplementary Information for: Sequence diversity and evolution of Infectious Bursal Disease Virus IBDV in Iraq. https://doi.org/10.5061/dryad.s7h44j167 (Abbas, 2021).\n\nThis project contains the following extended data:\n\n• TextFileToShow_connection_iTol_VP2. (Connections datasets allow the drawing of straight or curved lines between any two nodes in the tree. Width, colour, and opacity can be set for each line).\n\n• TextFileToShow_GRADIENT_iTol_VP2. (In gradient datasets, each ID is associated to a single numeric value which is converted to a coloured box based on the gradient defined).\n\n• IraqiVP2_pairwiseDistance.csv. (Pairwise distance of VP2 aligned region among strains isolated from Iraq).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiverhttps://creativecommons.org/publicdomain/zero/1.0/ (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nThe authors thank the Faculty of Veterinary Medicine, University of Kufa.\n\n\nReferences\n\nAbbas AH: Supplementary Information for: Sequence diversity and evolution of Infectious Bursal Disease Virus IBDV in Iraq. Dryad, Dataset. 2021. Publisher Full Text\n\nAli Khan RS, et al.: Phylogenetic analysis of Infectious Bursal Disease viruses according to newly proposed model of classification into geno-groups. J Infect Public Health. King Saud Bin Abdulaziz University for Health Sciences;2019; 12(3): 410–418. Publisher Full Text\n\nAli N, et al.: Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BioMed Research International. 2017. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAltschul SF, et al.: Basic local alignment search tool. J Mol Biol. 1990; 215(3): 403–410. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nKJ Fahey, E K, C J: A Conformational lmmunogen on VP-2 of Infectious Bursal Disease Virus that Induces Virus-neutralizing Antibodies that Passively Protect Chickens. CSIRO Division of Animal Health, Animal Health Research Laboratory, Private Bag No. 1 1989; pp. 1473–1481. PubMed Abstract | Publisher Full Text\n\nCamilotti E, et al.: Infectious bursal disease: Pathogenicity and immunogenicity of vaccines. Revista Brasileira de Ciencia Avicola. 2016; Publisher Full Text\n\nCosgrove AS: An Apparently New Disease of Chickens: Avian Nephrosis. Avian Diseases. 1962. Publisher Full Text\n\nCoulibaly F, et al.: The Birnavirus Crystal Structure Reveals Structural Relationships among Icosahedral Viruses.2005; 120, pp. 761–772. Publisher Full Text\n\nDobos P, et al.: Biophysical and Biochemical Characterization of Five Animal Viruses with Bisegmented Double-Stranded RNA Genomes.1979; 32(2): 593–605. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC353591/pdf/jvirol00191-0245.pdfPubMed Abstract | Publisher Full Text | Free Full Text\n\nEdgar RC, Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5): 1792–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvon Einem UI, et al.: VP1 of infectious bursal disease virus is an RNA-dependent RNA polymerase. J Gen Virol. 2004. PubMed Abstract | Publisher Full Text\n\nEterradossi N, et al.: Modified activity of a VP2-located neutralizing epitope on various vaccine, pathogenic and hypervirulent strains of infectious bursal disease virus.1997; 2, pp. 255–270. PubMed Abstract | Publisher Full Text\n\nEterradossi N, et al.: Critical amino acid changes in VP2 variable domain are associated with typical and atypical antigenicity in very virulent.1998; 14955, pp. 1627–1636. PubMed Abstract | Publisher Full Text\n\nEterradossi N, Saif YM: Infectious Bursal Disease. In: Diseases of Poultry: Thirteenth Edition. 2017. Publisher Full Text\n\nFelsenstein J: Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution. 1985. PubMed Abstract | Publisher Full Text\n\nIbdv B, Jackwood DJ, Sommer-wagner SE: Amino acids contributing to antigenic drift in the infectious bursal disease. Virology. Elsevier Inc;2011; 409(1): 33–37. PubMed Abstract | Publisher Full Text\n\nIslam MR, et al.: Differentiation of infectious bursal disease virus (IBDV) genome segment B of very virulent and classical lineage by RT-PCR amplification and restriction enzyme analysis. Arch Virol. 2012. PubMed Abstract | Publisher Full Text\n\nJackwood DJ, Sreedevi B, Lefever LJ: Studies on naturally occurring infectious bursal disease viruses suggest that a single amino acid substitution at position 253 in VP2 increases pathogenicity.2008; 377, pp. 110–116. PubMed Abstract | Publisher Full Text\n\nKumar S, et al.: MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLetunic I, Bork P: Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahgoub HA: An overview of infectious bursal disease. Arch Virol. 2012. PubMed Abstract | Publisher Full Text\n\nMichel LO, Jackwood DJ: Classification of infectious bursal disease virus into genogroups. Arch Virol. Springer Vienna;2017; 162(12): 3661–3670. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMichel LO, Kimber ML, Jackwood DJ: New introduction of a very virulent infectious bursal disease virus in New York, USA. Avian Pathol. 2019. PubMed Abstract | Publisher Full Text\n\nMüller H, et al.: Current status of vaccines against infectious bursal disease. Avian Pathol. 2012. PubMed Abstract | Publisher Full Text\n\nOkonechnikov K, et al.: Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics. 2012. PubMed Abstract | Publisher Full Text\n\nOwoade AA, et al.: High sequence diversity in infectious bursal disease virus serotype 1 in poultry and turkey suggests West-African origin of very virulent strains. Arch Virol. 2004; 149(4): 653–672. PubMed Abstract | Publisher Full Text\n\nRautenschlein S, et al.: Role of intrabursal T cells in infectious bursal disease virus (IBDV) infection: T cells promote viral clearance but delay follicular recovery.2002; pp. 285–304. PubMed Abstract | Publisher Full Text\n\nSaitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987. PubMed Abstract | Publisher Full Text\n\nTamura K, et al.: Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A. 2012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993. PubMed Abstract | Publisher Full Text\n\nTamura K, Tao Q, Kumar S: Theoretical foundation of the reltime method for estimating divergence times from variable evolutionary rates. Mol Biol Evol. 2018. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "83455",
"date": "07 May 2021",
"name": "Daral J. Jackwood",
"expertise": [
"Reviewer Expertise Molecular Virology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper describes the phylogenetic relationship of a vvIBDV strain identified in Iraq with known IBDV strains from the region and around the world. It is also compared to vaccine strains used to protect against IBD.\n\nThere are three different phylogenetic tree types Traditional, Radiation and Circle used in this paper. It is recommended that only one type of tree be used throughout the manuscript.\n\nIn the discussion, the authors indicate that the genetic sequence data of the vvIBDV from Iraq suggests a genetic reassortment. It is not clear from the data why this virus is a reassorted strain. Both genome segments aligned with vvIBDV. Reassorted vvIBDV typically have a genome segment B from a non-vvIBDV strain. That does not seem to be the case here.\n\nThe New York strain of vvIBDV is not from New York City, it is from the state of New York (see the bottom of page 8).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7060",
"date": "02 Sep 2021",
"name": "Ali Abbas",
"role": "Author Response",
"response": "Thank you very much for your valuable comments. Please have a look to the following response to your comments: There are three different phylogenetic tree types Traditional, Radiation and Circle used in this paper. It is recommended that only one type of tree be used throughout the manuscript? The phylogenetic trees in figure 1 and figure 2 were reformatted to the standard phylogenetic tree to be replacing the radial and circular format, respectively. However, for figure five it is crucial to keep it as is, in order to show the links between taxa. In the discussion, the authors indicate that the genetic sequence data of the vvIBDV from Iraq suggests a genetic reassortment. It is not clear from the data why this virus is a reassorted strain. Both genome segments aligned with vvIBDV. Reassorted vvIBDV typically have a genome segment B from a non-vvIBDV strain. That does not seem to be the case here? We'd liked to emphasise that the similarity between strains of IBDV in VP1 gene does not necessarily have sequence similarity in hvVP2 region. Nonetheless, we've omitted the text to remove the confusion. The New York strain of vvIBDV is not from New York City, it is from the state of New York? This has been corrected."
}
]
},
{
"id": "89761",
"date": "30 Jul 2021",
"name": "Fatma Abdallah",
"expertise": [
"Reviewer Expertise Molecular Virology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors explore the sequences diversity of IBDV in Iraq and compared it with other local and global sequences from GenBank, as well as, compared to available vaccine strains in Iraq.\n\nHowever, I have significant reservations, as outlined below; please address the following comments in your consideration before acceptance:\nPage 5, the circular unrooted phylogenetic tree of vp1 is not at all clear; please change the phylogenetic tree into another form as traditional to become better and expressive.\n\nPlease, you can unite the drawing of the all phylogenetic tree in the manuscript as a traditional form to become clearer.\n\nIn the discussion section, please explain with what motives you have led to suggest that there is a genetic reassortment in IBDV strain in Iraq because the genetic reassortment is not based on genetic drift in the protein coding region.\n\nIn the conclusion section, you cannot judge that the available vaccinations against Gumboro disease in Iraq are enough to prevent the current IBDV infection through sequence analysis of all available IBDV sequence strains in Iraq. Indeed, you are needed to isolate circulating IBDV strains from different outbreaks across different regions of your country and then track evolution changes in these strains through studying the pathogenicity and virulence of these strain in vivo; Thus, you can control whether these new isolated IBDV strains are controlled with these available vaccine strains or not. so, I recommend you adjust your conclusion with your results and 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?\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": "7063",
"date": "02 Sep 2021",
"name": "Ali Abbas",
"role": "Author Response",
"response": "Thank you very much for your valuable comments. Please have a look to the following response to your comments: For comment one and two: We reformatted the phylogenetic trees in figure 1 and 2 to the standard phylogenetic tree to be replacing the radial and circular format, respectively. However, for figure five it is crucial to keep it as is, in order to show the links between different strains. 3. We'd liked to emphasise that the similarity between strains of IBDV in VP1 gene does not necessarily have sequence similarity in hvVP2 region. Nonetheless, we've omitted the text to remove the confusion. 4. I've appended a statement, which illuminates the importance of experimental work to be involved in future studies to assess the efficacy of vaccines against local strains. However, a cross country molecular study is important to show the diversity of IBDV to reduce the time, cost and labour to achieve the experimental work."
}
]
}
] | 1
|
https://f1000research.com/articles/10-293
|
https://f1000research.com/articles/10-875/v1
|
01 Sep 21
|
{
"type": "Research Article",
"title": "Alteration in surface roughness of reciprocating endodontic instruments",
"authors": [
"Khoa Van Pham"
],
"abstract": "Background: Surface roughness is one of the most important characteristics of endodontic instruments, correlating to instrument fracture. The purpose of this study was to measure the surface roughness values of these instruments before and after resin root canal preparation without previous glide path preparation, with the new method. Data was obtained from field emission scanning electron microscopes (FE-SEM) combined with independent ImageJ software (NIH, Bethesda, MD, USA). Methods: A total of 20 simulated J-shape resin blocks with a radius of 4.5 mm, length of 16 mm, and angle of inflection of 600 were chosen and distributed into two equal groups. Each group was prepared by the WaveOne Gold Primary (Dentsply Sirona, Maillefer, Ballaigues, Switzerland) or the Reciproc Blue R25 (VDW, Munich, Germany) instruments, without glide path preparation. Special molds were used to confirm the same areas on the cutting blade at 3 mm and the instruments’ tips were scanned by FE-SEM, at different observed times. The parameters of Ra, Rq, and Rz in each sample were collected using the ImageJ software for analyses. The data was processed using the paired t-test with a significance level of 0.05. Results: Right after the first resin canal instrumentation, the surface roughness parameters of the two reciprocating investigated instruments were decreased. Conclusions: The FE-SEM images processed using the ImageJ software offered a trustworthy and suitable method for assessment of the NiTi endodontic file surface roughness.",
"keywords": [
"FE-SEM",
"root canal instrumentation",
"surface roughness",
"reciprocating"
],
"content": "Introduction\n\nRoot canal preparation plays an important role in endodontic treatment. This step is critical and facilitates obturation.1 Advancements in science and technics have led to the production of the rotary nickel-titanium (NiTi) root canal instruments using two manners of movement: continuous or reciprocating motion. To reduce time required, complicatedness of the process, and exhaustion of clinicians in root canal preparation, the single-file instruments are introduced using continuous or reciprocating rotation.2 Since the first introduction of the single-file system with proprietary integrated technique, the system has been continuously developed in material improvement, taper modification, and cross-sectional geometry, especially in distinctive heat treatment processes.\n\nMean and standard deviations of Ra, Rq, Rz parameters before and after instrumentation of experimental instruments (μm).\n\na,b,c,d,e,f,g,h Different superscript letters (in the same group and scanning area) indicate statistically significant differences at 5% level.\n\nRecently, the Reciproc Blue (RB) (VDW, Munich, Germany) and WaveOne Gold (WOG) (Dentsply Sirona, Maillefer, Ballaigues, Switzerland) instruments have been developed with many distinctive features in designs and thermal treatments.3 The instruments are subjected to the proprietary post-machining heat processes after being ground by machine. This treatment produces the oxide layer with the specific blue or gold.4\n\nThe risk of fracture is inherent in an endodontic instrument, especially for rotary nickel-titanium files. Both brittleness or ductility are a possible cause of breakage.5 Typically, a beginning crack on the material facet could lead to the fracture of the file.5 Defect on the surface of the material could be the crack beginning.6 There could be a correlation between surface characteristics and the breakage mechanism of the root canal rotary file.7\n\nSo far, there are limited studies of the root canal instrument surface roughness,8–11 especially using the data obtained from the field emission scanning electronic microscope (FE-SEM).12 There is modest data available for the surface roughness parameters of the WOG Primary (WOGP) and RB R25 (RBR25) instruments for root canal preparation with the previous glide path preparation using the FE-SEM.12 The purpose of this study was to measure the surface roughness values of these instruments before and after resin root canal preparation without previous glide path preparation, with the new method, using the data obtained from FE-SEM combined with independent ImageJ software (NIH, Bethesda, MD, USA).\n\n\nMethods\n\nThe present study was performed in 2019, at the University of Medicine and Pharmacy at Ho Chi Minh City, Viet Nam. The method used for the present study was introduced in a previous study.12 An acrylonitrile butadiene styrene (ABS) former was produced using automatically computerized controlled apparatus for ensuring the root canal file at the exact location before and after resin root canal preparation with dimethicone (Sylgard 184, Dow Corning Corp., USA) impression.12 The combination of the ABS mold and the polydimethylsiloxane (PDMS) impression with instrument inside was then introduced and fastened into the gear of the vacuum room of the FE-SEM (NOVA NanoSEM 450, FEI, UNSW, Sydney, Australia) after complete removal of bubbles and drying at 60°C in 3 hours using the vacuum extractor (Diener Electronic, Germany).12\n\nSample size was calculated using the data of the previous study12 with a total of 20 J-shape limpid plastic blocks for endodontic training (Dentsply Sirona, Maillefer, Ballaigues, Switzerland). Ten blocks were used for each group. Clear resin simulated root canal was a radius of 4.5 mm, length of 16 mm, and 60° angle of inflection, using the Pruett’s manner.13 All endodontic preparations were conducted by an endodontist. The resin root canal was first explored using the ISO #10 K-file (Dentsply Sirona, Maillefer, Ballaigues, Switzerland) to confirm the patency of the entire plastic canal. X-Smart IQ cordless handpiece (Dentsply Sirona, Maillefer, Ballaigues, Switzerland) combined with an iPad Mini were operated using proper modules for root canal instrumentation.\n\nIn total, ten WOGP (lot no. 1493642) and ten RB25 (lot no. 258192) files were chosen for the study. The marks on the shanks of all files were produced with the tiny round bur #014 ISO (Dentsply Sirona, Maillefer, Ballaigues, Switzerland). These marks assisted in reintroducing the files into the mold after preparation and in inspecting the identical sectors on the file before and after preparation.12\n\nGroup 1 was prepared (without the glide path preparation) by the WOGP (Dentsply Sirona, Maillefer, Ballaigues, Switzerland) and group 2 was prepared (without the glide path preparation) by the RB25 (VDW, Munich, Germany) until the working length was reached with the gentle in-and-out pecking movement to approach clinical settings. Plastic root canal was thoroughly irrigated using 3% NaOCl solution (Canal Pro, Coltene Whaledent, Altstätten, Switzerland). One reciprocating file was only used for each plastic canal. After complete instrumentation, the instrument’s surface was wiped off using moisture gauze, then the instrument was placed into an ultrasonic cleaner to be vibrated with alcohol solution for further cleansing and dried using gauze afterward.\n\nThe files were captured before and after endodontic preparation using the FE-SEM (×1000, 10kV). The surface of the instrument pinpointed at 3 mm from the peak of the file was assessed using the method described the previous study.12 The marks on the shank of the file were used as reference points. The evaluated sections were located, first by displacing the gear containing specimen from the mark on the instrument’s shaft, toward the peak until it could be observed. Then, the backward movement of the gear was performed with the distance of 3 mm, and at this position, the cutting blade was evaluated and captured with the dimensions of 150 μm × 150 μm. These figures were analyzed using the ImageJ 1.52 (NIH, Bethesda, MD, USA). The mean roughness parameters (Ra), root-mean-square roughness (Rq), the average length in the range of the highest tip and lowest groove in each length of specimen (Rz), and the three-dimension graphs were calculated and obtained from the ImageJ.12\n\nShapiro-Wilk statistic was performed initially to check the distribution of the data and the paired t-test was executed to interpret the data using the SPSS 22.0 package (IBM-SPSS Inc, Armonk, NY, USA).\n\n\nResults\n\nThe statistical values of the Ra, Rq, and Rz were showed in the Table 1.22 All data were normally distribution using the Shapiro-Wilk test. Ra and Rq parameters of the group 1 decreased after root canal instrumentation (P > 0.05). For the group 2, all these values decreased after endodontic, and these values were significantly different (P < 0.05).\n\n\nDiscussion\n\nThe result of the present study showed that almost all of the surface roughness parameters of both experimental instruments were decreased after root canal instrumentation. In the WOGP group, two of three valueswere reduced. In the RBR25 group, all values were decreased significantly. This result showed that surface changes, for such small sample of ten instruments, in the very beginning stage of root canal instrumentation, even the tiniest ones, could be discovered by this alternative modality with the FE-SEM at superior preciseness.\n\nThe atomic force microscope (AFM) and the conventional SEM were used for assessment of the surface of the root canal file before and after endodontic instrumentation. Although the three-dimension reconstruction feature of the AFM was been highly evaluated, this modality could just be used for scanning on tiny and absolute square, flat and rigid surfaces, whilst the conventional SEM could only capture the two-dimensional figures.10 In the touch mode of the AFM, the tiny end of the stylus might be damaged itself or it could destruct the scanned surface, affecting the outcome, and increasing the considerable time required for image building as well.10\n\nRecently, a touchless profilometer has been reported by Ferreira et al. for investigation of the root canal instrument topography.10 However, this technique has been found to give inaccurate outcomes when scanning in extreme slope inclines or intermissions.14 One important shortcoming of this modality is that it does not properly work on the breakage areas.15 The contemporary profilometer does not work properly without integrated software supplied by the manufacturer.\n\nThe extreme tiny resolution of 1.4 mm was one of the most advantage of this modern FE-SEM and the specimen treatment was unnecessary. One of the utmost significant advantage of the FE-SEM is the integration of the data obtained from the FE-SEM and the calculation using the ImageJ program in reconstruction of the three-dimension figures and automatic production of the surface roughness values.12\n\nSome other studies have affirmed the correctness and reliability of the integration of the data obtained from FE-SEM and the ImageJ program in calculation of the material surface roughness.16–18 In the present study, the above viewpoint was securely confirmed with the results of precise and reliable surface roughness and reconstructed three-dimension figures using the data obtained from FE-SEM and the independent ImageJ program.\n\nAll surface roughness parameters of the RBR25 group were significantly reduced, these reductions might be emerged from the efficacy of the instruments in root canal preparation.\n\nAlmost all surface roughness values in the WOGP group were receded after endodontic instrumentation, however, the differences were not statistically significant. This showed that the RBR25 files were subjected to the friction more than the WOGP instruments did. This could be led from the discrepancies in the construction, proportions, and substance of the two experimental NiTi instruments.\n\nAlthough there were still certain disadvantages of resin blocks used for root canal experiments,8,19 the plastic blocks might still be used appropriately for endodontic investigation.12\n\nThe results of the present study were similar to those of the two previous studies.11,20 The surface roughness parameters of the WaveOne Primary (WOP) and Reciproc R25 (RR25) were increased after resin root canal preparation in the study using the AFM and those of the ProTaper F2 (Dentsply Sirona, Mailefer, Ballaigues, Switzerland) instruments were reduced.11 The ProTaper F2 instruments were performed following the F1 instruments, therefore, the F2 instruments were subjected to less load than the WaveOne Primary and Reciproc R25. In the present study, the two instruments were subjected to a heavy load when using the resin root canal at the beginning of the preparation without any previous glide path preparation. However, they had the reduced surface roughness after first utilization, therefore; the difference came from the construction, dimension, and substance of these instruments. In the previous study using a non-contact optical profilometer for investigation of the surface roughness of the WOP and RR25, these roughness values also reduced from the second use to the first use and from the second use to the unused instruments after resin root canal preparation.20 This result agreed with the outcome of the present study, came from the wear of cutting blades of the files after root canal preparation.\n\nOpposed to the result of the present study, other studies have reported that the surface roughness of the endodontic instruments increased after endodontic instrumentation.8,9,21 All these previous studies used the extracted human teeth, one investigated the files used in the clinical setting,9 and two others used the extracted human teeth for the in vitro evaluations.8,21 The instruments were used five times and sterilized six times in the other study,9 and the instruments were used in the severely curved canals for three times before examining under the AFM8 or four-time utilizations and subjected to one sterilization cycle before investigation under the non-contact optical profilometer.21 All the above different conditions affected the surface roughness of the instruments after instrumentation. Further research on the WOGP and RBR25 using many times both in-vitro or in-vivo situations needed to be performed to explore more characteristics of these instruments’ surface.\n\n\nConclusion\n\nThe FE-SEM images processed using the ImageJ software offered a trustworthy and suitable method for assessment of the NiTi endodontic file surface roughness. In total, two of the three surface roughness parameters of the WOGP and RBR25 were significantly decreased after the first manipulation in plastic root canal preparation.\n\n\nData availability\n\nMendeley Data: WOGP RB wo GlidePath with FE-SEM Images. http://doi.org/10.17632/xr749xdwkn.2.22\n\nThis project contains the following underlying data:\n\n- WOGP RB without Glide Path\n\n- Ket Qua Do Roughness WOGP RB wo GlidePath.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nPham K, Phan T: Evaluation of root canal preparation using two nickel-titanium instrument systems via cone-beam computed tomography. Saudi Endodontic J. 2019 September 1; 9(3): 210–5. Publisher Full Text\n\nPham K, Nguyen N: Cutting efficiency and dentinal defects using two single-file continuous rotary nickel-titanium instruments. Saudi Endodontic J. 2020 January 1; 10(1): 56–60. Publisher Full Text\n\nSantos CB, Simões-Carvalho M, Perez R, et al.: Torsional fatigue resistance of R-Pilot and WaveOne Gold Glider NiTi glide path reciprocating systems. Int Endod J. 2019; 52(6): 874–9. Epub 2019/01/21. eng. PubMed Abstract | Publisher Full Text\n\nZupanc J, Vahdat-Pajouh N, Schäfer E: New thermomechanically treated NiTi alloys – a review. Int Endod J. 2018 2018/10/01; 51(10): 1088–103. PubMed Abstract | Publisher Full Text\n\nParashos P, Messer HH: Rotary NiTi Instrument Fracture and its Consequences. J Endod. 2006; 32(11): 1031–43. PubMed Abstract | Publisher Full Text\n\nKuhn G, Tavernier B, Jordan L: Influence of Structure on Nickel-Titanium Endodontic Instruments Failure. J Endod. 2001 2001/08/01/; 27(8): 516–20. PubMed Abstract | Publisher Full Text\n\nValois CRA, Silva LP, Azevedo RB: Multiple Autoclave Cycles Affect the Surface of Rotary Nickel-Titanium Files: An Atomic Force Microscopy Study. J Endod. 2008; 34(7): 859–62. PubMed Abstract | Publisher Full Text\n\nÖzyürek T, Yılmaz K, Uslu G, et al.: The effect of root canal preparation on the surface roughness of WaveOne and WaveOne Gold files: atomic force microscopy study. Restor Dent Endod. 2018; 43(1): e10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInan U, Aydin C, Uzun O, et al.: Evaluation of the Surface Characteristics of Used and New ProTaper Instruments: An Atomic Force Microscopy Study. J Endod. 2007; 33(11): 1334–7. PubMed Abstract | Publisher Full Text\n\nFerreira F, Barbosa I, Scelza P, et al.: A new method for the assessment of the surface topography of NiTi rotary instruments. Int Endod J. 2017 2017/09/01; 50(9): 902–9. PubMed Abstract | Publisher Full Text\n\nFatma Y, Ozgur U: Evaluation of surface topography changes in three NiTi file systems using rotary and reciprocal motion: An atomic force microscopy study. Microsc Res Tech. 2014 2014/03/01; 77(3): 177–82. PubMed Abstract | Publisher Full Text\n\nPham VK, Vo CQ: A new method for assessment of nickel-titanium endodontic instrument surface roughness using field emission scanning electronic microscope. BMC Oral Health. 2020 2020/08/31; 20(1): 240. Epub 2020/09/02. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPruett JP, Clement DJ, Carnes DL Jr: Cyclic fatigue testing of nickel-titanium endodontic instruments. J Endod. 1997; 23(2): 77–85. PubMed Abstract | Publisher Full Text\n\nLeach R: Surface Topography Measurement Instrumentation. In: Leach R, editor. Fundamental Principles of Engineering Nanometrology. Second ed.Oxford: William Andrew Publishing; 2014. p. 133–204.\n\nKhokhlov M, Fischer A, Rittel D: Multi-Scale Stereo-Photogrammetry System for Fractographic Analysis Using Scanning Electron Microscopy. Experimental Mechanics. Springer US; 2011 2012; 52(8): 975–91. Publisher Full Text\n\nSafdar A: Effect of process parameters settings and thickness on surface roughness of EBM produced Ti-6Al-4V. Rapid Prototyping J. 2012; 18(5): 401–8. Publisher Full Text\n\nErsoy O, Aydar E, Gourgaud A, et al.: Quantitative analysis on volcanic ash surfaces: Application of extended depth-of-field (focus) algorithm for light and scanning electron microscopy and 3D reconstruction. Micron. 2008 2008/02/01/; 39(2): 128–36. PubMed Abstract | Publisher Full Text\n\nChinga G, Johnsen PO, Dougherty R, et al.: Quantification of the 3D microstructure of SC surfaces. J Microsc. 2007 2007/09/01; 227(3): 254–65. PubMed Abstract | Publisher Full Text\n\nKum KY, Spängberg L, Cha BY, et al.: Shaping ability of three ProFile rotary instrumentation techniques in simulated resin root canals. J Endod. 2000 Dec; 26(12): 719–23. Epub 2001/07/27. eng. PubMed Abstract | Publisher Full Text\n\nFerreira FG, Barbosa IB, Scelza P, et al.: Noncontact three-dimensional evaluation of surface alterations and wear in NiTi endodontic instruments. Braz Oral Res. 2017; 31. PubMed Abstract | Publisher Full Text\n\nUslu G, Özyürek T, Yılmaz K: Comparison of Alterations in the Surface Topographies of HyFlex CM and HyFlex EDM Nickel-titanium Files after Root Canal Preparation: A Three-dimensional Optical Profilometry Study. J Endod. 2018; 44(1): 115–9. Epub 2017/10/09. eng. PubMed Abstract | Publisher Full Text\n\nPham K: WOGP RB wo GlidePath with FE-SEM Images. Mendeley Data . 2021: V2. Publisher Full Text"
}
|
[
{
"id": "93259",
"date": "19 Oct 2021",
"name": "Gianluca Gambarini",
"expertise": [
"Reviewer Expertise Endodontology"
],
"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 is interesting but in present form is only partially developed:\nIndeed the sample size is small and is not clear if there is any clinically significance for the present results.\n\nDespite the study is realized without a glide path establishment, the resin block diameter is usually up to 15.02. Moreover the authors, to verify the patency have shaped the canal up to 10.02, that can be considered a glide path. Moreover, the resin could influence the results of the study.\n\nPlease repeat the study using extracted teeth if possible, moreover add some statistical test such as cyclic fatigue, torsional resistance and cutting efficiency. This way you can make a clinical translation of these 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? Yes\n\nAre 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": "119267",
"date": "17 Jan 2022",
"name": "Murilo Priori Alcalde",
"expertise": [
"Reviewer Expertise Endodontics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors should discuss better the limitation of the use of resin blocks in comparison with human teeth. Do you really rely that this method simulate similar condition using human teeth?\n\nThis method to evaluate the surface roughness is different then use profilometer. Therefore, the authors should compare the results using the same methods. Please include in the discussion section why this method can replace the profilometer? And the limitation of this method. The discussion of this part is so poor. The are SEVERAL articles using the profilometer method. The authors should discuss better this section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-875
|
https://f1000research.com/articles/10-180/v1
|
04 Mar 21
|
{
"type": "Research Article",
"title": "Accuracy of digital dental models and three-dimensional printed dental models in linear measurements and Bolton analysis",
"authors": [
"William Suryajaya",
"Maria Purbiati",
"Nada Ismah",
"Maria Purbiati"
],
"abstract": "Background: Due to advances in digital technology, it is possible to obtain digital dental models through intraoral scanning. The stereolithographic data collected from the scanner can subsequently be printed into a three-dimensional dental model in resinic material. However, the accuracy between digital dental models and printed dental models needs to be evaluated since it might affect diagnosis and treatment planning in orthodontic treatment. This study aimed to evaluate the accuracy of digital models scanned by a Trios intraoral scanner and three-dimensional dental models printed using a Formlabs 2 3D printer in linear measurements and Bolton analysis. Methods: A total of 35 subjects were included in this study. All subjects were scanned using a Trios intraoral scanner to obtain digital study models. Stereolithographic data from previous scanning was printed using a Formlabs 2 3D printer to obtain printed study models. Mesiodistal, intercanine, intermolar, and Bolton analysis from all types of study models were measured. The intraclass correlation coefficient was used to assess intraobserver and interobserver reliability. All data were then statistically analyzed. Results: The reliability tests were high for both intraobserver and interobserver reliability, which demonstrates high reproducibility for all measurements on all model types. Most of the data compared between study models showed no statistically significant differences, though some data differed significantly. However, the differences are considered clinically insignificant. Conclusion: Digital dental models and three-dimensional printed dental models may be used interchangeably with plaster dental models for diagnostic and treatment planning purposes. Keywords: Accuracy, 3D printing, digital dental model, printed dental model.",
"keywords": [
"Accuracy",
"3D printing",
"digital dental model",
"printed dental model"
],
"content": "Introduction\n\nDental models are essential in the process of determining diagnosis and treatment planning in orthodontic treatment1–3. Commonly used dental models are made of plaster, which can easily be fractured and lost4. Aside from that, plaster models require storage room, which can be problematic since typical dental practices have limited space, and the number of models will continue to grow as the number of patients treated grows5. Moreover, the process of obtaining plaster models requires taking impressions with impression material, which can be an unpleasant experience for patients6.\n\nRecent developments in digital technology have made digitalization of dental models possible. Using an intraoral scanner, a patient’s oral condition, especially the teeth, can be registered and stored in a computer7. The scanned data is in the form of stereolithographic data that can be retrieved from the computer storage system almost instantly. The advantage of digital study models is that they are not prone to damage, fracture, or loss. Not only is no extra space needed to store the models, digital models also make setting up models and sending models for referral easy8–10.\n\nGenerally, intraoral scanners record intraoral structures with a camera located on the tip of a wand that emits light. The light is then reflected back by the surface of the intraoral structures and recaptured by the camera to create digital objects11. There are several intraoral scanners available on the market, such as iTero (Align Technologies, San Jose, CA), Lava Chairside Oral Scanner (COS) (3M ESPE, Seefeld, Germany), and Trios (3Shape, Copenhagen, Denmark). Of these scanners, Lava COS requires the addition of titanium oxide to opacify the tooth surface so that the light from the camera on the wand can be optimally reflected. This addition may affect the accuracy of the recorded digital model since it adds thickness to the teeth12.\n\nStereolithographic data obtained from previous scanning can be printed using a 3D printer to produce a printed model8,9. When necessary, the printed model is especially beneficial in diagnosing complex cases when a tangible model would make the diagnosis easier. There are several 3D printer technologies available, such as Fusion Deposition Modelling, an inkjet-based system or 3DP, and stereolithography (SLA). Each 3D printer has its own method of producing 3D objects13. However, the accuracy of a printed model may be altered since two steps are required to produce the printed model: scanning from the intraoral structure and printing it into resinic material.\n\nThe accuracy of dental models in recording intraoral structures is paramount since inaccuracy may lead to inaccurate diagnosis and treatment planning14. Hence, it is important to evaluate the accuracy of various dental models compared to the commonly accepted instrument: plaster models. Several studies have confirmed that digital models are suitable to replace plaster models11,14,15. However, limited studies are available that assess the accuracy of printed models, which have to go through the two steps of scanning and printing. This study aims to evaluate the linear accuracy and Bolton analysis16 of digital dental models scanned using Trios and resinic dental models printed using Formlabs 2 and compare them to plaster dental models.\n\n\nMethods\n\nThis prospective observational analytical study was approved by the Ethical Committee of the University of Indonesia (approval number of 49/Ethical Approval/FKG UI/VI/2019). The subjects were graduate and undergraduate dental students at the University of Indonesia who agreed to participate in the study and signed informed consents after being briefed about the details of the study. Sample size was calculated using Gpower Software version 3.1 for windows with the premises: normal data distribution, α = 0.05, β = 80%, and effect size = 0.5 and the result signified a minimum sample of 34. Based on convenience sampling, a total of 35 subjects (mean age: 24.85 ± 3.9 years old), five males and 30 females, were selected based on the following inclusion criteria: (1) 16–50 years old, (2) total crowding on each jaw not exceeding 3 mm, and (3) all teeth from central incisors to first molars on each quadrant are present. The exclusion criteria were: (1) large filling or restoration on the proximal side of the measured teeth and (2) incomplete impression or scanning results. This study was conducted at Graduate Orthodontic Clinic at the University of Indonesia Teaching Dental Hospital between June 2019 until August 2019.\n\nAll subjects were scanned using Trios (3Shape, Copenhagen, Denmark) on both the maxilla and mandible. All teeth from the central incisors to the first molars were thoroughly scanned so as to produce complete sets of teeth on the digital model. Stereolithographic data from the scanning procedure were saved on a computer hard drive.\n\nAll stereolithographic data were subsequently printed using a Formlabs 2 SLA 3D printer (Formlabs, Somerville, MA) to produce printed dental models of both the upper and lower jaws of all subjects.\n\nAfter the scanning procedure was complete, impressions were taken from all subjects with alginate impression material (Hydrogum, Zhermack Dental, Badia Polesine, Italy). The impression was consequently poured with type II dental stone (Pro Model Super 11, Saint Gobain, France) to obtain a plaster dental model.\n\nThe mesiodistal widths of all teeth from the central incisors to the first molars on each quadrant of all models were measured. Subsequently, the intercanine and intermolar widths were also measured. All measurements on the plaster and printed models were measured using a digital caliper (Mitutoyo, Japan), while the digital models were measured using built-in measurement tools on Autodesk Netfabb Premium 2019 (RRID:SCR_019812) software as described in previous study by Akyalcin et al.17 Approximately 10% of each model was measured by another observer (MP) to assess interobserver reliability. Interobserver reliability was assessed using the intraclass coefficient (ICC) and showed almost perfect agreement (ICC > 0.9). Within two weeks after the first measurements, 10% of all models were measured again by the same observer (WS) to assess intraobserver reliability. Intraobserver reliability was assessed using the ICC and reached almost perfect agreement (ICC > 0.9) between the first and second observations. Bolton analysis was then measured using the collected mesiodistal width data.\n\nAll data were analyzed using the Statistical Package for the Social Sciences (SPSS) version 20.0 for Windows (RRID:SCR_019096). The data normality of each group was assessed using the Shapiro-Wilk test. Repeated measures ANOVA was used for parametric numeric data, while the Friedman test was used to compare nonparametric numeric data. Within-group differences were assessed using the paired t-test for parametric data sets, while the Wilcoxon test was used for nonparametric data sets. A p-value < 0.05 was considered statistically significant.\n\n\nResults\n\nThe flow of participants is shown in Figure 1.\n\nThe reliability of all criteria in this study was tested using the ICC. All data tested, including mesiodistal, intercanine, and intermolar width for both interobserver and intraobserver, were found to be reliable with high agreement (Table 1 and Table 2).\n\n*: ICC: <0.20: poor agreement | 0.21–0.40: fair agreement | 0.41–0.60: moderate agreement | 0.61–0.80: substantial agreement | 0.81–1.00: almost perfect agreement\n\n*: ICC: <0.20: poor agreement | 0.21–0.40: fair agreement | 0.41–0.60: moderate agreement | 0.61–0.80: substantial agreement | 0.81–1.00: almost perfect agreement\n\nA total of eight different teeth (11, 13, 14, 16, 31, 33, 34, 36) were chosen to represent each of the tooth types on each jaw. Almost all data were normally distributed except 11 and 31. This is probably due to the various tooth sizes between individual subjects. All group comparisons (Table 3) showed statistically significant differences (p<0.05) on 13 and 16. Further within-group analysis (Table 4) revealed statistically significant differences (p<0.05) between printed models and plaster models on both teeth.\n\nThe intercanine and intermolar widths of all groups were compared, and significant differences (p<0.05) were found for mandibular intercanine, maxillary intermolar, and mandibular intermolar (Table 5 and Table 6). Further comparison analysis between groups revealed a significant difference for maxillary intercanine between the digital model-printed model and printed model-plaster model (Table 7). Significant differences (p<0.05) between groups were found for the digital model-printed model and the printed model-plaster model for the maxillary intermolar teeth and for the printed model-plaster model and plaster model-digital model for mandibular intermolar teeth.\n\nThe data collected for the Bolton analysis were compared. A significant difference (p<0.05) was found on anterior Bolton analysis (Table 8). A positive result showed tooth excess on maxillary teeth, and a negative result showed tooth excess on mandibular teeth. Comparisons between groups showed significant differences for the printed model-plaster model and the plaster model-digital model on anterior Bolton analysis (Table 9).\n\n**: excess on mandibular teeth\n\n\nDiscussion\n\nMesiodistal width, intercanine width, intermolar width, and Bolton analysis were compared between the plaster models, digital models, and printed models. Measurements on the digital models were found to be challenging, as a digital model is a three-dimensional object to be seen on the two-dimensional spectrum of a computer screen. All measurements were conducted by one observer, which makes the measurements more reliable8.\n\nWhile the comparison of the mesiodistal widths of the measured teeth showed varied results, most of the teeth measured had no statistically significant difference. If the difference was found to be significant, it was within the range of 0.15 mm, which was deemed clinically insignificant. It must be noted that between-group comparison revealed the difference was between the plaster models and printed models. The same result was found by Brown et al.18 The difference is probably due to instability of alginate impressions. Alginate is unstable at room temperature, so it can absorb water from the air through the process of imbibition, which causes alginate to enlarge19. Moreover, 3D printer minimum thickness may play a role in the difference. The minimum thickness can cause the printed model to be bigger than usual even though the minimum thickness is relatively small (25 μm). The differences for mesiodistal width between the plaster models and digital models were found to be insignificant.\n\nIntercanine and intermolar comparison in this study showed statistically significant differences for mandibular intercanine, maxillary intermolar, and mandibular intermolar. However, even though the differences were statistically significant, they were rendered clinically insignificant since the mean difference was not more than 1.5 mm. De Waard et al.20 found a similar result, although the digital models in their study were obtained from cone-beam computed tomography scanning of plaster models. Another study by Brown et al.18 found that there were no statistically significant differences between printed models and plaster models. However, the 3D printer used in that study was a polyjet and DLP printer, which has a minimum thickness ranging from 15 μm to 50 μm, while the printer used in the present study was an SLA printer, which has a minimum thickness of 50 μm.\n\nBolton analysis measurement showed a statistically significant difference for anterior Bolton analysis. Even though the difference was significant, the Bolton analysis measurement difference was not more than 1.5 mm, which is clinically insignificant21. Several studies have revealed the same result as this study for Bolton analysis comparison between different dental models8,11. Bolton analysis is a very sensitive technique. Measurement by the same observer on the same model may produce a different result22. Hence, the statistically significant difference in this study was rendered clinically insignificant.\n\nSeveral limitations and difficulties were present on this study. Plaster model as gold standard reference measurement does not represent the actual size of each tooth since both the impression material and the plaster used in the making of plaster model may shrink and cause disparity from actual tooth size. Measurement on dry skull as reference might be more appropriate on similar future study since measurement on patient is both difficult and inconvenience. Moreover, selection of 3D printer model might enhance the accuracy of the study. 3D printer that can print 3D object with less minimum thickness than that of used in this study is preferable to produce more accurate resin model.\n\n\nConclusion\n\nDigital models and printed models may be considered to replace plaster models to diagnose and plan treatment for orthodontic cases because the linear measurement and Bolton analysis between the different study models mostly showed no statistically significant differences. Even when the difference was statistically significant, it was negligible clinically.\n\n\nConsent\n\nAll participants provided written informed consent before involvement in the study.\n\n\nData availability\n\nFigshare: Research Data, https://doi.org/10.6084/m9.figshare.13469160.v123\n\nThis project contains the following underlying data:\n\n- Linear measurements\n\n- Bolton Analysis of dental stone, digital, and printed models\n\nFigshare: Stereolihographic Data, https://doi.org/10.6084/m9.figshare.13469172.v124\n\nThis project contains the following underlying data:\n\n- Stereolithographic data obtained from scanning subjects’ dentition.\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\nCoubourne MT, DiBiase AT: Handbook of Orthodontics. 2nd Edition. Edinburgh: Mosby; 2016; 143. Reference Source\n\nHan UK, Vig KWL, Weintraub JA, et al.: Consistency of orthodontic treatment decisions relative to diagnostic records. Am J Orthod Dentofac Orthop. 1991; 100(3): 212–219. PubMed Abstract | Publisher Full Text\n\nSofyanti E, Boel T, Satria D, et al.: Differences in dental arch characteristics between genders in patients with suspected condylar hyperplasia in a North Sumatra subpopulation: a cross-sectional study [version 3 ; peer review : 3 approved]. F1000Res. 2020; 9: 263. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJacob HB, Wyatt GD, Buschang PH: Reliability and validity of intraoral and extraoral scanners. Prog Orthod. 2015; 16: 38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl-zanaty HM, El-beialy AR, El-ezz AMA, et al.: Three-dimensional dental measurements: An alternative to plaster models. Am J Orthod Dentofac Orthop. 2010; 137(2): 259–265. PubMed Abstract | Publisher Full Text\n\nBurhardt L, Livas C, Kerdijk W, et al.: Treatment comfort, time perception, and preference for conventional and digital impression techniques: A comparative study in young patients. Am J Orthod Dentofac Orthop. 2016; 150(2): 261–267. PubMed Abstract | Publisher Full Text\n\nPeluso MJ, Josell SD, Levine SW, et al.: Digital Models: An Introduction. Semin Orthod. 2004; 10(3): 226–238. Publisher Full Text\n\nWiranto MG, Engelbrecht WP, Tutein Nolthenius HE, et al.: Validity, reliability, and reproducibility of linear measurements on digital models obtained from intraoral and cone-beam computed tomography scans of alginate impressions. Am J Orthod Dentofac Orthop. 2013; 143(1): 140–147. PubMed Abstract | Publisher Full Text\n\nGrünheid T, McCarthy SD, Larson BE: Clinical use of a direct chairside oral scanner: An assessment of accuracy, time, and patient acceptance. Am J Orthod Dentofac Orthop. 2014; 146(5): 673–682. PubMed Abstract | Publisher Full Text\n\nKo H, Liu W, Hou D, et al.: Agreement of treatment recommendations based on digital vs plaster dental models. Am J Orthod Dentofac Orthop. 2019; 155(1): 135–142. PubMed Abstract | Publisher Full Text\n\nAtia MA, El-Gheriani AA, Ferguson DJ: Validity of 3 Shape Scanner Techniques: A Comparison with the Actual Plaster Study casts. Biometrics Biostat Int J. 2015; 2(2): 64–69. Publisher Full Text\n\nMeyer BJ, Mörmann WH, Lutz F: Optimization of the powder application in the Cerec method with environment-friendly propellant systems. Schweiz Monatsschr Zahnmed. 1990; 100(12): 1462–1468. PubMed Abstract\n\nTorabi K, Farjood E, Hamedani S: Rapid Prototyping Technologies and their Applications in Prosthodontics, a Review of Literature. J Dent (Shiraz). 2015; 16(1): 1–9. PubMed Abstract | Free Full Text\n\nFleming PS, Marinho V, Johal A: Orthodontic measurements on digital study models compared with plaster models: A systematic review. Orthod Craniofacial Res. 2011; 14(1): 1–16. PubMed Abstract | Publisher Full Text\n\nRossini G, Parrini S, Castroflorio T, et al.: Diagnostic accuracy and measurement sensitivity of digital models for orthodontic purposes: A systematic review. Am J Orthod Dentofac Orthop. 2016; 149(2): 161–170. PubMed Abstract | Publisher Full Text\n\nBolton WA: Disharmony in tooth size and its relation to the analysis and treatment of malocclusion. Angle Orthod. 1958; 28(3): 113–130. Publisher Full Text\n\nAkyalcin S, Cozad BE, English JD, et al.: Diagnostic accuracy of impression-free digital models. Am J Orthod Dentofac Orthop. 2013; 144(6): 916–922. PubMed Abstract | Publisher Full Text\n\nBrown GB, Currier GF, Kadioglu O, et al.: Accuracy of 3-dimensional printed dental models reconstructed from digital intraoral impressions. Am J Orthod Dentofac Orthop. 2018; 154(5): 733–739. PubMed Abstract | Publisher Full Text\n\nTodd JA, Oesterle LJ, Newman SM, et al.: Dimensional changes of extended-pour alginate impression materials. Am J Orthod Dentofac Orthop. 143(4 Suppl): S55–S63. PubMed Abstract | Publisher Full Text\n\nde Waard O, Rangel FA, Fudalej PS, et al.: Reproducibility and accuracy of linear measurements on dental models derived from cone-beam computed tomography compared with digital dental casts. Am J Orthod Dentofac Orthop. 2014; 146(3): 328–336. PubMed Abstract | Publisher Full Text\n\nProffit W: Contemporary Orthodontics. 5th Edition. St. Louis: Mosby; 2012. Reference Source\n\nTomassetti JJ, Taloumis LJ, Denny JM, et al.: A Comparison of 3 Computerized Bolton Tooth-Size Analyses with a Commonly Used Method. Angle Orthod. 2001; 71(5): 351–357. PubMed Abstract | Publisher Full Text\n\nSuryajaya W: Research Data. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.13469160.v1\n\nSuryajaya W: Stereolithographic Data. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.13469172.v1"
}
|
[
{
"id": "80961",
"date": "17 Mar 2021",
"name": "Ida Bagus Narmada",
"expertise": [
"Reviewer Expertise Orthodontics and Orthopaedic Dentofacial"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors of this study have evaluated the linear accuracy and Bolton analysis of digital dental models scanned using Trios and resinic dental models printed using Formlabs 2 and compare them to plaster dental models. The results are certainly interesting and the authors are commended for executing this study.\n\nHowever, the authors need to address the following minor concerns:\n\nGeneral:\nThe paper is well organized and easy to follow.\n\nNovelty is sufficient and high impact.\n\nTo improve the readability, it is recommended that the text is checked by a native English speaking person as many of the sentences might be misunderstood. I suggest a revision of the English grammar structures by an expert editor in revising manuscripts.\nIntroduction:\nNo revision is needed.\nResults:\nPlease provide and add some information about standard deviation of the data.\n\nIs it possible to combine the tables to reduce the number of the tables? (9 tables are too many).\nDiscussion:\nDiscussion of the results is quite comprehensive. In analyzing the results, the authors also show citations from the previous study to support the explanation of these results.\n\nThe answer to the hypothesis of this study should be included at the beginning of the discussion section.\n\nPlease mention the limitation of this study and the suggestion for future study in the discussion section.\nConclusion:\nThe conclusion section is quite comprehensive. However, please add the clinical implication from this study result.\nReferences:\nThe supporting references are adequate for the medium 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?\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": "7074",
"date": "01 Sep 2021",
"name": "William Suryajaya",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for the valuable suggestions. Here are our response: We have made revisions accordingly. Notably, We replaced the tables with graphs so as to limit the number of the tables in the article. Thank you"
}
]
},
{
"id": "80964",
"date": "29 Mar 2021",
"name": "Cortino Sukotjo",
"expertise": [
"Reviewer Expertise 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\nDear authors, thank you very much for your article.\nPlease convert table 3-9 to graphs, so that you can include p-value comparisons between group.\n\nThe gold standard is plaster model, however, you mentioned many disadvantages of plaster model, which could confuse the reader who is not orthodontist.\n\nYou mentioned that some values were significantly different, but were they clinically significant?\n\nIn your conclusion, you mentioned that: \"Digital models and printed models may be considered to replace plaster models to diagnose and plan treatment for orthodontic cases\". Actually, in many developed countries, digital models have been used in orthodontic offices daily. Please revise your conclusion.\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? No",
"responses": [
{
"c_id": "7072",
"date": "01 Sep 2021",
"name": "William Suryajaya",
"role": "Author Response",
"response": "Dear reviewer, Thank you for the valuable input and here are our response: 1. Yes, we have replaced the tables with graphs so as to make the reader easier to compare between the p-values. 2. Plaster model is still the gold-standard study models in most parts of the worlds, especially in the less developed country. However, since it has many disadvantages, efforts to replace them with a more precise and accurate models has been very rigorous. One of the effort is to replace them with digital models and printed models. 3. As mentioned, a couple of times in the article and citing some references, we mentioned that the differences are clinically insignificant though statistically significant. 4. We have made revision accordingly. Thank you."
}
]
},
{
"id": "80963",
"date": "26 Apr 2021",
"name": "Ashok Karad",
"expertise": [
"Reviewer Expertise Orthodontic clinical work and research"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDental study models are one of the important diagnostic aids and their accuracy affects the diagnosis and treatment planning. This study has evaluated the linear accuracy and Bolton analysis of digital dental models and printed models and compared them to plaster dental models. The authors have done good work in analysing various parameters and providing a useful and clinically-relevant information. The contents have been clearly and accurately presented in the manuscript. The results of the study have been discussed comprehensively and are supported with appropriate references.\nHowever, the following minor concerns need to be addressed by the authors to provide more clarity and better understanding:\nThe manuscript requires one more round of linguistic/ grammatical editing.\n\nIn ‘Methods’ section, it is appropriate to use the term ‘Ethics committee’ instead of ‘Ethical committee’.\n\nThe figure 1 legend should be ‘Flow of events’ instead of ‘Flow of participants’. Make corresponding changes in the manuscript as well.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "7073",
"date": "01 Sep 2021",
"name": "William Suryajaya",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for your valuable inputs. Here are our response: 1. We have made an attempt to cross this article through a professional grammar editing process. 2. Noted and will be revised. 3. Noted and will be revised. Thank you"
}
]
}
] | 1
|
https://f1000research.com/articles/10-180
|
https://f1000research.com/articles/10-437/v1
|
03 Jun 21
|
{
"type": "Research Article",
"title": "Regional disparities and their contribution to the coverage of the tetanus toxoid vaccine among women aged 15–49 years in Indonesia",
"authors": [
"Hidayat Arifin",
"Restuning Widiasih",
"Rifky Octavia Pradipta",
"Yulia Kurniawati",
"Restuning Widiasih",
"Rifky Octavia Pradipta",
"Yulia Kurniawati"
],
"abstract": "Background: The prevention of Clostridium tetani bacterial infection through the administration of the tetanus toxoid (TT) vaccine in women is important. The purpose of this study was to determine the regional disparities and factors associated with TT vaccine coverage in women aged 15–49 years in Indonesia. Methods: The Indonesian Demographic Health Survey (IDHS) 2017 data was used in this study. A total of 36,028 women, aged 15–49 years were recruited using the two-stage stratified cluster sampling technique. The questionnaire used was based on the DHS Questionnaire Phase 7. Chi-squared and binary logistic regression were used in this study as part of the analysis. Results: We found that the TT vaccine coverage was 75.32% and that the majority were spread across several provinces. The provinces of Bali and Nusa Tenggara, the richer respondents, living in a rural area, visiting the health facility, having health insurance, and those currently working were factors making it more likely that the women would receive the TT vaccine. The respondents aged 15–24 years with a primary education level and the respondents who were divorced were less likely to receive the TT vaccine. Conclusion: The coverage of the TT vaccine among women can be increased by considering the regional disparities in Indonesia and the socio-economic demographic details of the respondents. Strengthening the policies from the central government in the local governments can improve the screening process and vaccine delivery outcomes. In addition, the importance of giving the TT vaccine to women needs to be relayed through health education in collaboration between health workers and the public.",
"keywords": [
"vaccine",
"tetanus toxoid",
"tetanus vaccine",
"demographic health survey",
"women"
],
"content": "Introduction\n\nNeonatal tetanus (NT) is a disease that can be prevented. It has become a global health problem with both high case and high fatality rates among neonates.1 NT refers to tetanus that occurs at 28 days of early life.2 NT occurs due to the toxins produced by Clostridium tetani alongside an unhygienic labor agent. It spreads through the umbilical cord.3 One of the efforts to prevent the incidence of NT is the provision of an adequate tetanus toxoid (TT) vaccine for women of reproductive age.4 In 2006, WHO developed guidelines for the TT vaccine for pregnant women to prevent NT.5 The Indonesian government through the Ministry of Health Regulation number 42 of 2017 also launched the TT vaccine program as an advanced vaccine with a national and regional vaccine target coverage of at least 90% and 80%, respectively.6\n\nTwo doses of the TT vaccine can provide immunity and reduce neonatal mortality by 94%.7,8 One case–control study also reported that the administration of two doses of the TT vaccine was associated with a decrease in the incidence of NT9,10 and vice versa.11 Infant mortality was predicted to decrease by 46% after the mother received their first dose of the TT vaccine and by 45% after the second dose.12 The Indonesian Health Profile data from the years 2013–2015 show the trend that not receiving the TT vaccine is the leading cause of neonatal mortality.13–15 Although NT can be prevented by the TT vaccine, the number of cases is still high. Globally, it is estimated that as many as 3.6 million neonates die every year, among which 59,000 die from tetanus.16 The infant mortality rate in Indonesia according to the Indonesian Demographic and Health Survey in 2007 was 34 deaths per 1,000 live births with the highest number of deaths occurring during the neonatal period.17 The neonatal mortality rate in Indonesia in 2007 was 19 per 1000 live births and NT was one of the main causes of death.18,19\n\nThere are still cases of NT in line with the coverage of the national and regional TT vaccines not yet reaching the target. Nationally, the coverage of the TT vaccine for both pregnant and reproductive age women tends to fluctuate and has not yet reached the target. The TT vaccine coverage for pregnant and reproductive age women from 2007 to 2011 was 26% and 27.1%, 65.2% and 24.7%, 73.5% and 11.2%, 69.5% and 8, 6%, and 63.6% and 11.8%, respectively.17 If the regional data is examined randomly, the coverage of the TT vaccine in select regions has also not reached the target.20\n\nThe low coverage of the TT vaccine is largely influenced by inadequate knowledge.21,22 Women of reproductive age with knowledge of maternal and neonatal tetanus (MNT) and low TT vaccine are 0.435 times more likely to receive the TT vaccine.23 Insufficient knowledge of the TT vaccine among prospective brides of reproductive age are one of the factors for the low TT vaccine coverage.24 Based on the data above, to overcome this inadequate knowledge, health education about TT is needed. Good health education pays attention to and identifies people’s characteristics in the intended category so then the health education provided can be more effective.25 This study is focused on revealing TT vaccine coverage and the determinant factors of the TT vaccine being received in relation to women of reproductive age.\n\nSeveral previous Indonesian studies have revealed the coverage and determinants of the TT vaccine. Research into the TT coverage is still reported on a regional scale.26,27 Research on the determinants of the vaccine for women of childbearing age specifically includes knowledge, family support, attitudes, and the behavior of the health workers.22,28,29 This study used available national data including age, education level, wealth quintile, residence, marital status, visiting the health facilities, health insurance, occupational status, the sex of the household head, pregnancy, and the different regional areas in relation to the TT vaccine. It is expected that the results of this study can be used when devising effective approaches for the education of women of reproductive age to promote the TT vaccine.\n\n\nMethods\n\nA cross-sectional study design was undertaken. We used secondary data from the Indonesian Demographic Health Survey (IDHS) 2017 and parts of the Inner-City Fund (ICF) International data.\n\nThe survey was conducted in December 2017. We used the IDIR71FL dataset (Indonesian Individual Recode phase 7). The total study population was 49,627 women aged 15–49 years. We then weighted the data based on the number of provinces in Indonesia in order to obtain the average for each region. We managed to reach 36,028 women aged 15–49 years who have not received the TT vaccine in Indonesia. Furthermore, there was missing data. Two-stage stratified cluster sampling was used in this study by selecting clusters from each stratum and a list of families from the selected clusters. Then the families’ questionnaire responses were investigated (Demographic Health Survey, 2017).\n\nThe independent variables in this study included age, education level, wealth quintile, residence, marital status, visiting the health facility, health insurance, occupational status, sex of household head, pregnancy, regional disparities. Age was categorized into 15–24 years old, 25–34 years old and 35–49 years old (Health Ministry of Republic Indonesia, 2009). Based on Law No. 20 of 2003 concerning the National Education System in Indonesia, education level was categorized into high, secondary, primary, and no education.30 The respondents’ wealth quintile was categorized into poorest, poorer, middle, richer, and richest respectively.31,32 Residence was categorized into either an urban or rural area.33 Marital status was classified as either married, partnered, widowed, divorced or separated. The respondents who had visited a health facility in the last six months, whether they had health insurance, if they were currently working, and their pregnancy status were all categorized as either yes or no.31 We identified the sex of the household head as either male or female. For the regions in Indonesia, we classified the country based on the big islands as follows: Sumatera, Riau, Java, Bali and Nusa Tenggara, Kalimantan, Sulawesi, Maluku, and Papua.34\n\nThe dependent variable in this study was the TT vaccine. We identified women aged 15–49 years who either received or did not receive the TT Vaccine. Then we categorized them according to their answer of either yes or no (Demographic Health Survey, 2017). To enhance the quality and transparency of reporting the study results, the researchers applied The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE).35\n\nWe used the STATA version 16.1: “A Software resource for statistical analysis and presentation of graphics (Stata, RRID:SCR_012763)”. We used Chi-squared to analyze the bivariate data and binary logistic regression to analyze the multivariate data. We used the adjusted odds ratio (AOR) with a 95% confidence interval (CI) and a significance level of p < 0.05.\n\nEthical approval for the secondary dataset was not required. The dataset policy is available on the official website. We received approval to use the dataset from ICF International with number AuthLetter_154679.\n\n\nResults\n\nIn this study, we found that the coverage of the TT vaccine in Indonesia reached 75.32% out of the 36,028 respondents. More than half of the total respondents who received the vaccine aged 35–49 years were educated to secondary school level. The distribution of wealth quintiles was almost the same, ranging from poorest to richest. The majority were in the poorest quintile. In addition, the distribution of residence was almost the same across both urban and rural areas. The majority of the respondents in this study were married and they had regularly visited health facilities in the last six months. We found that the majority of respondents had health insurance, were working, and were not pregnant. The majority of the household heads were male. According to the regional data, the majority of the respondents were spread across the large islands in Indonesia such as Java and Sumatra (Table 1).\n\nUpon examining the regional distribution data in Indonesia, the TT vaccine coverage was more than 70% in Riau, Java, Bali and Nusa Tenggara, Kalimantan, Sulawesi, and Papua. The majority of respondents aged 35–49 years were spread across Indonesia. The distribution data indicate that the majority of respondents were educated to secondary school level, followed by those with primary education. The majority of respondents in the richest quintile and living in an urban area in Riau and Java. The majority of respondents in the poorest quintile and living in a rural area were in Bali and Nusa Tenggara, Sulawesi, Maluku, and Papua. Most of the respondents were married, had health insurance, were working, were not pregnant, and the household head was male. The respondents in Riau, Maluku, and the Papua islands responded stating that they had rarely visited the health facilities in the last six months (Table 2).\n\nThe bivariate analysis showed that the regional variables, age, education level, wealth quintile, residence, marital status, whether they visited the health facilities, health insurance, whether they were currently working, and the sex of the household head have a significant relationship with TT vaccine coverage in women aged 15–49 years. However, the pregnancy variable did not have a significant relationship with TT vaccine coverage (Table 3).\n\n*** p < 0.01.\n\n** p < 0.05.\n\n* p < 0.1.\n\nTable 4 shows the results of the multivariate analysis. The data indicate that regional disparities, age, education level, wealth quintile, residence, marital status, whether they had visited the health facilities recently, and health insurance are likely to be associated with TT vaccine coverage in women aged 15–49 years in Indonesia. The regional data shows that the respondents in Bali and Nusa Tenggara are 3.363-times more likely to receive the TT vaccine than the respondents in Sumatera (AOR = 3.363; 95%CI = 2.997–3.773). The respondents aged –24 years old are 0.71-times less likely to receive the TT vaccine than those aged 35–49 years (AOR = 0.71; 95%CI = 0.653–0.772). Regarding education level, the respondents with a primary school level of education were 0.544-times less likely to receive the TT vaccine than the respondents with a higher level of education (AOR = 0.544; 95%CI = 0.494–0.599). Furthermore, the richer respondents were 1.645-times more likely to receive the TT vaccine than the poorest respondents (AOR = 1.645; 95%CI = 1.506–1.798). The respondents living in rural areas were 1.106-times more likely to have had the TT vaccine than those living in urban areas (AOR = 1.106; 95%CI = 1.044–1.173). Divorced respondents were 0.693-times less likely to receive the TT vaccine than married respondents (AOR = 0.693; 95%CI = 0.608–0.79). The respondents who had regularly visited a health facility in the last six months were 1.693-times more likely to receive the vaccine than those who had not (AOR = 1.693; 95%CI = 1.609–1.781). The respondents who had health insurance were 1.176-times more likely to receive the vaccine than those who did not (AOR = 1.176; 95%CI = 1.117–1.239). The respondents who worked were 1.147-times more likely to receive the vaccine than those who did not (AOR = 1.147; 95%CI = 1.088–1.208).\n\n*** p < 0.01.\n\n** p < 0.05.\n\n* p < 0.1.\n\n\nDiscussion\n\nIn this study, we discussed the gap in the reception of the TT vaccine among women aged 15–49 years in Indonesia by looking at the regional disparities. We also were able to determine the contributions behind the achievement of the TT vaccine coverage in Indonesia as it stands. We found that regional disparities were significantly associated with TT vaccine performance. In addition, the factors of age, education level, wealth quintile, residence, marital status, whether they visited the health facilities, health insurance, and whether they were currently working also contribute to the TT vaccine coverage among women aged 15–49 years in Indonesia.\n\nRegional disparities are one of the demographic factors that contribute greatly to the TT vaccine coverage among women. Indonesia, which is an archipelago region, can be an inhibiting factor regarding vaccine coverage.36,37 Differences in culture, region, ethnicity, language, knowledge, and access are important factors to consider when seeking to facilitate access to a vaccine.38,39 According to this study, the Bali and Nusa Tenggara regions have a greater chance of administering the TT vaccine to their respective populations than other regions. When viewed according to socio-economic development, Bali and Nusa Tenggara, which are included within Eastern Indonesia, are far behind compared with the Java, Sumatera and Riau.40,41 However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high. This is consistent with the previous research which states that vaccine coverage can be influenced by region, development, knowledge and self-awareness.42,43\n\nWe found that the younger respondents, aged 15–24 years, were less likely to receive the TT vaccine than the respondents who were older (35–49 years old). A previous study showed that age is related to the knowledge of the importance of vaccines and the ability to make decisions.44,45 Therefore, health education is needed among those of a young age about the importance of vaccines. In addition, in this study it is also known that this is less likely for those of a primary education level compared with those with a higher level of education. This is because with a good level of knowledge, TT vaccination coverage can be achieved. In this case, the government and health workers have an important role in distributing knowledge about vaccines to the public. The previous study has shown that vaccine performance is influenced by a good level of knowledge.46,47\n\nIn this study, we found that economic status contributed to the achievement of TT vaccine coverage in women. It is known that respondents with a wealth quintile that is higher and those with a job are more likely to receive the TT vaccine compared with the respondents whose economic level is low and who do not work. Previous research has shown that the respondents with a stable income can easily access private and government health facilities and get vaccines.48,49 In addition, the respondents who had health insurance were found to be more likely to receive the TT vaccine. This is because the respondent feels calm that their medical costs will be covered by their health insurance. Previous research has shown that with health insurance, vaccine coverage can increase.50–52\n\nIn terms of the rural areas, the study found that the residents of these areas are more likely to receive the TT vaccine. This is related to the obedience of the rural population where doctors, nurses and midwives have been able to gain the trust of the community.53 This closeness is also obtained through the routine outreach process used to engage with the community members.54 The information obtained by the rural residents tends to be more centralized and there is no intervention from other sources such as the internet and minimizing false news; the information will be centered on the doctors, nurses and midwives visited at the health facility as a result. This is in contrast to the urban residents who prefer to obtain their health-related information independently. They tend to compare the results of the information obtained from the internet with that of the doctors, nurses and midwives at the health facilities. The gaps in the information obtained trigger doubts about the TT vaccine and in the end, there is a delay in getting the vaccine even after marriage.\n\nThis study found that the women who visit the health facility are more likely to receive the TT vaccine. Visiting the health facility will increase their information and knowledge related to vaccines.55 In addition, each visit can increase their closeness and bond with the health workers. This can convince the women aged 15–49 years old to have the TT vaccine. Routine visits to the health facilities can also overcome obstacles that have previously been a barrier to vaccines, including a lack of knowledge and excessive concern about the side effects of the vaccine. Rumors circulating in the community regarding the TT vaccine can be explained through counselling during visits to the health facilities. One of the rumors is that the content of the vaccine material is not halal, so there is resistance from some women. Health workers like the doctors and nurses are needed to clarify the problem.\n\nThose with a divorced status were found to be less likely to receive the TT vaccine. This is associated by the decrease or non-existence of motivation from a partner. Divorced women do not feel the need to receive the TT vaccine. This is because one of the goals of this vaccine is to reduce the risk of tetanus in women and their unborn baby.56 If they are divorced, there is no need for the TT vaccine. Although the TT vaccine is actually a requirement before marriage takes place, this vaccine can be missed because of the assumption that you have received the vaccine before. There is still the assumption that the vaccine is not necessary.\n\nThe strength of our study is that it provides information on the TT vaccine coverage nationally while highlighting the regional disparities in Indonesia. The results of this study can become basic data for the Indonesian government to use to determine further policies to achieve an improved level of TT vaccine coverage among women. However, this study has limitations in that the researchers looked at the distribution based only on the major islands in Indonesia. Descriptions at the provincial level are needed for the formulation of more specific policies.\n\n\nConclusion\n\nIn this study, we found there to be a gap in the TT vaccine uptake among women aged –49 years old in Indonesia. Indonesia as a whole, which is an archipelago, is one of the considerations and constraints involved in the coverage of the TT vaccine among women. The findings of this study provide an overview about the TT vaccine coverage according to several factors such as the regional disparities and the respondents’ socio-economic demographic information. Furthermore, the government can collaborate across different sectors between the central and local governments to achieve the desired TT vaccine coverage. Providing accurate and precise information about the TT vaccine needs to be promoted by healthcare workers in collaboration with the community through online methods to reach the urban population areas in Indonesia. An in-depth exploration with additional factors and sectors involved is needed in terms of the direction of further research.\n\n\nData availability\n\nData used in this study is available online from the Indonesian 2017 Demographic and Health Survey (DHS) website under the ‘Individual Recode’ section. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.",
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}
|
[
{
"id": "87631",
"date": "23 Jul 2021",
"name": "Heri Kuswanto",
"expertise": [
"Reviewer Expertise Statistical data analysis",
"econometrics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 has been written very well, with a structure that is easily understood. However, there is a minor comment that might be considered to improve the quality of the paper:\nThe interpretation of the logistic regression model is done partially without trying to interrelate the finding on another variable. In this paper, since the authors did not conduct a collinearity test, some findings need to be clarified further. For instance, I guess women in rural areas are mostly without insurance, but the statistical test showed that either women in rural areas or women with insurance are likely to be vaccinated. This finding seems to contradict each other which might be caused by a high degree of correlation between variables (considering the fact that the odds ratio is also very close to 1). If it is difficult to be done, I would suggest that the authors state the assumption of no significant correlation among predictors.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7065",
"date": "02 Sep 2021",
"name": "Hidayat Arifin",
"role": "Author Response",
"response": "Dear Prof. Heri Kuswanto Thank you very much for your comments and suggestion to improve the quality of our manuscript. we have added in the limitations of the study that there is the assumption of no significant correlation among predictors."
}
]
},
{
"id": "87930",
"date": "09 Aug 2021",
"name": "Muhammad Hardhantyo",
"expertise": [
"Reviewer Expertise Health Policy",
"Epidemiology",
"Child Health",
"Maternal Health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPlease clarify the sudden increase of pregnant TT vaccine coverage in Indonesia from 2007 to 2008. It was mentioned that the vaccine coverage was 26% in 2007 and significantly increased to 65.2% in 2008. The strategies might benefit to improve the coverage in reproductive age women vaccination also.\n\nPlease determine the framework or theoretical model to decide the independent variables used in the study.\n\nHow was the categorization of household wealth determined by the authors of this article?\n\nPlease clarify the sampling method used in the articles, in the sample section the authors managed to reach 36,028 women aged 15– 49 years who have not received the TT vaccine in Indonesia. However, in the results section, the authors found that the coverage of the TT vaccine in Indonesia reached 75.32% out of the 36,028 respondents. Both statements were contradictory.\n\nPlease explain the process of handling the missing data and whether these might cause a bias in the estimation of parameters.\n\nTo reduce the number of tables, Tables 1 and 2 could be combined together.\n\nNeed to add 1 row to correct the position of the p-value and 95% Confidence Interval column in Table 4.\n\nUnderprivileged communities such as poor, low-educated women, single parents did not have any health insurance and the unemployed were less likely to have received TT vaccination compared to their counterparts. However, an interesting finding in the rural area where rural women are more likely to have received TT vaccination. Authors need to find more explanations and references.\n\nPlease provide reference to this statement \"The information obtained by the rural residents tends to be more centralized and there is no intervention from other sources such as the internet and minimizing false news; the information will be centered on the doctors, nurses and midwives visited at the health facility as a result. This is in contrast to the urban residents who prefer to obtain their health-related information independently. They tend to compare the results of the information obtained from the internet with that of the doctors, nurses, and midwives at the health facilities.\"\n\nIn the Discussion section, please have a comment on any current public health efforts from the Indonesian government to increase immunization coverage?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7066",
"date": "02 Sep 2021",
"name": "Hidayat Arifin",
"role": "Author Response",
"response": "Dear Muhammad Hardhantyo, PhD. Thank you very much for the comments and suggestions. Here we put some revisions based on your suggestions. 1. Please clarify the sudden increase of pregnant TT vaccine coverage in Indonesia from 2007 to 2008. It was mentioned that the vaccine coverage was 26% in 2007 and significantly increased to 65.2% in 2008. The strategies might benefit to improve the coverage in reproductive age women vaccination also. Thank you for the suggestion. The difference in coverage from the highest and lowest during the period was possible due to differences in perceptions of the operational definition, problems in recording, reporting formats, and others. So there needs to be an effort to organize a recording and reporting system for pregnant women TT vaccination. 2. Please determine the framework or theoretical model to decide the independent variables used in the study. Thank you for the suggestion. The independent variables in this study were obtained from similar previous research variables, then adjusted to the demographic data in Indonesia. 3. How was the categorization of household wealth determined by the authors of this article? The wealth quintiles were divided into five categories based on principal component analysis (PCA). The wealth quintiles were measured by the percentage distribution of the de jure population using the wealth quintiles and the Gini coefficient. For the percentage distribution, the numerators were divided by the denominators multiplied by 100. The results were then divided into five equal parts from quintile one (poorest) to quintile five (richest); each included 20% of the total population. Then, it was categorized into the poorest, poorer, middle, richer, and richest respectively. 4. Please clarify the sampling method used in the articles, in the sample section the authors managed to reach 36,028 women aged 15– 49 years who have not received the TT vaccine in Indonesia. However, in the results section, the authors found that the coverage of the TT vaccine in Indonesia reached 75.32% out of the 36,028 respondents. Both statements were contradictory. Thank you for the correction. We have mistaken the sentences. We reached 36,028 women aged 15– 49 years who have and have not received the TT vaccine in Indonesia. 5. Please explain the process of handling the missing data and whether these might cause a bias in the estimation of parameters. In the beginning, we weighted the data set to make sure the equal portion in each province of Indonesia. Then, we used syntax “keep if” in STATA to exclude the missing data from the analysis. 6. To reduce the number of tables, Tables 1 and 2 could be combined together. We combined Table 1 and Table 2. 7. Need to add 1 row to correct the position of the p-value and 95% Confidence Interval column in Table 4. Yes, we have added the suggestion. 8. Underprivileged communities such as poor, low-educated women, single parents did not have any health insurance and the unemployed were less likely to have received TT vaccination compared to their counterparts. However, an interesting finding in the rural area where rural women are more likely to have received TT vaccination. Authors need to find more explanations and references. Thank you for the suggestion. “Number of midwives in rural to remote areas facilitate access for pregnant women to check up pregnancy, including the TT vaccine”. 9. Please provide reference to this statement \"The information obtained by the rural residents tends to be more centralized and there is no intervention from other sources such as the internet and minimizing false news; the information will be centered on the doctors, nurses and midwives visited at the health facility as a result. This is in contrast to the urban residents who prefer to obtain their health-related information independently. They tend to compare the results of the information obtained from the internet with that of the doctors, nurses, and midwives at the health facilities.\" Thank you for the suggestion. We have added the references. \"The information obtained by the rural residents tends to be more centralized and there is no intervention from other sources such as the internet and minimizing false news; the information will be centered on the doctors, nurses and midwives visited at the health facility as a result. This is in contrast to the urban residents who prefer to obtain their health-related information independently. They tend to compare the results of the information obtained from the internet with that of the doctors, nurses, and midwives at the health facilities.\" 10. In the Discussion section, please have a comment on any current public health efforts from the Indonesian government to increase immunization coverage? Thank you for the suggestion. The Indonesian government has many efforts to increase the TT vaccination coverage, such as equitable availability of midwives in rural to remote areas and regulations that require brides to be vaccinated TT according to government regulation number 02 of 1989 about Tetanus Toxoid Immunization before marriage."
}
]
},
{
"id": "90139",
"date": "19 Aug 2021",
"name": "Azza Mehanna",
"expertise": [
"Reviewer Expertise Behavioral Sciences",
"Health promotion",
"Health 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\nIntroduction:\nParagraph 1, last line: Reference 6 is not in English, and on opening it, it seemed to lack some important details such as the target year for national and regional vaccine coverage of at least 90% and 80% respectively and it (target year) was not mentioned in the manuscript either.\nAlso: \"as an advanced vaccine”, what do you mean?\n\nParagraph 2, line 4: Reference 12 is rather old, aren’t there more recent updates for these figures?\nAlso: \"and by 45% after the second dose”, I don’t think this percentage is correct, infant mortality shows more decrease after the second dose.\n\nParagraph 2, line 7: Reference 16 is rather old, try to find more recent data.\n\nParagraph 2, lines 7-8: you got the data from DHS 2007, isn’t there a more recent DHS? You mentioned DHS 2017 in methodology, why haven’t you used it in your review?\n\nParagraph 3, line 1: “There are still cases of NT in line with the coverage of the national and regional TT vaccines not yet reaching the target.” This statement is not clear and needs to be rephrased.\n\nParagraph 4, lines 1-2: “Women of reproductive age with knowledge of maternal and neonatal tetanus (MNT)”, you probably mean poor knowledge, please clarify.\n\nParagraph 4, line 2: “low TT vaccine are 0.435 times more likely to receive the TT”, what do you mean by low tetanus toxoid vaccine? \"0.435 times more likely to receive the TT vaccine\": this is not a good interpretation of the odds ratio.\n\nI found some difficulty checking on some references, e.g references 6 and 27, as they were written in a different language.\nMethods:\nYou need to elaborate more on methods as follows:\nSample, lines 3-4: “We managed to reach 36,028 women aged 15– 49 years who have not received the TT vaccine in Indonesia”, how did you reach them? Did you give them questionnaires? Please clarify.\n\nWhy haven’t you been able to study the whole population mentioned (49,627)? Please clarify.\n\nThis sample of women (36,028) comprises those who received and those who did not receive the vaccine according to Table 1 and not only those who have not received the vaccine as you mentioned.\n\nSample, line 4: “Two-stage stratified cluster sampling was used”, what are the two stages? Stratified according to what?\n\nResults:\nTables 3 and 4: You don’t need to put *P<0.1 in the footnotes.\n\nTable 3, last row: Is the value “0.091” the correct value of χ2? Please check.\n\nTable 3: Why have you calculated percent from total not from independent variable?\n\nTable 4, line 2: “and health insurance”, it is better to say \"and having health insurance\".\nDiscussion:\nParagraph 2, line 2: “Indonesia, which is an archipelago region, can be an inhibiting factor regarding vaccine coverage”. This statement needs rephrasing and clarification.\n\nParagraph 2, lines 7-9: “However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high. This is consistent with the previous research which states that vaccine coverage can be influenced by region, development, knowledge and self-awareness”:\n\n“vaccine coverage can be influenced by region, development”: From the context, it seems that you refer to a direct relationship. However, this contradicts your findings as vaccine coverage in Bali and Nusa Tenggara is high (83.66%), despite having a high percentage of the poorest (48.38%) and a relatively low percentage of the richest (10.94%).\n\n\"self-awareness”: Self-awareness was not studied in this research and it is a totally different concept, I think you mean awareness of the disease and vaccine.\n\n“it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high”: Awareness of the vaccine and of its importance was not studied in this research, in fact, awareness of the vaccine and of its importance could just be some of the possible factors underlying high coverage rates. You may point to awareness as an inference not as a finding. Please note that awareness of the vaccine is not the same as awareness of the importance of the vaccine.\n\nParagraph 3: Why do you relate your studied variables as age and education to knowledge and you continue referring to it (knowledge) despite not being studied in this research? In fact, many other variables could underlie and explain high coverage, such as: applying a good coverage policy, life experiences and beliefs, culture, physicians’ attitude and behavior regarding vaccine, availability and accessibility of vaccine, and social support/pressure.\n\nParagraph 3, line 7: “the previous study”, which study? You put two references not one.\n\nParagraph 4, lines 1-2: “It is known that respondents with a wealth quintile that is higher and those with a job are more likely to receive the TT vaccine compared with the respondents whose economic level is low and who do not work”:\n\n“it is known that\": From where? Opposite findings are displayed in other studies, for example, Mehanna A, Ali MH, Kharboush I: Knowledge and health beliefs of reproductive-age women in Alexandria about tetanus toxoid immunization. J Egypt Public Health Assoc. 2020; 95(1): 1–11 (Reference 23).\n\nParagraph 4, lines 6-7: “Previous research has shown that with health insurance, vaccine coverage can increase”, this statement may be too simple, it needs rephrasing.\n\nParagraph 5: You pointed out that residents of rural areas are more likely to receive the TT vaccine, and you attributed that to their obedience to their doctors and nurses. Well, perhaps there are other justifications; maybe physicians in rural areas - who usually work in health units or hospitals affiliated to the ministry of health (MOH) - are more committed to vaccinate or recommend vaccination to their female clients. Maybe females in urban areas rely more on private physicians who may not always adhere to the instructions and regulations of the MOH regarding vaccination.\n\nParagraph 6: You found that women who visited the health facility were more likely to receive the TT vaccine, then you started explaining your finding. You gave a good interpretation, however, some information was repeated, e.g “Routine visits to the health facilities can also overcome obstacles that have previously been a barrier to vaccines, including a lack of knowledge and excessive concern about the side effects of the vaccine”. This is a repetition of what you have just said. You may rephrase this paragraph to explain your point without redundancy.\n\nParagraph 7: The same comment as paragraph 6. Please rephrase this paragraph to avoid redundancy.\n\nParagraph 7, line 4 “Although the TT vaccine is actually a requirement before marriage takes place”, please identify the regulations and policy of the Ministry of Health in Indonesia regarding TT vaccination for females.\n\nParagraph 7, line 5 “vaccine can be missed because of the assumption that you have received the vaccine before”, isn’t there vaccination cards or records to refer to by the health personnel to make sure that the female client has been vaccinated? Is vaccine given only in health facilities affiliated with the MOH or it may be administered in private clinics? Please clarify.\n\nParagraph 7, lines 5-6: “There is still the assumption that the vaccine is not necessary”, you need to elaborate a little more on this point and identify the rationale beyond this assumption.\nConclusion\nLine 1: “we found there to be a gap in the TT vaccine uptake among women aged –49 years old in Indonesia”, if you mean the age group 35-49 then this conclusion contradicts your findings as this group is the highest in vaccine uptake. If you mean 15-49 then you need to explain your conclusion, especially that your results (Table 2) and your Discussion (\"However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high\") referred to the high TT vaccine coverage rates.\n\nLines 2-3: “Indonesia as a whole, which is an archipelago, is one of the considerations and constraints involved in the coverage of the TT vaccine among women”, you need to clarify this point a little.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7067",
"date": "02 Sep 2021",
"name": "Hidayat Arifin",
"role": "Author Response",
"response": "Dear Dr. Azza Mehanna, Thank you very much for the comments and suggestions. Here we put some revisions based on your suggestions. Paragraph 1, last line: Reference 6 is not in English, and on opening it, it seemed to lack some important details such as the target year for national and regional vaccine coverage of at least 90% and 80% respectively and it (target year) was not mentioned in the manuscript either. Thank you for the correction. The Government of Indonesia through the regulation of the Minister of Health no 12 of 2017 concerning the implementation of immunization stipulates a national immunization coverage of at least 90% and immunization coverage in districts/cities of at least 80%. Also: \"as an advanced vaccine”, what do you mean? Thank you for the correction. We mean \"continued vaccine\". Paragraph 2, line 4: Reference 12 is rather old, aren’t there more recent updates for these figures? Thank you for the suggestion. We have found and added the more recent data. “Minimum 2 doses of TT vaccine were identified can reduce neonatal mortality” Also: \"and by 45% after the second dose”, I don’t think this percentage is correct, infant mortality shows more decrease after the second dose. Thank you for the correction. In line with the addition of recent data in references 1 and 12 (paragraph 2), we also update this percentage. “TT vaccination contributes to the reduction of neonatal mortality due to tetanus by 85% from 2000 to 2018”. Paragraph 2, line 7: Reference 16 is rather old, try to find more recent data. Thank you for the suggestion. We have found and added the more recent data. “TT vaccination contributes to the reduction of neonatal mortality due to tetanus by 85% from 2000 to 2018”. Paragraph 2, lines 7-8: you got the data from DHS 2007, isn’t there a more recent DHS? You mentioned DHS 2017 in methodology, why haven’t you used it in your review? We used 2007 DHS data as an initial overview of TT immunization coverage in the introduction. DHS 2017 data is the data we analyzed, so the review is only written in the method, result, discussion section. Paragraph 3, line 1: “There are still cases of NT in line with the coverage of the national and regional TT vaccines not yet reaching the target.” This statement is not clear and needs to be rephrased. Thank you for the correction, we have paraphrased the sentence. Paragraph 4, lines 1-2: “Women of reproductive age with knowledge of maternal and neonatal tetanus (MNT)”, you probably mean poor knowledge, please clarify. Thank you for the correction. “Women with poor knowledge of MNT and TT vaccine”. Paragraph 4, line 2: “low TT vaccine are 0.435 times more likely to receive the TT”, what do you mean by low tetanus toxoid vaccine? \"0.435 times more likely to receive the TT vaccine\": this is not a good interpretation of the odds ratio. Thank you for the correction. We have revised it to be less likely to receive the TT vaccine. I found some difficulty checking on some references, e.g references 6 and 27, as they were written in a different language. Thank you for your attention. We used those references because they are related to the statements. Sample, lines 3-4: “We managed to reach 36,028 women aged 15– 49 years who have not received the TT vaccine in Indonesia”, how did you reach them? Did you give them questionnaires? Please clarify. In this study, we used secondary data from the Indonesian Demographic Health Survey (IDHS) 2017 that is part of the Inner-City Fund (ICF) International data. All the data collection was collected by questionnaire and managed by IDHS. Thus, we managed to reach 36,028 women aged 15– 49 years who have and have not received the TT vaccine in Indonesia. Why haven’t you been able to study the whole population mentioned (49,627)? Please clarify. We were not the whole population to be analyzed because we found many missing data and should be excluded. We weighted the data set to make sure the equal portion in each province of Indonesia. Then, we used syntax “keep if” in STATA to exclude the missing data from the analysis. This sample of women (36,028) comprises those who received and those who did not receive the vaccine according to Table 1 and not only those who have not received the vaccine as you mentioned. Thank you, we have revised it. We managed to reach 36,028 women aged 15– 49 years who received and did not receive the TT vaccine in Indonesia. Sample, line 4: “Two-stage stratified cluster sampling was used”, what are the two stages? Stratified according to what? The sample was obtained through a two-stage stratified cluster sampling technique including select clusters from each stratum and a list of households in selected clusters. The researchers then selected the households to be interviewed. Tables 3 and 4: You don’t need to put *P<0.1 in the footnotes. Thank you for the correction. Table 3, last row: Is the value “0.091” the correct value of χ2? Please check. Yes, the analysis is correct based on chi-square analysis. Table 3: Why have you calculated percent from total not from independent variable? Because we would like to know the distribution of the percentage of each category. Table 4, line 2: “and health insurance”, it is better to say \"and having health insurance\". Thank you for the correction. Paragraph 2, line 2: “Indonesia, which is an archipelago region, can be an inhibiting factor regarding vaccine coverage”. This statement needs rephrasing and clarification. Thank you for your suggestion. Indonesia is a country that has many islands. This geographical condition can affect the coverage in vaccination because it affects the access, availability, distribution of the vaccine supply chain between islands. Paragraph 2, lines 7-9: “However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high. This is consistent with the previous research which states that vaccine coverage can be influenced by region, development, knowledge and self-awareness”: “vaccine coverage can be influenced by region, development”: From the context, it seems that you refer to a direct relationship. However, this contradicts your findings as vaccine coverage in Bali and Nusa Tenggara is high (83.66%), despite having a high percentage of the poorest (48.38%) and a relatively low percentage of the richest (10.94%). Thank you for the correction. We have deleted the sentence because of incoherence with the previous sentences. \"self-awareness”: Self-awareness was not studied in this research and it is a totally different concept, I think you mean awareness of the disease and vaccine. Thank you for the correction. “it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high”: Awareness of the vaccine and of its importance was not studied in this research, in fact, awareness of the vaccine and of its importance could just be some of the possible factors underlying high coverage rates. You may point to awareness as an inference not as a finding. Please note that awareness of the vaccine is not the same as awareness of the importance of the vaccine. Thank you for the correction. We have deleted the sentence because of incoherence with the previous sentences. Paragraph 3: Why do you relate your studied variables as age and education to knowledge and you continue referring to it (knowledge) despite not being studied in this research? In fact, many other variables could underlie and explain high coverage, such as: applying a good coverage policy, life experiences and beliefs, culture, physicians’ attitude and behavior regarding vaccine, availability and accessibility of vaccine, and social support/pressure. We discussed age, knowledge, and level of education because we found many references about it. Moreover, we added that less experience, beliefs, and support from family are also related in this case. Paragraph 3, line 7: “the previous study”, which study? You put two references not one. We mean both previous studies. Paragraph 4, lines 1-2: “It is known that respondents with a wealth quintile that is higher and those with a job are more likely to receive the TT vaccine compared with the respondents whose economic level is low and who do not work”: “it is known that\": From where? Opposite findings are displayed in other studies, for example, Mehanna A, Ali MH, Kharboush I: Knowledge and health beliefs of reproductive-age women in Alexandria about tetanus toxoid immunization. J Egypt Public Health Assoc. 2020; 95(1): 1–11 (Reference 23). We wrote the sentence referring to the result of our study. Paragraph 4, lines 6-7: “Previous research has shown that with health insurance, vaccine coverage can increase”, this statement may be too simple, it needs rephrasing. Previous research has shown that with health insurance, vaccine coverage can increase. It was because people should not think about the payment for the TT vaccine. It can be one of the programs from the government to reach high vaccination coverage. Paragraph 5: You pointed out that residents of rural areas are more likely to receive the TT vaccine, and you attributed that to their obedience to their doctors and nurses. Well, perhaps there are other justifications; maybe physicians in rural areas - who usually work in health units or hospitals affiliated to the ministry of health (MOH) - are more committed to vaccinate or recommend vaccination to their female clients. Maybe females in urban areas rely more on private physicians who may not always adhere to the instructions and regulations of the MOH regarding vaccination. Thank you for the suggestion. We have elaborated the sentence. Rural residents rely more on health workers where they live. In this context, it is the midwife who mostly works in remote villages. Rural residents trust these midwives and regard the midwife as a link between them and the health care facilities provided by the government. Paragraph 6: You found that women who visited the health facility were more likely to receive the TT vaccine, then you started explaining your finding. You gave a good interpretation, however, some information was repeated, e.g “Routine visits to the health facilities can also overcome obstacles that have previously been a barrier to vaccines, including a lack of knowledge and excessive concern about the side effects of the vaccine”. This is a repetition of what you have just said. You may rephrase this paragraph to explain your point without redundancy. Thank you for your suggestion. We have paraphrased the sentence. This study found that the women who visit the health facility are more likely to receive the TT vaccine. Visiting the health facility will increase their information and knowledge related to vaccines. In addition, each visit can increase their closeness and bond with the health workers. This can convince the women aged 15–49 years old to have the TT vaccine. A visit to a health care facility provides an opportunity for women to clarify and address their concerns regarding the side effects of vaccines by consulting directly with their doctor or nurse. Rumors circulating in the community regarding the TT vaccine also can be explained through counselling during the visits. One of the rumors is that the content of the vaccine material is not halal, so there is resistance from some women. Health workers like the doctors and nurses are needed to clarify the problem. Paragraph 7: The same comment as paragraph 6. Please rephrase this paragraph to avoid redundancy. Thank you for your suggestion. We have paraphrased the sentence. Those who are divorced are less likely to receive the TT vaccine. This is related to the decrease or absence of motivation from the partner. Women who have lived alone tend to have different views after a divorce. Focus and priorities in life may no longer lead to the fulfillment of health support such as vaccines, but rather to be economically independent and able to meet the needs of daily life. Paragraph 7, line 4 “Although the TT vaccine is actually a requirement before marriage takes place”, please identify the regulations and policy of the Ministry of Health in Indonesia regarding TT vaccination for females. Thank you, we have deleted the sentences because they are not relevant to the previous sentences. Paragraph 7, line 5 “vaccine can be missed because of the assumption that you have received the vaccine before”, isn’t there vaccination cards or records to refer to by the health personnel to make sure that the female client has been vaccinated? Is vaccine given only in health facilities affiliated with the MOH or it may be administered in private clinics? Please clarify. Thank you, we have deleted the sentences because they are not relevant to the previous sentences. Paragraph 7, lines 5-6: “There is still the assumption that the vaccine is not necessary”, you need to elaborate a little more on this point and identify the rationale beyond this assumption. Thank you for your correction, we have rewritten the sentence. Line 1: “we found there to be a gap in the TT vaccine uptake among women aged –49 years old in Indonesia”, if you mean the age group 35-49 then this conclusion contradicts your findings as this group is the highest in vaccine uptake. If you mean 15-49 then you need to explain your conclusion, especially that your results (Table 2) and your Discussion (\"However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high\") referred to the high TT vaccine coverage rates. Thank you, we mean gaps among women aged 15-49 years. We have revised the sentences. \"However, it can be seen in this study that the respondents' awareness of the importance of the TT vaccine is very high\" referred to the high TT vaccine coverage rates in Bali and Nusa Tenggara regions. Lines 2-3: “Indonesia as a whole, which is an archipelago, is one of the considerations and constraints involved in the coverage of the TT vaccine among women”, you need to clarify this point a little. Thank you, we have clarified it."
}
]
}
] | 1
|
https://f1000research.com/articles/10-437
|
https://f1000research.com/articles/9-1030/v1
|
24 Aug 20
|
{
"type": "Research Article",
"title": "maxRatio improves the detection of samples with abnormal amplification profiles on QIAgen’s artus HIV-1 qPCR assay",
"authors": [
"Luigi Marongiu",
"Eric B. Shain",
"Marianna Martinelli",
"Matteo Pagliari",
"Heike Allgayer",
"Eric B. Shain",
"Marianna Martinelli",
"Matteo Pagliari",
"Heike Allgayer"
],
"abstract": "Background: Accurate viral load (VL) determination is paramount to determine the efficacy of anti-HIV-1 therapy. The conventional method used, fit-point (FP), assumes an equal efficiency in the polymerase chain reaction (PCR) among samples that might not hold for low-input templates. An alternative approach, maxRatio, was introduced to compensate for inhibition in PCR. Methods: Herein, we assessed whether maxRatio could improve VL quantification using 2,544 QIAgen artus HI virus-1 RT-PCR reactions. The assay’s standard dilutions were used to build external standard curves with either FP or maxRatio that re-calculated the VLs. Results: FP and maxRatio were highly comparable (Pearson’s ρ=0.994, Cohen’s κ=0.885), and the combination of the two methods identified samples (n=41) with aberrant amplification profiles. Conclusions: The combination of maxRatio and FP could improve the predictive value of the assay.",
"keywords": [
"HIV",
"qPCR",
"quantification",
"maxRatio",
"viral load."
],
"content": "Introduction\n\nInfection with HIV-1 accounts for a global prevalence of 38 million cases and a one million deaths yearly1. An accurate viral load (VL), typically carried out by quantitative polymerase chain reaction (qPCR), is pivotal for addressing the efficacy of antiviral therapies2. The threshold level of detection for the HIV-1 (VL) has been reported in the range 20–44 viral genomic copies per milliliter (c/mL)3,4.\n\nqPCR data are usually analyzed by the fit-point (FP) method, which assumes equal amplification efficiency between samples5. However, anomalies in the background fluorescence at low template input, can affect the quantification6–8. An alternative method, maxRatio, was introduced to overcome these issues9. It has been reported that maxRatio conferred a marginal increase in assay accuracy over FP10,11.\n\nFP provides only a quantification cycle (Cq) value, which is then used to calculate VL. MaxRatio, instead, gives two parameters: one associated with the reaction’s efficiency (MR) and one equivalent to, albeit distinct from, Cq. These two parameters can be linked to bestow a quantitative cycle (FCNA) compensated for inhibition.\n\nIn the present work, we aimed to determine whether maxRatio could improve the determination of HIV-1 VL. We compared the quantification of HIV-1 VL computed by FP and maxRatio on a dataset generated with the QIAgen artus HIV assay, which has a reported limit of detection of 35.5 c/mL, and we showed that maxRatio could pinpoint samples with abnormal amplification profiles.\n\n\nMethods\n\nThe amplification data (see Underlying data12) obtained with the QIAgen artus HI Virus-1 RT-PCR kit were collected by the Public Health England Clinical Microbiology and Public Health Laboratory, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QW, UK, during the year 2016. All data were anonymized before use. The reactions were subdivided into clinical samples, control dilutions (CDs), and non-template controls (NTCs). The CDs were based on known dilutions of in vitro transcribed HIV-1 RNA provided by the artus kit, corresponding to 405, 4,050, 40,500, and 405,000 c/mL.\n\nThe FP method generated the Cq by registering the fractional cycle where the fluorescence passed the threshold of 0.2 units. The maxRatio transform of the amplification data and determination of the cut-offs were computed as previously described9,10. Different operators visually inspected the reaction’s profiles and classified each reaction as either passed or failed. Using R v.3.6, linear models (standard curves, SC) were built on the CDs and applied to calculate the copy numbers according to the formula 10(x – b)/m where x is the quantitative cycle (either Cq or FCNA), b and m are the intercept and slope, respectively, of the linear models13. VL correlation was obtained with the Pearson product-moment coefficient ρ14 and agreement between methods was tested with the Cohen’s κ15; both are reported with their 95% confidence interval (CI).\n\n\nResults\n\nThe present dataset was derived from 122 individual artus HIV-1 runs, corresponding to 2,544 reactions (480 CDs, 122 NTCs and 1,931 clinical samples). The cut-offs obtained by EM analysis were multiplied by 2.7 to generate the values used to filter the maxRatio data, as depicted in Figure 1.\n\nClinical samples (○) and CDs (◊) are plotted on the maxRatio plane; the numbers report the obtained cut-offs for MR (horizontal lines) and FCNA (vertical lines). A. MR/FCNA pairs for the HIV-1 target. To note how the CDs form four distinct clusters, corresponding to the different standard dilutions. B. MR/FCNA pairs for the IC target. To note that the data form a single cloud because the IC input was virtually the same for all reactions. The presence of two outlier groups at low and high FCNA values required to instantiate two cut-offs.\n\nThe CDs were used to build SCs (Figure 2) that quantified both the CDs (Table 1 and Figure 3) and the clinical samples (Figure 4). Overall, the VLs obtained with the two methods were very strongly correlated (ρ = 0.994, 95% CI: 0.993-0.994) and the agreement in the stratification of the reactions into reactive and non-reactive was almost perfect (κ = 0.885, 95% CI: 0.863-0.907). Both methods identified 307 (15.9%) and 28 (1.5%) samples within and above the quantification range 405–405,000 c/mL (ρ = 0.988, 95% CI: 0.985-0.991 and ρ = 0.992, 95% CI: 0.982-0.996, respectively), and 1,571 (81.3%) below this range (ρ = 0.844, 95% CI: 0.829-0.858).\n\nDevelopment of the linear models. The Cq (○) and FCNA (●) were used to build SCs for FP (dashed line) and maxRatio (dotted line). The dots and bars represent the mean and standard deviation of the data, respectively. The characteristics of the models are reported.\n\nThe mean VL is reported together with the 95% CI (calculated), the difference between the calculated and the expected concentration (difference), and the result of the t-test (p-value). Statistical significance is represented by * and ** for values below 0.05 and 0.01, respectively. The copy numbers are given in c/mL.\n\nThe four panels represent the calculated copy numbers obtained using FP (○) or maxRatio (●) for each dilution. The dots and bars represent the mean and the 95% CI of the data, respectively.\n\nThe external standard curves were used to calculate the VL for the clinical samples. The following thresholds are depicted: lower (solid lines) and upper (double solid lines) limits of the quantification range; limit of detection of HIV-1 diagnostic in general (dashed line) and artus HI Virus-1 assay in particular (dotted line).\n\nFP identified 22 reactions above the limit of detection of 20 c/mL, while maxRatio failed the quantification; conversely, maxRatio identified 18 reactions below 20 c/mL while FP quantified them above this level. Visual inspection of the amplification profiles of the reactions failed by FP showed that 10 of them (43.4%) had a proper sigmoid outlook for the internal control (IC) signal that, however, was discarded by the FP (as exemplified in Figure. 5A). In contrast, the others had a low signal for either HIV-1 or IC recovered by maxRatio (Figure 5B). Conversely, 15 (83.3%) of the reactions failed by maxRatio showed either a low IC or HIV-1 input (Figure 6A), whereas the FCNA of the remainder of the reactions produced fractional VL that were rounded to 0 c/mL (Figure 6B).\n\nExample of raw amplification profiles for the samples whose FP did not provide a VL. The panels displays the FP (left) the maxRatio (right) transforms of the amplification data. The solid line represents the HIV-1 template and the dashed line the IC template. (A) The majority of the samples had a proper IC profile but the output was undetermined. (B) The minority of the samples showed low target inputs.\n\nExample of raw amplification profiles for the samples whose maxRatio did not provide a VL. The panels displays the FP (left) the maxRatio (right) transforms of the amplification data. The solid line represents the HIV-1 template and the dashed line the IC template. (A) The majority of the samples had abnormal IC profiles that were overlooked by FP. (B) The minority of the samples showed proper amplification profiles, but the calculation provided fractional VLs that were rounded to zero.\n\n\nDiscussion\n\nThe purpose of the present work was to assess the potential benefits of maxRatio in determining HIV-1 VL given its inherent compensation of PCR inhibition. Contrary to our expectation, the SCs we built with either FP or maxRatio were virtually the same. Both methods gave SD VLs significantly divergent from the expected copy numbers at the lower and upper CDs, and maxRatio was, in general, more discrepant from the expected copy numbers than FP. Even concerning the samples’ quantification, the two methods produced essentially the same VLs.\n\nThe main difference between the two methods was in terms of sample’s reactivity. By accepting the reactions identified as non-reactive by FP, but reactive by maxRatio, there would have been 18 false-negative results. Conversely, 15 samples identified as non-reactive by maxRatio showed aberrant IC that raised quality control, rather than false-positive, issues overlooked by FP.\n\nThe current use of maxRatio is to confirm the reactivity determined by FP on the Abbott m2000rt platform. Our data supported this combination as the most effective approach for screening purposes. Samples in disagreement between FP and maxRatio would require further assessment that could reduce the workload involved in issuing the results and minimize the risk of providing false results.\n\nThe present work had some limitations. Firstly, the sample size was small. Secondly, the CDs were prepared by diluting the control samples provided in the kit, but the actual concentration was not measured. Finally, we did not have access to the actual issued results; thus, we could not confirm the official VL values.\n\nIn conclusion, we compared FP and maxRatio in providing HIV-1 VL. Contrary to our expectations, maxRatio did not give a better quantification than FP, but combining the two methods could minimize issuing false results.\n\n\nData availability\n\nHarvard Dataverse: artusHIV_amplificationData. https://doi.org/10.7910/DVN/0QQNPF\n\nThis project contains the following underlying data:\n\namplificationDataRaw.tab. (Raw amplification data.)\n\nviralLoads.tab. (Raw viral loads data.)\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nWe would like to thank Dr. Martin D. Curran (Public Health England, Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge UK) for providing the amplification data.\n\nWe would also like to thank Prof. Clementina Elvezia Cocuzza (University of Milano Bicocca, Department of Medicine and Surgery, Monza, Italy) and Dr. Maria Serena Beato (‘Istituto Zooprofilattico Sperimentale delle Venezie’, Department of Diagnostics in Animal Health, Legnaro, Italy) for their moral support.\n\n\nReferences\n\nWang H, Wolock TM, Carter A, et al.: Estimates of global, regional, and national incidence, prevalence, and mortality of HIV 1980–2015: the Global Burden of Disease Study 2015. Lancet HIV. 2016; 3(8): e361–87. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarschner IC, Collier AC, Coombs RW, et al.: Use of Changes in Plasma Levels of Human Immunodeficiency Virus Type 1 RNA to Assess the Clinical Benefit of Antiretroviral Therapy. J Infect Dis. 1998; 177(1): 40–7. PubMed Abstract | Publisher Full Text\n\nAdams P, Vancutsem E, Nicolaizeau C, et al.: Multicenter evaluation of the cobas® HIV-1 quantitative nucleic acid test for use on the cobas® 4800 system for the quantification of HIV-1 plasma viral load. J Clin Virol. 2019; 114: 43–9. PubMed Abstract | Publisher Full Text\n\nSizmann D, Glaubitz J, Simon CO, et al.: Improved HIV-1 RNA quantitation by COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test, v2.0 using a novel dual-target approach. J Clin Virol. 2010; 49(1): 41–6. PubMed Abstract | Publisher Full Text\n\nBustin SA: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000; 25(2): 169–93. PubMed Abstract | Publisher Full Text\n\nBar T, Kubista M, Tichopad A: Validation of kinetics similarity in qPCR. Nucleic Acids Res. 2012; 40(4): 1395–406. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen P, Huang X: Comparison of Analytic Methods for Quantitative Real-Time Polymerase Chain Reaction Data. J Comput Biol. 2015; 22(11): 988–96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamakers C, Ruijter JM, Lekanne Deprez RH, et al.: Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett. 2003; 339(1): 62–6. PubMed Abstract | Publisher Full Text\n\nShain EB, Clemens JM: A new method for robust quantitative and qualitative analysis of real-time PCR. Nucleic Acids Res. 2008; 36(14): e91. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarongiu L, Shain E, Drumright L, et al.: Analysis of TaqMan Array Cards Data by an Assumption-Free Improvement of the maxRatio Algorithm Is More Accurate than the Cycle-Threshold Method. PLoS One. 2016; 11(11): e0165282. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarongiu L, Shain E, Shain K, et al.: Filtering maxRatio results with machine learning models increases quantitative PCR accuracy over the fit point method. J Microbiol Methods. 2020; 169(1): 105803. PubMed Abstract | Publisher Full Text\n\nMarongiu L: \"artusHIV_amplificationData\". Harvard Dataverse, V1, 2020. http://www.doi.org/10.7910/DVN/0QQNPF\n\nScott Adams P: Data Analysis and Reporting. In: Dorak T editor. Real-time PCR. 1st ed. New: Taylor & Francis; 2006; 39–62. Reference Source\n\nSchober P, Schwarte LA: Correlation coefficients: Appropriate use and interpretation. Anesth Analg. 2018; 126(5): 1763–8. PubMed Abstract | Publisher Full Text\n\nViera AJ, Garrett JM: Understanding interobserver agreement: The kappa statistic. Fam Med. 2005; 37(5): 360–3. PubMed Abstract"
}
|
[
{
"id": "83772",
"date": "10 Jun 2021",
"name": "Emiliano Panieri",
"expertise": [
"Reviewer Expertise Oncology",
"cellular and molecular biology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment: The paper from Marongiu et al. presents an alternative approach to the conventional use of fit-point (FP) or MaxRatio methods, which can be used to accurately determine the viral load of HIV-1 patients under experimental conditions wherein the amplification efficiency might vary across the samples, as in the case of low-copy number of viral RNA or in presence of PCR inhibitors. This is a clinically relevant issue since the VLs widely differ among HIV-1 infected individuals, potentially leading to issues of false-positive/negative results when the viremia is very low or the efficiency of PCR reactions is not uniform. It is therefore of utmost importance to improve not only the analytical sensitivity of qPCR methods but also their predictive value to avoid that a substantial fraction of HIV-1 patients will be incorrectly diagnosed, causing a negative impact on their prognosis and treatment monitoring. In this regard, the approach proposed by the authors, based on both FP and MaxRatio is straightforward and when correctly applied can represent a cost-effective alternative to the time-consuming and labor-intensive work required to validate false positive and false negative results. In general, the manuscript is well written, concise and presented in a clear, scientifically-sound way. The data are quite exhaustive, corroborated by appropriate statistical analysis and firmly support the authors’ conclusions.\nHowever, some minor changes will be required to improve the MS quality, which are listed below:\nThe authors correctly indicate that the small-size of the tested samples represents a limitation to their study. Can also the authors discuss whether increasing the sample size is expected to proportionally increase the accuracy of the proposed method? In other words, in the authors’ opinion, is the number of tested samples expected to influence the predictive value of the FP + MaxRatio use? It might be useful to further elaborate this aspect in the discussion to help the readers to gain insights on this limitation.\n\nThe authors should indicate which kind of t-test was used to assess the statistical significance of the data contained in Table 1 (i.e paired or unpaired, with or without other corrections such as Welch’s or Bonferroni’s) and which software was used to perform the statistical analysis.\n\nIn the Results paragraph it is suggested to mitigate the following statement: ”…the agreement in the stratification of the reactions into reactive and non-reactive was almost perfect (κ = 0.885, 95% CI:0.863-0.907). ”. Instead, “noticeably robust” can be a good alternative.\n\nFew lines below it is suggested to slightly rearrange the sentence “…the FP identified 22 reactions above the limit of detection of 20 c/mL, while maxRatio failed the quantification” (i.e. while Max Ratio was unsuccessful).\n\nFew lines below it is suggested to substitute “sigmoid outlook” with “sigmoidal shape”.\n\nFew lines below it is suggested to change “…of the remainder of the reactions” into “…of the remaining reactions”.\n\nIn the Figure 1 legend, the authors describe a panel A (MR/FCNA pairs for the HIV-1 target) and a panel B (MR/FCNA pairs for the IC) which are however absent in the Figure 1. Please add the correct indication or either refer to the panels as upper and lower.\n\nIn the Figure 5-6 legend, it should be corrected “the panels displays” with “the panels display”.\n\nIn the last three lines of the Discussion section please rephrase the sentence: “…maxRatio did not give a better quantification than FP, but combining the two methods could minimize issuing false results” into “maxRatio did not result in a better quantification than FP but when combined together these two methods could…”\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/9-1030
|
https://f1000research.com/articles/10-204/v1
|
11 Mar 21
|
{
"type": "Research Article",
"title": "Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia",
"authors": [
"Adewale J. Ogunleye",
"Ekaterina Romanova",
"Yulia A. Medvedeva",
"Ekaterina Romanova",
"Yulia A. Medvedeva"
],
"abstract": "Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that ecCEBPα (extra coding CEBPα) - a lncRNA transcribed in the same direction as CEBPα gene - regulates DNA methylation of CEBPα promoter in cis. Here, we hypothesize that ecCEBPα could participate in the regulation of DNA methylation in trans. Method: First, we retrieved the methylation profile of AML patients with mutated CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the ecCEBPα secondary structure in order to check the potential of ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated CEBPα locus, we show that ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions. ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.",
"keywords": [
"Acute myeloid leukemia",
"Triplex",
"DNA methylation",
"long non coding RNA",
"extra-coding CEBPα"
],
"content": "Introduction\n\nAcute myeloid leukemia (AML) is a malignant tumor characterized by the proliferation of undifferentiated myeloblasts1,2. It is the most prevalent form of leukemia in older adults (>60 years) with an annual mortality rate of 50% and a 5-year survival rate of 24%2,3. With the combined effects of the global increase in average life expectancy and AML drug inefficiency, the number of patients is expected to significantly increase in the coming years4,5.\n\nThe current understanding of the molecular interplay in AML has been defined under two distinct categories; (i) genetic abnormalities and (ii) non-random chromosomal rearrangements. Cases of AML with chromosomal rearrangements as t(15;17) [PML-RARA], t(9;22) [BCR-ABL], inv(16) [CBFB-MYH11], t(8;21) [RUNX1-ETO] are called cytogenetically abnormal (CA-AML), while cases with genetic abnormalities (including frequent mutations in DNMT3A, NPM1, CEBPα, IDH1/2, TET2, FLT3-ITD) are called cytogenetically normal (CN-AML)1,4. The former accounts for 50–55%, while the latter accounts for 45–50% of diagnosed AML cases6,7. Even though these mutations and chromosomal alterations are crucial for initiating AML, they are not sufficient to explain AML progression, heterogeneity, and relapse8.\n\nRecently, studies have identified the role of non-coding RNAs, especially long non-coding RNAs (lncRNA) in the initiation and progression of cancers9–11. LncRNAs are emerging functional transcriptional products of at least 200 nucleotides lacking an open reading frame. Although they account for a large proportion of transcriptional products in mammals (about 58,000 loci)12, only a small number of lncRNAs have been well characterized. Although lncRNAs are mostly not conserved evolutionarily, they are heavily regulated suggesting their functional role12,13. They may function either as signal transducers, protein guides, or molecular scaffolds to regulate transcriptional and epigenetic events14–16. Some lncRNAs perform these functions in cis- by modulating transcription of nearby genes (Dum)17 or act in trans-, by modulating genes at multiple distant loci (MALAT1)18, while some can do both (HOTAIR)9,19.\n\nRecent studies have identified lncRNAs for their remarkable role in regulating major epigenetic processes such as DNA methylation and chromatin remodeling. DNA methylation in mammals is coordinated by one of the three DNA methyl-transferases (DNMT); DNMT1, DNMT3A, and DNMT3B7,17,20. LncRNAs have been identified in recent studies as important agents that can modulate DNA methylation, either by activating or repressing DNMTs. For example, the lncRNA Dum was discovered to repress a nearby gene Dppa2 by recruiting multiple DNMTs leading to methylation of a promoter region, thus promoting myoblast differentiation17. Conversely, the lncRNA H19 represses the activity of DNMT3B by interacting with SAHH which hydrolyzes SAH, a step required for DNMT3B activation21. ecCEBPα, which is transcribed from the CEBPα locus, directly blocks DNMT1 to prevent methylation of proximal and distal located promoters, thus promoting CEBPα-mediated granulocyte differentiation20. Mechanistic studies via reduced representation bisulfite sequencing and RNA immunoprecipitation sequencing shows that ecCEBPα suppresses DNA methylation in cis- by acting as a shield that sequesters DNMT1 from the CEBPα promoter. We speculate that ecCEBPα could regulate DNMT1 activities in distant DNA regions (in trans-) as well. The mechanism of this potential interaction is to be determined.\n\n\nMethods\n\nIn the recent version of GENCODE, ecCEBPα is not annotated most likely due to an overlap with a protein-coding gene CEBPα on the same strand. We retrieved the complete ecCEBPα sequence from the human genome (hg19, chr19: 33298573-33303358) based on information reported in the work of Di Ruscio et al.20. ecCEBPα is approximately 4.8kb and it overlaps with the intronless CEBPα gene (~2.6kb) on the same strand. ecCEBPα does not share either the same transcription start site (TSS) or transcription end site (TES) with CEBPα, starting ~0.89kb upstream and ending ~1.46kb downstream of the CEBPα gene.\n\nCpG methylation (Illumina 450K array) and CEBPα mutation data for 186 AML patients were retrieved from the Cancer Genome Atlas (TCGA: http://firebrowse.org). CpG methylation levels were measured in 307796 unique loci. We split all the AML patients into two groups based on CEBPα mutation status (13 patients with a CEBPα mutation and 173 patients without a mutation). We classified a CpG position as hypermethylated (HM) in patients with a CEBPα locus mutation if DNA methylation level was significantly increased in the case of a CEBPα mutation (t-test, FDR ≤0.05 and Δ-value ≥0.1) and all non-hypermethylated (NHM) CpG in the case of a CEBPα mutation were classified as non-hypermethylated CpGs (t-test, FDR >0.05 and |Δ-value| <0.1). As a result, we obtained 11955 HM and 261433 NHM CpGs.\n\nAs suggested in a previous study22, unpaired RNA nucleotides are more likely to form triplexes with DNA. We predicted RNA secondary structure using RNAplfold (V 2.4.14), from the Vienna suite using a cut-off for pairing probability (-c) of 0.123,24. To search for potential interactions between ecCEBPα and DNA target regions we used only unpaired nucleotides, while the nucleotides predicted to pair were replaced with ‘N’.\n\nDNA target regions were defined as 100 nucleotides centered at each CpG. To predict ecCEBPα triplex formation with DNA target regions, we used Triplexator (V 1.3.2)25, since it has higher accuracy of prediction14, with the following optimization parameters suggested in 22: minimum length = 10 nucleotides, error rate = 20%, G-C content = 70%, and filter-repeats = off. Using these parameters out of 307796 unique CpG loci, we predicted 272131 loci with at least one triplex and 35715 without any. Among them, 10351 and 222105 potential triplex targets were predicted in the HM and NHM regions respectively.\n\nTo estimate the statistical significance of predicted triplexes we used Triplex domain finder (TDF v 0.12.3), which clusters RNA triplex-forming oligonucleotide (TFO) into DNA binding domains (DBD)26. Briefly, all 272131 CpG loci with at least one predicted triplex were taken as input target regions. By predicting triplexes in the background regions, TDF is capable of estimating the statistical significance of ecCEBPα binding between target regions and other non-target CpGs regions. Since TDF allows only to mask regions in the genomic background rather than to select the background explicitly we had to prepare a special mask for the non-target regions. To do so we removed 35715 CpG loci with zero triplex predictions from the human genome using BEDtools subtract (BEDTools v2.29.2). TDF was implemented with a minimum triplex length (-l) of 10 nucleotides, an error rate (-e) of 20%, and (-f) to mask background loci in 100 random samplings (-n).\n\nTo validate the predicted interactions we used RNA:chromatin interactome obtained with iMARGI method capturing chromatin-associated RNA (caRNA) and their genomic interaction loci27. The data was downloaded from GEO (GSM3478205). The iMARGI dataset was mapped to the hg38 genome assembly. We used UCSC Liftover to convert ecCEBPα sequence coordinates from hg19 to hg38 sequences28. We expanded the DNA coordinates of CpGs by 3.0kb nucleotides upstream and downstream. IntersectBed from BEDTools was used to check the co-location of predicted triplexes and experimentally validated interactions of ecCEBPα29. Fisher’s exact test was calculated for the number of confirmed ecCEBPα interactions between TDF and iMARGI data.\n\nFinally, since Illumina 450K array probes are located close to genes, we performed functional enrichment using BiNGO (v 3.0.3) (binomial test)30 to infer the biological significance of the genes potentially affected by ecCEBPα binding.\n\nAll statistical analyses were performed using R 4.0 or SciPy v1.5.1 library. Visualization was done in Cytoscape 3.2.031 and Python 3.7. Code is available at https://zenodo.org/record/438525932.\n\n\nResults\n\nThe current study explores the potential of the lncRNA ecCEBPα in the modulation of global CpG methylation status in trans via direct interaction with DNA regions. ecCEBPα (extra coding CEBPα), reported in work by Di Russio et al.20, is located on chromosome 19 and transcribed from the CEBPα locus (Figure 1a).\n\n(a) Schematic diagram for transcriptional products in the CEBPα locus; CEBPα is represented by an orange arrow and ecCEBPα is represented by the blue line. (b) Global change in DNA methylation (c) Difference in DNA methylation levels between patients with and without CEBPα mutation in the regions of ecCEBPα predicted binding (non parametric t-test, p-value >1E-10) (d) Number of DNA Triplex Target Site (y-axis) and a location of the corresponding TFO on the ecCEBPα (TFO: RNA; x-axis). (e) Number of Triplex Target sites per TFO predicted for NHM and HM CpG regions.\n\nMutations in CEBPα locus are a common feature of AML leading to whole genome hypermethylation (Figure 1b). Since TCGA is focused on protein-coding genes, all reported mutations are located within the CEBPα gene and could affect both CEBPα and ecCEBPα. To investigate if ecCEBPα could affect DNA methylation in trans, first we checked if it is capable of interaction via forming triple helices (triplexes) with its binding sites and if such interactions affect DNA methylation. We observed that regions capable of forming triplexes with ecCEBPα remain protected from global DNA hypermethylation observed in case of a mutation in a CEBPα locus (Figure 1c, Fisher’s exact test, p-value <0.001). This result suggests a negative relationship between DNMT access to promoter sites and ecCEBPα binding.\n\nTo investigate deeper the potential of ecCEBPα to form triplexes we used Triplex Domain Finder (TDF) - a triplex prediction tool that refines the resolution of predicted TFOs in RNA into DNA binding domains (DBD) and calculates the significance of the number of predicted triplexes for each DBD. Overall, 17 significant DBDs were identified within ecCEBPα, interspaced between sequences 4086 and 4968 towards the 3’ end of the lncRNA (Figure 1d). These DBDs form triplexes with the majority of regions protected from hypermethylation in patients with a CEBPα mutation (Figure 1e, Extended data: Supplementary Table 1). The DBD region is located downstream from the CEBPα gene suggesting that ecCEBPα binding region is not affected by the mutation in the CEBPα locus. The predicted secondary structure of the ecCEBPα sequence showed that more than 95% of sequence positions from 4087-4987 (~0.5kb from CEBPα TES) (Figure 1d) were unpaired and potentially capable of forming triple helices with the target DNA region (Figure 2a).\n\n(a) Predicted secondary structure of ecCEBPα. Nucleotide color represents base pairing probabilities as predicted by RNAplfold. (b) Experimentally validated ecCEBPα triplexes per chromosome. The x-axis represents the chromosome and y-axis represents the triplex potential relative to TTS. Blue points represent all TDF predictions that are present in the iMARGI dataset (c) Functional enrichment of genes located nearby CpG with predicted triplexes. (d) Schematic representation of ecCEBPα:DNA interactions in trans and its implication on DNA methylation. The presence of ecCEBPα inhibits DNA methylation process.\n\nSince we use relatively relaxed thresholds for triplex prediction, we decided to validate the predicted RNA:DNA triplexes using experimental data obtained with the iMARGI method, allowing detection of RNA-chromatin interactions. We identified 157 ecCEBPα contacts within the iMARGI dataset and 29 of them contained predicted triplexes. Altogether, these 29 iMARGI interactions were made up of 182 predicted TTS (Fisher’s exact test, p-value < 2.2E-16) located in cis and in trans on 14 chromosomes (Figure 2b). Chromosomes 19 (the native chromosome for ecCEBPα) are accounted for by all predictions.\n\nWe performed gene ontology analysis on the genes located nearby 182 ecCEBPα triplexes supported by iMARGI. Key gene ontology categories such as nucleic acid binding and transcription factor activities were enriched among putative ecCEBPα targets (Figure 2c). Representative genes among transcription factors include MLF2, SUV39H2, RBM5, UBTF, and among sequence-specific DNA binding proteins include POU2F2, MED12L, and DNASE1L1. The enrichment in transcription factors (TF) suggests that triplex formation may represent a possible mechanism employed by ecCEBPα to regulate TF methylation and as a consequence, their expression.\n\n\nDiscussion\n\nUnlike other forms of cancers, AML progression is often mutation-independent but may be explained by altered epigenetic regulation, DNA methylation specifically1,8. In this study, we elucidate a putative mechanism for the regulation of DNA methylation by ecCEBPα. In a previous study, ecCEBPα, which accompanies the transcription of CEBPα on the same locus, was shown to protect the promoter of CEBPα from DNA methylation leading to active expression20. We speculated that ecCEBPα might perform a similar function in trans. We demonstrated that ecCEBPα-DNA triplex formation might provide the molecular basis of this interaction. ecCEBPα binding presumably protects the region from genome-wide hypermethylation induced by CEBPα mutation in AML patients. ecCEBPα contains a TFO/DBD-rich region at its 3’ end, with low pairing probability, suggesting that it is capable of triplex formation. Several of the predicted ecCEBPα binding sites, which include transcription factors such as MLF2, SUV39H2, RBM5, UBTF, and sequence-specific DNA binding proteins include POU2F2, MED12L, and DNASE1L1, were supported by experimental iMARGI RNA:chromatin interactions data.\n\nCurrently, the understanding of lncRNA function and mechanisms of action is limited to a few dozen well-annotated lncRNA transcripts. A few functional characterization attempts are based on the ‘guilt by association’ hypothesis, which may not resonate well with the ability of lncRNA to interact in trans33. As thoroughly reviewed previously, lncRNAs such as ecCEBPα, Dum, Dali, Dacor1, and LINCRNA-P21 interact with DNA in trans to regulate DNA methylation34. The results presented herein further demonstrate that triplex formation between ecCEBPα and CpG containing DNA regions could indeed be regulatory and protect CpG sites from DNMT activity.\n\nUnfortunately, RNA:chromatin interaction protocols are relatively new and the data is available only for a few cell types. Since RNA:chromatin interactions are highly cell-type specific35 and lowly expressed, it is not surprising that we could validate only a few of the predicted interactions. Nevertheless, based on our results, we suggest a model of potential ecCEBPα chromatin interaction in trans (Figure 2d). In this model, ecCEBPα uses its unpaired regions to directly bind to specific DNA sequences by forming triplexes and in this way prevents DNA methylation in the region of binding. ecCEBPα binding to distant regions could be mediated either by 3-dimensional chromatin organization17 which brings them close to ecCEBPα.\n\nRecent studies have observed that promoter or transcription start sites (TSS) regions, which tend to be rich in CpG dinucleotides, are TTS-rich and potential triplex-forming hotspots36,37. Through functional enrichment analysis, we observed that transcription factors might be preferential targets of ecCEBPα. Interestingly, previous studies have shown that the suppression of a myeloid leukemia factor (MLF2), an oncogene in breast cancer and myeloid leukemia38,39 as well as UBTF which controls rDNA expression40,41 contributes significantly to cancers upon promoter hypermethylation40,42. The suppressor of variegation 3-9 homolog 2 (SUV39H2), a histone-lysine-N-methyltransferase which regulates the hypermethylation H3K9 has also been reported to indirectly influence over 450 promoters in AML43. Having in mind that ecCEBPα is transcribed from CEBPα locus - a key transcription factor of hematopoiesis - this lncRNA could participate in the formation of a hub in the hematopoiesis regulatory network.\n\n\nConclusion\n\nIn conclusion, we have shown that ecCEBPα could serve as a trans-acting regulatory agent protecting its binding sites from genome-wide CpG methylation, and its dysregulation could contribute to aberrant methylation profile in AML patients. These results suggest a novel regulatory mechanism for ecCEBPα as a modulator of DNA methylation through triplex formation providing a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.\n\n\nData availability\n\nComplete ecCEBPα sequence retrieved from the human genome (hg19, chr19: 33298573-33303358): https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/\n\nCEBPα mutation data for 186 AML patients retrieved from the Cancer Genome Atlas (TCGA): http://firebrowse.org.\n\nGEO: Embryonic kidney that expresses SV40 large T antigen, Accession number GSM3478205: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3478205\n\nZenodo: josoga2/eccebp-alpha-project: F1000 Code Release, https://doi.org/10.5281/zenodo.438525932\n\nThis project contains the following underlying data:\n\n- DNA_BINDING_DOMAINS_ID.tsv\n\n- predicted_secondary_structure_of_ecCEBPA.fa\n\n- probes.csv (main data)\n\nCode used for analysis available from: https://github.com/josoga2/eccebp-alpha-project/tree/f1000\n\nArchived code as at time of publication: https://doi.org/10.5281/zenodo.438525932\n\nZenodo: Supplementary Data for Secondary structure and DNA binding domain prediction, http://doi.org/10.5281/zenodo.443322244.\n\nThis project contains the following extended data:\n\nSupplementary Table 1: Summary table of DNA binding domains (DBD), the counts of target regions within the genome and statistical analysis.\n\necCEBPα secondary structure prediction with RNAplfold\n\nData and code are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nGoldman SL, Hassan C, Khunte M, et al.: Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity. Front Genet. 2019; 10: 133. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGambacorta V, Gnani D, Vago L, et al.: Epigenetic Therapies for Acute Myeloid Leukemia and Their Immune-Related Effects. Front Cell Dev Biol. 2019; 7: 207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan Oosterwijk JG, Buelow DR, Drenberg CD, et al.: Hypoxia-induced upregulation of BMX kinase mediates therapeutic resistance in acute myeloid leukemia. J Clin Invest. 2018; 128(1): 369–380. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang J, Gu Y, Chen B: Mechanisms of drug resistance in acute myeloid leukemia. Onco Targets Ther. 2019; 12: 1937–1945. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nHe B, Peng F, Li W, et al.: Interaction of lncRNA-MALAT1 and miR-124 regulates HBx-induced cancer stem cell properties in HepG2 through PI3K/Akt signaling. J Cell Biochem. 2019; 120(3): 2908–2918. PubMed Abstract | Publisher Full Text\n\nBotti G, Scognamiglio G, Aquino G, et al.: LncRNA HOTAIR in Tumor Microenvironment: What Role? Int J Mol Sci. 2019; 20(9): 2279. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDi Ruscio A, Ebralidze AK, Benoukraf T, et al.: DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013; 503(7476): 371–376. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou J, Yang L, Zhong T, et al.: H19 lncRNA alters DNA methylation genome wide by regulating S-adenosylhomocysteine hydrolase. Nat Commun. 2015; 6: 10221. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu W, Yan Z, Nguyen TC, et al.: Mapping RNA-chromatin interactions by sequencing with iMARGI. Nat Protoc. 2019; 14(11): 3243–3272. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKuhn RM, Haussler D, Kent WJ: The UCSC genome browser and associated tools. Brief Bioinform. 2013; 14(2): 144–161. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6): 841–842. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaere S, Heymans K, Kuiper M: BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 2005; 21(16): 3448–3449. PubMed Abstract | Publisher Full Text\n\nShannon P, Markiel A, Ozier O, et al.: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11): 2498–2504. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgunleye AJ: josoga2/eccebp-alpha-project: F1000 Code Release (Version f1000). Zenodo. 2020. http://www.doi.org/10.5281/zenodo.4385259\n\nJalali S, Singh A, Maiti S, et al.: Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the human genome. J Transl Med. 2017; 15(1): 186. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao Y, Sun H, Wang H: Long noncoding RNAs in DNA methylation: new players stepping into the old game. Cell Biosci. 2016; 6: 45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBonetti A, Agostini F, Suzuki AM, et al.: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions. Nat Commun. 2020; 11(1): 1018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSridhar B, Rivas-Astroza M, Nguyen TC, et al.: Systematic Mapping of RNA-Chromatin Interactions In Vivo. Curr Biol. 2017; 27(4): 602–609. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAntonov I, Medvedeva YA: Purine-rich low complexity regions are potential RNA binding hubs in the human genome [version 2; peer review: 3 approved]. F1000Res. 2018; 7: 76. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDave B, Granados-Principal S, Zhu R, et al.: Targeting RPL39 and MLF2 reduces tumor initiation and metastasis in breast cancer by inhibiting nitric oxide synthase signaling. Proc Natl Acad Sci U S A. 2014; 111(24): 8838–8843. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGobert V, Haenlin M, Waltzer L: Myeloid leukemia factor: a return ticket from human leukemia to fly hematopoiesis. Transcription. 2012; 3(5): 250–254. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen LXT, Raval A, Garcia JS, et al.: Regulation of ribosomal gene expression in cancer. J Cell Physiol. 2015; 230(6): 1181–1188. PubMed Abstract | Publisher Full Text\n\nSantoro R, Grummt I: Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol Cell. 2001; 8(3): 719–725. PubMed Abstract | Publisher Full Text\n\nLeshchenko VV, Kuo PY, Shaknovich R, et al.: Genomewide DNA methylation analysis reveals novel targets for drug development in mantle cell lymphoma. Blood. 2010; 116(7): 1025–1034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMonaghan L, Massett ME, Bunschoten RP, et al.: The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia. Front Oncol. 2019; 9: 705. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgunleye AJ: Supplementary Data for Secondary structure and DNA binding domain prediction [Data set]. Zenodo. 2021. http://www.doi.org/10.5281/zenodo.4433222"
}
|
[
{
"id": "81314",
"date": "15 Apr 2021",
"name": "Amrita Singh",
"expertise": [
"Reviewer Expertise Structure function relationship of noncoding RNA",
"with major focus on LncRNA function via triple helical structures."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 addressed an important question of the ability of a lncRNA to act in trans and regulate a multitude of genes, which might be affecting the progression of acute myeloid leukemia. The authors have also highlighted the possibility of a triplex structure for defining the binding of lncRNA at its target gene CpG region. However, there are certain parts wherein the authors haven't been able to convey their points properly.\nIn Figure 1(b), a global DNA hypermethylation has been represented in AML patients with CEBPα mutation, but the numbers of the HM and NHM sites in the methods section do not reflect the same. It shows higher sites for NHM, than the HM sites, kindly check if some mislabeling is there at the authors part.\n\nAlso, the reviewer has failed to understand Figure 1(c). In both the x-axis and the side legend, binding and non-binding have been depicted, but which one is the AML patients with and without mutation isn't clear from the figure.\n\nThere are few other key points that were not clear;\n(a) what is the level of ecCEBPα expression in AML patients with and without mutation.\n(b) Additionally, if the expression of the lncRNA remains the same in both cases, how does one explain the increase in binding of the lncRNA and subsequent higher NHM sites, in the case of AML patients with CEBPα mutation?\n(c) Moreover, a previous report (Di Ruscio et.al1) on ecCEBPα had also analyzed genome-wide methylation, in which they report that methylation levels remain unchanged even when ecCEBPα was overexpressed. This is in contrast with the major theme of the paper i.e., methylation of genes in trans is affected by the ecCEBPα. The authors should comment on this in the discussion part.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6998",
"date": "31 Aug 2021",
"name": "ADEWALE OGUNLEYE",
"role": "Author Response",
"response": "Response to Reviewer One Comment One: In Figure 1(b), a global DNA hypermethylation has been represented in AML patients with CEBPα mutation, but the numbers of the HM and NHM sites in the methods section do not reflect the same. It shows higher sites for NHM, than the HM sites, kindly check if some mislabeling is there at the authors part. Response Two: We believe that there is a confusion here. The plot was correct and reflected the change in DNA methylation in all CpG positions including those that were not statistically differentially methylated. We counted hypermethylated CpG (t-test, FDR ≤0.05 and Δ-value ≥0.1) and those that were not hypermethylated (t-test, FDR >0.05 and |Δ-value| <0.1). In this way, we refer to non-hypermethylated (NHM) to any CpG with DNA methylation change less than 0.1, which includes either not changing or hypomethylated and not only hypomethylated. To avoid this confusion we suggest replacing the plot with the one below. We specified a 0.1 mid-point to aid visualization. (Figure 1b). Comment Two: Also, the reviewer has failed to understand Figure 1(c). In both the x-axis and the side legend, binding and non-binding have been depicted, but which one is the AML patients with and without mutation isn't clear from the figure. Response Two: Each violin in Figure 1(c) is a representation of the differential methylation score between CpGs of AML patients with and without CEBPa mutation. The blue violin represents all CpGs that are located in ecCEBPA binding sites, while the orange violin represents CpGs that do not bind with ecCEBPA. To provide clarity, we corrected the labels on the X and Y axes and added explicit explanation in the legend of the figure (Figure 1c). Difference in methylation = Mean methylation of CpGs in AML patients with CEBPA mutation - Mean methylation of CpGs in AML patients without CEBPA mutation. Comment 3: There are few other key points that were not clear; (a) what is the level of ecCEBPα expression in AML patients with and without mutation. (b) Additionally, if the expression of the lncRNA remains the same in both cases, how does one explain the increase in binding of the lncRNA and subsequent higher NHM sites, in the case of AML patients with CEBPα mutation? (c) Moreover, a previous report (Di Ruscio et.al1) on ecCEBPα had also analyzed genome-wide methylation, in which they report that methylation levels remain unchanged even when ecCEBPα was overexpressed. This is in contrast with the major theme of the paper i.e., methylation of genes in trans is affected by the ecCEBPα. The authors should comment on this in the discussion part. Response: (a&b): It is relatively difficult to estimate the expression level of ecCEBPA since this gene is not in the annotation used by TCGA. The raw data is not freely available in TCGA. ecCEBPA gene also overlaps with the CEBPA gene making the estimation of expression of each of the genes even more complicated. Since the mutation in AML patients happens in the body of CEBPA gene, we do not expect a significant change in the expression of either CEBPA or ecCEBPA. We explained the relationship between ecCEBPA binding and methylation in the first result section (Figures 1c,d&e). We suggested that the mutation(s) in CEBPA does not affect the expression of the lncRNA, but rather the ability to bind its targets. We further emphasize this point in the paper with this line (discussion): “Di Ruscio et al. confirmed that most mutations in CEBPα do not influence the expression of ecCEBPα but rather, its ability of the RNA to fold properly. We suggest that the inability to fold properly even in overexpressed cases may affect its structural ability to bind its targets.” (c): We are very grateful to the reviewer for this valuable comment. In response to this, we retrieved the DNA methylation data (RRBS) for wild-type HL-60 cells (ENCODE Dataset) and overexpressed HL-60 cells (Di Ruscio et al). We then calculated the methylation difference between the two cell states and compared it between the ecCEBPA binding sites versus the non-binding sites. Non ecCEBPA binding sites were more methylated in comparison to ecCEBPA binding sites (Fisher Test: p-val = 1.24E-09). Bearing in mind that ecCEBPA targets are located genome-wide, it is tempting to suggest that “enforced overexpression” (which was achieved with the R1 variant of ecCEBPA; comprise of downstream ecCEBPA sequences) of ecCEBPA strongly protects local CpGs from methylation while the rest of the genome gain some methylation. We added the following statement to the results in the main text: \"Furthermore, the overexpression of ecCEBPA in HL-60 cells (Wang et al) lead to ecCEBPA binding sites stay unmethylated while non ecCEBPA binding sites gain methylation (Fisher Test: p-val = 1.24E-09) , suggesting a protective effect on ecCEBPA’s binding to its target locations (Fig 1d).\""
}
]
},
{
"id": "81320",
"date": "10 Jun 2021",
"name": "Oleg N. Demidov",
"expertise": [
"Reviewer Expertise Models of human diseases",
"cancer research",
"fibrosis",
"paging"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Ogunleye AF and co-authors describes a novel phenomenon of lncRNA ecCEBPα -dependent regulation of methylation in several genes. The authors analyzed the open datasets and showed that mutations in CEBPA gene (coding both, CEBPA transcriptional factor and lncRNA ecCEBPα) changed the global CpG methylation status in AML cells. The manuscript is nicely written, conclusions are logically justified. This work will be interesting to the readers in the epigenetic regulation and cancer research field.\nStill, I have several concerns about the analysis. There are a lot of predicted triplex target regions for ecCEBPA genome-wide. Some of them could be false-positive predictions. Is there any way to confirm the observed effect only of experimentally validated contacts? Or in regions where predictions are most reliable?\nAlso, it is unclear other genes, not only transcription factors, predicted to be regulated by ecCEBPA are related to hematopoiesis. It would be helpful to have at least some hypotheses in the discussion. If there is some link found between ecCEBPA targets and regulation of hematopoiesis, it would really strengthen the conclusions of the work. Probably, KEGG pathway enrichment analysis may help with that.\nMinor comments:\nIt is unclear on the figure with a secondary structure of ecCEBPA where the triplex-forming region is located.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "6999",
"date": "31 Aug 2021",
"name": "ADEWALE OGUNLEYE",
"role": "Author Response",
"response": "Response to Reviewer Two Comment one: There are a lot of predicted triplex target regions for ecCEBPA genome-wide. Some of them could be false-positive predictions. Is there any way to confirm the observed effect only of experimentally validated contacts? Or in regions where predictions are most reliable? Response one: We are grateful to the reviewer for this suggestion. We performed a validation for the most reliable predicted triplexes using only experimentally validated ecCEBPA:DNA contacts. Overall, a mean methylation delta score of only 0.01 (p-value < 1E-09) was observed which further emphasizes the protective effect of ecCEBPA. The following text and images were added to the main body of the paper: “Since these ecCEBPA contacts have been experimentally validated, we suggested that they are the most reliable regions where ecCEBPA might have a protective effect from DNA methylation. Overall, a mean methylation delta score of experimentally validated binding sites is significantly lower than that of the non-binding sites (p-value < 1E-09) (Figure 2C).” New figure panels (1&2) here: https://drive.google.com/file/d/1iynm-t0DfGkxLF5vsumG4iCcfo2u2xCJ/view?usp=sharing Comment two: Also, it is unclear if other genes, not only transcription factors, predicted to be regulated by ecCEBPA are related to hematopoiesis. It would be helpful to have at least some hypotheses in the discussion. If there is some link found between ecCEBPA targets and regulation of hematopoiesis, it would really strengthen the conclusions of the work. Probably, KEGG pathway enrichment analysis may help with that. Response two: We thank the reviewer for this important comment. Indeed, we discovered that other non-transcription factor genes have links to acute myeloid leukemia via literature mining. Unfortunately, this could not be enriched through KEGG. We suggest including a supplementary table that details the different roles of the identified genes. In the main text, we added: “Out of the 33 genes we identified to be targets of ecCEBPA, 16 genes (ICAM1, PDXK, etc.) are clearly related to hematopoiesis and various leukemias. A summary of the genes and their function is provided in Table 1.” Table 1: AML specific function of nearby genes that are protected by ecCEBPA (added to the paper)."
}
]
}
] | 1
|
https://f1000research.com/articles/10-204
|
https://f1000research.com/articles/10-556/v1
|
12 Jul 21
|
{
"type": "Research Article",
"title": "Psychological and clinical-epidemiological profile of poisoning in Nepal: an institutional experience",
"authors": [
"Angela Basnet",
"Dhan Shrestha",
"Sabin Chaulagain",
"Ashok Thapa",
"Manoj Khadka",
"Bishal Regmi",
"Manita Khadka",
"Kabita Adhikari",
"Anil Jung Thapa",
"Sakar Pokharel",
"Kaushal Kumar Singh",
"Prajwal Syangtang",
"Surakchha Adhikari",
"Angela Basnet",
"Sabin Chaulagain",
"Ashok Thapa",
"Manoj Khadka",
"Bishal Regmi",
"Manita Khadka",
"Kabita Adhikari",
"Anil Jung Thapa",
"Sakar Pokharel",
"Kaushal Kumar Singh",
"Prajwal Syangtang",
"Surakchha Adhikari"
],
"abstract": "Background Poisoning has become a major public health problem, with the intent in most cases being self-harm and commit suicide. This study highlights the psychological and clinical-epidemiological profile of patients visiting Scheer Memorial Adventist Hospital after poisoning. Methods This retrospective record-based study was done among poisoning patients of a hospital in Nepal from 1st January 2018 to 31st December 2020. Data were analyzed using STATA version-15. Results Out of 134 total poisoning cases, 71 had consumed organophosphate compounds. The majority of the cases were female (59.2% in organophosphate groups, 69.8% in non-organophosphate groups). The circumstances of poisoning were mostly suicidal (95.8% in organophosphate groups, 90.5% in non-organophosphate groups) and the reasons for this being mostly family disputes. Organophosphate groups had 8.41 times higher odds of having complications when compared to non-organophosphorus compounds.\n\nConclusions The majority of the poisoning cases were suicidal in nature and family disputes being the major reason for the intake of a poisonous substance. This demands that more attention be given to psychological and family counseling to resolve any disputes, as well as psychological management of poisoning cases after medical management. Also, a strong regulatory mechanism should be imposed to control the easy access to poisonous substances.",
"keywords": [
"organophosphates",
"Nepal",
"suicide"
],
"content": "Introduction\n\nAs per reports from the World Health Organization (WHO), about 0.3 million people die each year as a result of various acute poisonings.1 The substances most commonly used in poisoning are agricultural pesticides (mostly organophosphates) in developing countries and misuse of drugs in developed countries. The common reason for most of the poisoning cases is the intention of self-harm.1 WHO estimates that pesticide self-poisoning accounts for around 20% of global suicides.2 Around 60% of the estimated annual deaths from self-harm in rural Asia are due to pesticide poisoning, and organophosphates account for around two-thirds of these deaths.3 In low and middle-income countries (LMICs) like Nepal, where 66% population is directly engaged in agriculture, pesticides have become the preferred means of suicide due to agricultural intensification and their easy availability.4\n\nLimited information is available regarding the pesticide poisoning scenario in Nepal as the national routine Health Management and Information System (HMIS) doesn’t include it.5 Also, the psychological aspect associated with poisoning in Nepal is not addressed much in the literature although the medical aspect is given high priority.\n\nOur study aims to address the psychological issues of poisoning with main focus on its intent and the reasons behind it. Apart from this, the study also highlights the clinical and epidemiological profile among patients presenting to the emergency department of a hospital in Nepal following intentional or accidental poisoning.\n\n\nMethods\n\nThis is a retrospective hospital record-based study done among patients presenting to the emergency department of Scheer Memorial Adventist Hospital (SMAH) following confirmed or suspected poisoning.\n\nAll the patients presenting to the emergency department of SMAH following confirmed or suspected poisoning during the period of 1st January 2018 to 31st December 2020 were included in the study. The study was conducted from 28th February to 14th March 2021. Patients were either admitted to the ICU or General ward, referred to other centers, or were brought in already deceased. Patients who had not been exposed to poison were excluded from the study.\n\nDifferent sets of data extraction sheets were prepared for both general compound poisoning and organophosphorus compound poisoning respectively. Each questionnaire consists of demographic variables like age, sex, marital status, religion, profession, external variables like reasons for taking poisons, manner of taking poisons, history of suicide attempts, history of psychiatric illness (as reported by the patient), and clinical variables like presenting signs and symptoms, along with outcome and complications. The study instrument is available in Extended data. Data were recorded at the time of the clinical encounter through a combination of the physician, nurse, and social work documentation in hospital records.\n\nThe data were extracted to Microsoft Excel-13, then imported and analyzed using STATA-15 (Stata, RRID:SCR_012763). Descriptive variables were presented in simple frequency tables. Continuous variables were expressed in terms of mean, standard deviation. Binary logistic regression analysis was performed for the dependent outcome of ‘complications’ with the occurrence of complications as ‘1’ and no complications as ‘0’ among organophosphorus and non-organophosphorus compounds. Subsequently, further different independent variables studied were explored to get adjusted odds for the occurrence of complications within the organophosphorus compound group.\n\nThe study was approved by the Institutional Review Committee of SMAH (Ref no: 2608). The data were collected from the hospital records and as a part of the standard workup and treatment of the patients. The need for patient consent was waived by the ethics committee due to the retrospective and anonymous nature of the data.\n\n\nResults\n\nOut of 159 total poisoning cases, 71 had consumed organophosphate compounds while 63 had consumed non-organophosphate compounds like non-organophosphate pesticides, drugs, and rodenticides. Since Aluminum phosphide (n = 25) cases had unique findings (all cases being suicidal in intent and with a high case fatality rate of 84%) as compared to other non-organophosphate poisoning cases, aluminum phosphide cases have been reported elsewhere as a case series, hence they were not included in the analysis of the non-organophosphate group.\n\nThe mean age of study participants in the organophosphate (OP) group was 31.72 (±14.07) years, while that in the non-organophosphate (Non-OP) group was 27.41 (±9.79) years. More than half of the cases in both groups were female (59.2% in OP, 69.8% in Non-OP). The majority of the study participants were married (80.3% in OP and 47.6% in Non-OP). Hinduism was the major religion in both groups (56.3% in OP and 44.4% in Non-OP). The intent of intake of substance was mostly suicidal (95.8% in OP and 90.5% in Non-OP) although the majority of them had no prior suicide attempt (91.5% in OP and 96.8% in Non-OP) and had no psychiatric history (91.5% in OP and 95.2% in Non-OP). The reason for intake being mostly a dispute (63.4 % in OP group). More than half of the OP patients (56.3%) and the majority of the Non-OP group patients (95.2%) brought to the hospital were conscious. Emesis was induced at home in most of the patients of both groups (59.2% in OP and 41.3% in Non-OP). Likewise, most of the study participants had gastric lavage (85.9% in OP and 47.6% in Non-OP) and charcoal lavage (81.7% in OP and 20.6% in Non-OP) done in the emergency block of the hospital (Table 1).\n\nMore than half of the patients in the OP group had a normal pulse (n = 41, 57.7%), while 38 % had tachycardia. Likewise, more than three-fourths of the patients in the Non-OP group (79.4%) had a normal pulse. Among OP patients, the mean systolic blood pressure (SBP) was 124.93 (±22.66) mm Hg, and the mean diastolic blood pressure (DBP) was 79.13 (±13.47) mm Hg. Similarly in Non-OP patients, the mean SBP was 116.03 (±14.54) mm Hg and the mean DBP was 75.87 (±10.57) mm Hg. The majority of the patients had temperatures within the normal range (93.0% in OP and 95.2% in Non-OP). Most patients with OP poisoning (n = 43, 60.6%) had increased respiratory rate while Non-OP group patients (n = 40, 63.5%) had normal respiratory rate. The mean POP (Peradeniya Organophosphorus Poisoning) score for OP patients was 2.20 (±1.685), with more than three-fourths patients having mild scores (77.5%) and only 1.4% being severe. Almost all patients (97.2% in OP and 95.2% in Non-OP) were admitted to the ICU of the hospital. All patients with Non-OP poisoning improved and were sent home whereas 5.6 % of OP patients were dead either during treatment or brought dead to the hospital (Table 2).\n\nThe majority of the participants had their occupation not disclosed (57.7% in OP, 60.3% in Non-OP). Most of the remaining individuals in both OP and Non-OP groups were either house managers (18.3% in OP, 6.3% in Non-OP), students (11.3% in OP, 17.5% in Non-OP), or farmers (5.6% in OP, 6.3% in Non-OP) (Extended data Table 1 and 2).\n\nA family dispute was the most common reason for taking the substance among both OP groups (46.5%) and Non-OP groups (28.6%) (Extended data Table 1 and 2).\n\nThe common OP substances ingested were a combination of Chlorpyrifos and Cypermethrin (28.2 %), Chlorpyrifos (19.7%), Dichlorvos (18.3%), Methyl parathion (7.0%), a combination of Triazophos and Deltamethrin (2.8%), and Malathion (1.4%). Around a quarter of the individuals (22.5%) had the OP substance they ingested not specified (Extended data Table 3).\n\nAmong Non-OP groups, almost half of the participants ingested either non-organophosphate insecticides (25.4%) or drugs (22.2%). The most commonly ingested non-organophosphate insecticides were Cypermethrin (n = 4, 25%) and Emamectin benzoate (n = 3, 18.8%), whereas the most commonly ingested drug was NSAIDS (n = 11, 78.6 %), either along with other drugs or alone. Among NSAIDs, Paracetamol was the most commonly ingested drug (n = 9, 81.8%) (Extended data Table 2 and 3).\n\nMore than two-thirds of the participants presented with vomiting (n = 49, 69.0%), more than half with miosis (n = 42, 59.2%) and almost half with nausea (n = 34, 47.9%).\n\nThe most common nicotinic presentation was hypertension (n = 14, 19.7%) and tachycardia (n = 14, 19.7%), whereas the most common central presentation was confusion (n = 24, 33.8%) and anxiety (n = 18, 25.4%) (Extended data Table 4).\n\nMore than half of the participants (n = 40, 56.3%) in the OP group and 92.1 % participants in the Non-OP didn’t have complications. Among the participants who experienced complications, the most commonly encountered among OP groups was aspiration pneumonia (n = 12, 38.7%), either alone or in combination with other complications, and among the Non-OP group the most commonly encountered was bradycardia (n = 3, 60%) (Extended data Table 5 and 6).\n\nBinary Logistic Regression for dependent outcome complication (Yes = 1, No = 0) taking other poison categories as independent variables showed OP category has 8.41 times higher odds of having complications (95% CI: 2.999-23.581, P < 0.001) (Table 3).\n\nDifferent independent variables couldn’t show association of developing a complication among the OP poisoning group with good precision (Extended data Table 7).\n\n\nDiscussions\n\nAcute Pesticide Poisoning is a major health-care problem and a frequent medical emergency in developing countries with high case fatality.1,5,6 This retrospective hospital-based study intends to explore various factors contributing to the exposure of poison and the outcome. Recent national, as well as international studies, suggest that younger people have emerged as a high-risk age group.1,5–7 Our study also showed that the mean age in years in OP poisoning cases was 31.72 (±14.068). The fact that poisoning is more common among young adults reflects their vulnerability to stress, maladjustment, and immature psychological coping mechanisms at a time of life’s major stressors.8,9\n\nIn our study, females were more involved in organophosphate poisoning as well as in other acute poisonings which was consistent with other studies conducted in different national hospitals.5,10–12 In contrary to this finding, a study done at Liaquat University of Medical and Health Sciences, Pakistan over one year period showed only 22% were females.13 More vulnerability of females to suicide attempts than males in developing countries like Nepal points towards various social and cultural factors revealing inequality. Factors like early marriages, fewer opportunities for education, domestic violence, abusive spouses, problematic love and marital relationships, and unwanted pregnancies, contribute to more suicide attempts by women.7,9,14,15 According to the Nepal Maternal Mortality and Morbidity (MMM) study 2008/09, the leading cause of death among women of reproductive age was suicide, comprising 16 percent of all deaths increasing from 10.2 percent in 1998.\n\nThis study revealed that more than 90 percent of the patients intentionally consumed the poison (self-poisoning) as a suicidal attempt. A similar study was done in Bir Hospital, Nepal which showed 97% intentional poisoning.12 Also, a study done in Turkey revealed that deliberate self-poisoning was the most common cause of poisoning (58.6%), followed by accidental exposure (39.1%).16 A study from Nepal that examined attempted suicide showed that the commonest mode of suicide among all attempted cases was OP poisoning.17 Pesticides becoming the first choice of method of suicide in rural agricultural communities is attributed to easy availability and no restrictions on buying and selling.5,14,15,18 To support this, we can look at the fact that in Sri Lanka, the suicide rates halved in the mid 1990s after a series of legislative activities systematically banned the most highly toxic pesticides.19 The ease of availability of lethal means of self-harm may influence patterns of suicide. Suicidal impulses are often short-lived and if we can buy some time by making the means of suicide less readily available, a proportion of suicides will be prevented.18,20,21\n\nThe main triggering factor for attempting suicide was found to be interpersonal conflict (family disputes) in our study. In many other studies, interpersonal conflicts involving domestic problems are the main precipitating factors.22–24 However, various studies done in India, Sri Lanka, and other countries showed that psychiatric illnesses like depression are associated with high-risk attempts.25–27 It was not significant in our study due to inadequate data and incomplete history provided by the patient’s party. Since we relied completely on the history given by patients for psychiatric illness, its prevalence among them cannot be verified and can be more than what is reported. Evidence also suggests that there is a lesser prevalence of psychiatric disorders in individuals involved in suicidal behavior in LMICs. It may reflect the suicide methods used in LMICs (e.g., pesticide ingestion) which are mostly impulsive acts with low suicidal intent.28\n\nAs is commonly observed in different studies, organophosphorus compounds are common mode of poisoning in our study followed by drugs and rodenticides.5,10,29 However, some studies showed a higher percentage of rodenticides compared to drugs.11,30 Among different organophosphorus compounds, our study showed the combination of chlorpyrifos and cypermethrin to be the most common. Previous studies from Nepal and other countries report methyl parathion and dichlorvos as the commonest causes of OP poisoning.11 But contrary to these studies and as mentioned by the National Forensic Science Laboratory,29 the use of a combination of chlorpyrifos and cypermethrin seems to be increasing. This might be because compounds like methyl parathion and dichlorvos, previously very common compounds of poisoning, have been banned from the country.\n\nIn our study 77.5 percent of patients fall under mild severity as per POP score. It has been shown by Senanayeke et al. that the severity, morbidity, and mortality of OP poisoned patients can be predicted through the POP score.31 Perhaps we can conclude the pertinent factor for improved survival in our study was the mild severity status of the patients at presentation. A previous study from Karachi also showed a similar relation between POP score and severity.32\n\nIn this study, 26.86 per cent of all poisoning cases developed complications, very similar to one of the studies from Central Nepal.10 This shows that the majority of the patients recovered completely without any complications and sequelae which might be because of various reasons like adequate and proper management, ingestion of low doses, and induction of vomiting at home as seen in this study as well. Aspiration pneumonia was the commonest complication in the OP group with bradycardia being common in the Non-OP group. Other studies are also found in favor of these findings.10,33 The intermediate syndrome was also found in a good percentage (5 per cent) among the OP group similar to the findings of a study from eastern Nepal3 but significantly low compared to a study from India (29.4 percent).34\n\n90 per cent of patients with OP poisoning were recovered while 100 percent of patients recovered with other Non-OP poisoning. The case fatality was 4.4 percent among OP poisoning patients excluding the cases whose outcome couldn’t be evaluated such as referred cases and LAMA. The fatality rate was lower as compared to various studies done in Nepal and other South Asian countries.10,35,36\n\nThe study being retrospective and hospital based, some data were missing. Although the study has been conducted over the period of three years, the seasonal variation couldn’t be elicited because of lack of data. The severity of the patient is only based on POP score, but different toxicological parameters could have contributed to the complications.\n\n\nConclusion\n\nPesticides, commonly organophosphate compounds are used as the major means of self-poisoning. Our study showed that young adults and females are mostly involved in poisoning with the intent of suicide. Disputes with family members were found to be the main reason. Short-term suicidal impulses and the easy availability of pesticides also contributed to suicides. Limitations of a hospital-based study like ours can be overcome by a population-based study, which will provide true reflection about the problem of pesticide exposure and self-poisoning. Easy access to pesticides should be restricted with strong regulatory mechanisms and implementation of rules and regulations for pesticide handling. Early psychiatric consultation and identification of psychiatric disorders will help to reduce the incidence of self-harm. So, preventive strategies and mental health awareness programs should be conducted for high-risk populations.\n\n\nData availability\n\nFigshare. Psychological and clinical-epidemiological profile of poisoning in Nepal: an institutional experience. DOI: https://doi.org/10.6084/m9.figshare.14776344.v1.\n\nThis project contains the following underlying data:\n\n• Excel data OP.xlsx (de-identified data on psychological and clinical-epidemiological profile of patients visiting Scheer Memorial Adventist Hospital after poisoning presented from 1st January 2018 to 31st December 2020.)\n\n• Final Data.dta (de-identified data on psychological and clinical-epidemiological profiles of patients visiting Scheer Memorial Adventist Hospital after poisoning presented from 1st January 2018 to 31st December 2020.)\n\nAnd the following extended data:\n\n• Supplementary analysis.docx (tables with details on occupation, poison taken, symptoms at presentation, complications and binary logistic regression analysis)\n\n• Data collection sheets.docx (pre-specified data collection sheets which were used to collect data from individual patients file)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).\n\nAuthors’ contributions: AB, SC, and AT contributed to the concept, design, and interpretation of data. DBS guided, analyzed, and interpreted the finding. MK, BR, MK, KA, AJT, SP, KKS, PS, and SA contributed to the literature search, data extraction, and initial manuscript drafting. AB and DBS contributed in revising the manuscript for important intellectual content and approval of the final manuscript.\n\nAll authors were involved in drafting and revising the manuscript and approved the final version.",
"appendix": "References\n\nRajbanshi L, Arjyal B, Mandal R: Clinical profile and outcome of patients with acute poisoning admitted in intensive care unit of tertiary care center in Eastern Nepal. Indian J Crit Care Med. 2018 Oct; 22(10): 691–696. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSuicide.[cited 2021 Jun 14]. Reference Source\n\nAgrawal K, Karki P: Clinico-epidemiological Study on Pesticide Poisoning in a Tertiary Care Hospital in Eastern Nepal - PubMed. JNMA J Nepal Med Assoc. 2014 [cited 2021 Jun 14]: 972–976. PubMed Abstract\n\nKonradsen F: Acute pesticide poisoning--a global public health problem. Dan Med Bull. 2007 [cited 2021 Jun 14]: 58–59. PubMed Abstract\n\nGyenwali D, Vaidya A, Tiwari S, et al.: Pesticide poisoning in Chitwan, Nepal: A descriptive epidemiological study. BMC Public Health. 2017 Jul; 17(1): 619. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Yu B, Wang N, et al.: Acute poisoning in Shenyang, China: A retrospective and descriptive study from 2012 to 2016. BMJ Open. 2018 Aug; 8(8): 21881. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLicata C, Liu L, Mole D, et al.: Social and Cultural Factors Leading to Suicide Attempt via Organophosphate Poisoning in Nepal. Case Rep Psychiatry. 2019; 2019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFergusson DM, Woodward LJ, Horwood LJ: Risk factors and life processes associated with the onset of suicidal behaviour during adolescence and early adulthood. Psychol Med. 2000; 30(1): 23–39. PubMed Abstract | Publisher Full Text\n\nPradhan A, Poudel P, Thomas D, et al.: A review of the evidence: suicide among women in Nepal. Natl Heal Sect Support Progr. 2011: 1–113.\n\nPaudyal B: Poisoning: pattern and profile of admitted cases in a hospital in central Nepal - PubMed. JNMA J Nepal Med Assoc. 2005 [cited 2021 Jun 14]: 92–96. PubMed Abstract\n\nGupta SK, Joshi MP: Pesticide poisoning cases attending five major hospitals of Nepal. J Nepal Med Assoc. 2002 Jan 1 [cited 2021 Jun 14]; 41(144): 447–456. Reference Source\n\nSingh DP, Aacharya RP: Pattern of Poisoning Cases in Bir Hospital. J Inst Med Nepal. 2006 [cited 2021 Jun 14]; 28(1): 3–6. Publisher Full Text Reference Source\n\nShaikh MA: Mortality in patients presenting with organophosphorus poisoning at liaquat university of medical and health sciences. Pakistan J Med Sci. 2011; 27(5): 1022–1024.\n\nGunnell DJ, Eddleston M: Suicide by intentional ingestion of pesticides: A continuing tragedy in developing countries. Int J Epidemiol. Europe PMC Funders. 2003; 32: 902–909. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Der Hoek W, Konradsen F: Risk factors for acute pesticide poisoning in Sri Lanka. Trop Med Int Heal. 2005 Jun; 10(6): 589–596. PubMed Abstract | Publisher Full Text\n\nGüloǧlu C, Kara IH: Acute poisoning cases admitted to a university hospital emergency department in Diyarbakir, Turkey. Hum Exp Toxicol. 2005 Feb; 24(2): 49–54. PubMed Abstract | Publisher Full Text\n\nRawal N, Shrestha DB, Katuwal N, et al.: Attempted suicide: Mode and its distribution characteristics among soldiers and their family. J Kathmandu Med Coll. 2018 Nov 12 [cited 2021 Apr 4]; 7(2): 47–49. Reference Source\n\nBanerjee I, Tripathi SK, Roy AS, et al.: Pesticide use pattern among farmers in a rural district of West Bengal, India. J Nat Sci Biol Med. 2014; 5(2): 313–316. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGunnell D, Fernando R, Hewagama M, et al.: The impact of pesticide regulations on suicide in Sri Lanka. Int J Epidemiol. 2007 Dec; 36(6): 1235–1242. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen YY, Wu KCC, Wang Y, et al.: Suicide Prevention Through Restricting Access to Suicide Means and Hotspots. Int Handb Suicide Prev Second Ed. 2016; (October): 609–636. Publisher Full Text\n\nSuicide: Closing the Exits - Google Books.\n\nHettiarachchi J, Kodituwakku GCS: Self poisoning in Sri Lanka: Motivational aspects. Int J Soc Psychiatry. 1989 Jun; 35(2): 204–208. PubMed Abstract | Publisher Full Text\n\nManoranjitham SD, Rajkumar AP, Thangadurai P, et al.: Risk factors for suicide in rural south India. Br J Psychiatry. 2010 Jan; 196(1): 26–30. PubMed Abstract | Publisher Full Text\n\nPrashar A, Ramesh M: Assessment of pattern and outcomes of pesticides poisoning in a tertiary care hospital. Trop Med Int Heal. 2018 Dec; 23(12): 1401–1407. PubMed Abstract | Publisher Full Text\n\nA study of hopelessness, suicidal intent and depession in cases of attempted suicide. 21455374PMC2962835\n\nKar N: Profile of risk factors associated with suicide attempts: A study from Orissa, India. Indian J Psychiatry. 2010 Jan; 52(1): 48–56. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan MM, Mahmud S, Karim MS, et al.: Case-control study of suicide in Karachi, Pakistan. Br J Psychiatry. 2008: 402–405. PubMed Abstract | Publisher Full Text\n\nKnipe D, Williams AJ, Hannam-Swain S, et al.: Psychiatric morbidity and suicidal behaviour in low- And middle-income countries: A systematic review and meta-analysis. PLoS Med. 2019; Public Library of Science. p. e1002905. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShova TB, Tuladhar BS: Trends of Clinical Toxicology Cases in Nepal. J Forensic Res. 2014; 5(2): 217. Publisher Full Text\n\nKarki RK, Risal A: Study of poisoning cases in a tertiary care hospital. Kathmandu Univ Med J. 2012; 10(40): 70–73. PubMed Abstract | Publisher Full Text\n\nSenanayake N, de Silva HJ, Karalliedde L: A Scale to Assess Severity in Organophosphorus Intoxication: POP Scale. Hum Exp Toxicol. 1993; 12(4): 297–299. PubMed Abstract | Publisher Full Text\n\nAmir A, Raza A, Qureshi T, et al.: Organophosphate Poisoning: Demographics, Severity Scores and Outcomes From National Poisoning Control Centre, Karachi. Cureus. 2020 May; 12(5). PubMed Abstract | Publisher Full Text | Free Full Text\n\nHrabetz H, Thiermann H, Felgenhauer N, et al.: Organophosphate poisoning in the developed world - A single centre experience from here to the millennium. Chem Biol Interact. 2013 Dec; 206(3): 561–568. PubMed Abstract | Publisher Full Text\n\nDe Bleecker JL: Intermediate syndrome in organophosphate poisoning. Toxicol Organophosphate Carbamate Compd. 2006; 27(1): 371–380.\n\nJaiprakash H, Sarala N, Venkatarathnamma PN, et al.: Analysis of different types of poisoning in a tertiary care hospital in rural south india. Food Chem Toxicol. 2011 Jan; 49(1): 248–250. PubMed Abstract | Publisher Full Text\n\nAhuja H, Mathai AS, Pannu A, et al.: Acute poisonings admitted to a tertiary level intensive care unit in Northern India: Patient profile and outcomes. J Clin Diagnostic Res. 2015 Oct; 9(10): UC01–UC04. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "89442",
"date": "15 Jul 2021",
"name": "Swapnajeet Sahoo",
"expertise": [
"Reviewer Expertise Consultation Liasion Psychiatry",
"Schizophrenia",
"Acute Psychosis",
"Psychosexual disorders"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe materials and methods section should have a detailed summary of how the records are maintained in the hospital so that at any point of time these can be reverified. Like having unique registration number of the patient or a register where all poisoning cases are documented along with clinical variables and outcome parameters.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "89443",
"date": "02 Aug 2021",
"name": "Nishita Pathak",
"expertise": [
"Reviewer Expertise Substance use disorder",
"Depression and anxiety"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAs a reviewer, I would like to highlight that the authors have nicely elaborated the psychological aspects of suicide including female dominance, domestic violence as the main cause, and organophosphorus poisoning being the most common. However, some points that I feel are lacking in this study are as follows:\n\nWhether the suicidal cause was impulsive or planned. These incidences seem to be important because planned suicides are more common in underlying mental health problems like major depressive disorder, old age, divorced, and homeless individuals1. Impulsive suicides are more common in inter-personal conflicts which suggest a lack of coping.\n\nDomestic conflict if elaborated on with spouse or other family members would have been better. This point would strengthen the study as it would give some data as to the number of suicidal incidences when conflict would occur with spouse and other family members separately.2\n\n'\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-556
|
https://f1000research.com/articles/10-868/v1
|
27 Aug 21
|
{
"type": "Research Article",
"title": "Comparison of the effect on postoperative pain between instrumentation with and without connected electronic apex locator: a randomized clinical trial",
"authors": [
"Khoa Van Pham",
"Cuong Hoang",
"Cuong Hoang"
],
"abstract": "Background: The aim of the present study was to evaluate the postoperative pain between root canal instrumentation with unconnected electronic apex locator and instrumentation with connected electronic apex locator. Methods: Forty-two patients were randomly divided into two groups (n=21). Group 1 was treated using the traditional endodontic motor with unconnected electronic apex locator (EAL) and group 2 was treated using the endodontic motor with connected EAL. All teeth were treated in single-visit endodontic therapy. Postoperative pain levels at 6, 24, 48, 72 h and 1 week were recorded by patients. The data were collected and analyzed using the χ2, and Mann-Whitney U tests with significance at 0.05. Results: Postoperative pain levels were significantly reduced by half at 6 hours in both experimental groups; however, no significant differences were found in postoperative pain levels between the two groups at all considered times. The postoperative pain levels using a percussion test were reduced on day 7 in both groups, and there was no significant difference in this variable between two groups. Conclusions: Both groups have a similar effect on reduction of the postoperative pain for endodontic patients undergoing root canal.",
"keywords": [
"nickel-titanium",
"electronic apex locator",
"single-visit endodontic",
"postoperative pain"
],
"content": "Introduction\n\nOne of the most important stages in endodontic therapy is root canal preparation, which required a working length (WL) determination.1 Therefore, the measurement of root canal WL is one of the most important factors in root canal instrumentation and can affect the success of the endodontic treatment.1 The complexity of the situation is that the WL is not constant, it changes during root canal preparation.2 Because the root canal space cannot be shaped and cleaned appropriately if the WL is not exactly determined, this value must be controlled, measured, and adjusted continuously during the preparation. This task is time consuming and can cause procedural errors as it can produce more stress for the operator. Although the electronic apex locator (EAL), a device for WL determination, has shown high accuracy and facilitation,1 such as ProPex PiXi (Dentsply Sirona, Ballaigues, Switzerland), it is still hard to satisfy the operator’s demand for continuous monitoring of the WL in root canal preparation. The E Connect S motor combined with E-Pex Pro EAL (Changzhou Eighteeth Medical Technology Co., China) is a solution for continuous control of WL. This motor offers very special function for the operator when the instrument reaches the WL, that is, the motor automatically decreases the speed of, stops and/or reverses the instrument. Using such strictly controlled WL, this is expected to reduce the postoperative pain caused by apical extrusion. Postoperative pain is one of the most sensitive consequence in root canal therapy and there are many efforts to reduce the postoperative pain to enhance the patient’s comfort, cooperation, and trust. The unremitting efforts of manufacturers and advancements in technology and materials have led to improved rotary nickel-titanium (NiTi) instruments.3,4 An offset cross-sectional design has become dominant in recent years because of its multi-advantages, such as larger envelope movement and good debris collection, facilitating its utilization.4 ProTaper Next (PTN, Dentsply Sirona, Maillefer, Ballaigues, Switzerland) possesses this offset design and is made of M-Wire.\n\nThe aim of the present study was to evaluate the postoperative pain after root canal treatment between utilization of a traditional endodontic motor with unconnected EAL and the motor with connected EAL. The null hypothesis was that there would be no differences in pain intensities between the two experimental groups.\n\n\nMethods\n\nThis trial was registered at Thai Clinical Trials Registry with identification number of TCTR20200118001. The trial was registered retrospectively, as the study was started directly after receiving ethical approval; application for registration occurred after the enrollment of the first participant. The design of this study was a parallel group randomized, controlled trial with two arms, from May 2019 to March 2020.\n\nAccording to the data of a previous study,5 the sample size was calculated as 36. The sample size was calculated as the following formula for comparison of means from two independent samples:\n\nWith the power of 80%, significance of 0.05, the Z1−α2 = 1.96, Z1−β= 0.84.\n\nConsidering the number of lost patients during follow-up, 42 patients were aimed to be included in the study with allocation ratio of 1:1.\n\nSubjects of the study were enlisted from patients sent to the Department of Operative Dentistry and Endodontics of the University of Medicine and Pharmacy at Ho Chi Minh City for endodontic treatment from May 2019 to March 2020. Patients were asked prior to making an appointment for taking part in the study. Every patient was thoroughly informed about the study by the investigators, and each patient signed an informed consent form. The patients were blind to the modalities used for the endodontic treatment.\n\nPatients were randomly distributed into two groups (n = 21 per group) using an online randomiser program (available at www.randomizer.org). Group 1 was treated using the traditional endodontic motor with unconnected EAL and group 2 was treated using the endodontic motor with connected EAL. In total, 26 women and 16 men with maxillary and mandibular molars indicated for endodontic therapy (as assessed with preoperative radiographs) were included in the present study. For each patient, one molar was treated for the study (a total of 42 molars for the study).\n\nCriteria for subjects included in the present study were healthy patients without systemic diseases with symptomatic pulpal or periapical pathology of the first or second molar. Criteria for subjects excluded from the study were those with systematic diseases and other conditions, and those aged less than 18 years. The inclusion and exclusion criteria of patients for the present study were displayed in the Table 1.\n\nPatient preoperative pain was recorded using the Heft Parker visual analogue scale (VAS) of Heft & Parker.6 The VAS was 170 mm in length and divided into four categories: 0 mm, no pain; 0-54 mm, mild pain (within this category: faint pain = 23 mm; weak pain = 36 mm); 55-113 mm, moderate pain; 114-170, severe pain (within this category: strong pain = 114 mm; intense pain = 144 mm).7 The patients had the VAS explained to them so that they knew how to record their pain on the line without any numerical markings, but with various descriptive words. The patients could place a mark anywhere on the line and use the verbal descriptors as a guide. Each patient’s mark was assigned a value between 0 and 170 mm on the scale by measuring the distance from the left end to the mark with a ruler.\n\nThe patients were required to record their own pain level at 6, 24, 48, 72 hours and one week after treatment was complete using the VAS. The patient was scheduled for an appointment at one week after treatment for recording the postoperative pain by percussion test and for collecting the VAS. The age, gender, number of teeth, diagnosis, preoperative and postoperative pain levels at 6, 24, 48, 72, one week, preoperative and postoperative pain levels at one week on percussion using the Heft & Parker VAS (HP-VAS), and the analgesic intake after procedure were recorded.\n\nAll endodontic treatments were performed by one endodontist (C.M.H.). The indicated tooth was anesthetized using local anesthetic solution containing 2% lidocaine with 1:100,000 epinephrine (Lignospan Standard, Septodont, France). Inferior alveolar nerve block and buccal infiltration anesthesia technique were used for the mandibular molars and buccal and palatal infiltration anesthesia technique was used for the maxillary molars. After 10 minutes, the access cavity was prepared under the rubber dam and explored for all possible canal orifices. The canals were filled with 3% sodium hypochlorite (Canal Pro, Coltene Whaledent, Altstätten, Switzerland) and explored by the 10 ISO K-file (Dentsply Sirona, Maillefer, Ballaigues, Switzerland). The coronal third of the canals were pre-enlarged using the PTN X1 to the estimated lengths (determined by the preoperative digital X-ray images).\n\nFor subjects of the group 1, group of instrumentation with unconnected EAL, the root canal lengths were measured using ProPex Pixi EAL and teeth were treated using WaveOne endodontic motor with Proglider and PTN instruments (Dentsply Sirona, Maillefer, Ballaigues, Switzerland). After WL was determined and confirmed radiographically (short of the apex from 0.5—1 mm), rubber stop on the shaft of the Proglider was set at the WL, then the instrument was inserted into the handpiece of the WaveOne motor (velocity: 300 rpm; torque: 2 N.cm) and used in slow in-and-out pecking motions inside the canal until it reached the determined working length. The Proglider was replaced by the PTN X1 with the rubber stop on the shaft at working length. The PTN X1 was used in slow in-and-out pecking motion inside the canal until reaching the determined WL. This same procedure was used for the next PTN X2 (upper buccal or lower mesial canals) and PTN X3 (upper palatal and lower distal canals).\n\nFor subjects of the group 2, group of instrumentation with connected EAL, the teeth were treated using E Connect S endodontic motor combined with the E-Pex Pro EAL with Proglider and PTN instruments. The WL of each root canal was confirmed radiographically. The Proglider was inserted into the handpiece of the E Connect S motor (velocity: 300 rpm; torque: 2 N.cm) connected with the E-Pex Pro EAL (set at the apex, 0.0). The hook wire of the motor was hung into the corner of the patient’s mouth, and the preparation was started. The instrument was inserted into the canal and used in slow in-and-out motion toward the apex until it was automatically stopped and reversed from the apex. This same procedure was used for the next PTN X2 (upper buccal or lower mesial canals) and PTN X3 (upper palatal and lower distal canals).\n\nFor the subjects of both groups, the 10 ISO K-file was used for patency file during the preparation after every instrument change. The file was inserted just past the apical foramen, with the amplitude of less than 0.5 mm.\n\nThe root canals were irrigated a final time using 5 mL 3% sodium hypochlorite following 5 mL 17% EDTA solution, then dried using matched paper cones and obturated with matched single gutta percha cones with AH Plus (Dentsply Sirona, Maillefer, Ballaigues, Switzerland). Digital radiograph was taken to check the quality of obturation. If the root canal treatment acquired all requirements of good obturation, without extrusion of material, the tooth was treated for the next step. The access cavities were restored using SDR flowable composite and Ceram X SphereTec composite resin (Dentsply Sirona, Konstanz, Germany).\n\nA total of 400 mg ibuprofen (Stada, Vietnam) was prescribed for cases of unbearable pain.\n\nData were imported and stored in the Statistical Package for Social Sciences (SPSS) (IBM, Armonk, NY, USA) version 25.0. Data were first checked for normality of distribution using the Shapiro-Wilk test, however, almost all variables had not been distributed normally. Data transformation was performed using many arithmetical functions, however, there was not any successful transformation. Therefore, the Mann-Whitney U test was used for comparison between the two groups. Age, gender, tooth number, and analgesic intake data were analyzed using the χ2 test. All statistical analyses were performed at the significance of 0.05.\n\nThis study was approved by the Research Ethics Committee of the University of Medicine and Pharmacy at Ho Chi Minh City with the approval number of 306/ĐHYD-HĐĐĐ. Written informed consent was obtained from all subjects involved in the study. Written informed consent was been obtained from the patients to publish the article.\n\n\nResults\n\nThere was not any loss of patients during follow-up (Figure 1). Demographic data, preoperative and post-operative pain levels, and pain levels on percussion are displayed in the Table 2.\n\nMean age of patients was 28.24 and 30.52 years for the group 1 and group 2, respectively. There were no significant differences in the age, gender, tooth number between the groups (P > 0.05). The preoperative pain levels and those on percussion were around the moderate level (85 mm) in both groups, and no significant differences were found in preoperative pain levels and these on percussion between two groups (P > 0.05). The postoperative pain levels were significantly reduced by half at 6 hours for both groups (greater than 50 mm); however, no significant differences were found in postoperative pain levels between two groups at all considered times (P > 0.05). The postoperative pain levels on percussion were reduced on day 7 in both groups, and there was no significant difference in this variable between two groups. There was only one patient who needed to use analgesics postoperatively in the instrumentation with unconnected EAL group (group 1). There was no patient who needed to use analgesics in the instrumentation with connected EAL group (group 2). There were not any signs of swelling, sinus tract, or palpation pain in the patients, and there were not any unscheduled appointments for the patients in the study.\n\n\nDiscussion\n\nThe result of the present study showed that postoperative pain levels of patients were lower than the “weak” level. Because the root canal length is changed during root canal preparation, therefore, it must be measured, controlled and maintained continuously.2 This makes the operator fatigued and exhausted. Using a common, separate EAL, the operator must use a reference from the remaining tooth structure on the occlusal surface, incisal edge or even the root surface in teeth missing structure. This reference can be lost during treatment, especially in multiple-appointment treatment. In addition, using the rubber stop on the shaft of the instrument is improper in certain circumstances. This rubber stop can be displaced or worse than that, the rubber stop can be overpassed because of its elastic property without notice from the operator if the instrument is sucked into the canal (screw-in tendency). Instrumentation with a connected EAL device will overcome these shortcomings of previous methods in WL determination, control, and maintenance. Although there are many in vitro studies on the WL determination of EALs,1,8-10 there are few studies on endodontic motors with built-in or connected EAL up to now and therefore, there is not much data on the effect of an endodontic motor on root canal treatment.5,11 EAL connected to the endodontic motor in the present study has been investigated in a previous study, which shows that accuracy was at the highest level when compared with other EAL and cone beam computed tomography.1 In the present study, we showed that EAL’s accuracy is still at a high level when using with the endodontic motor.\n\nThe PTN is made of M-Wire with special offset design and unique dimensions in order to reduce operator’s fatigue and exhaustion, and procedure complexity and enhance effectiveness.4,12 In the two previous studies on causing apical extruded debris of PTN and other rotary NiTi instruments, the results showed that PTN caused significantly less apical debris extrusion than ProTaper Universal and PTN caused significantly more apical extruded debris than HyFlex CM.13,14 These studies of comparison between the continuous rotary NiTi and reciprocating instruments showed that there were not significant differences in apical extruded debris.13,15 Other authors reported that the continuous rotary NiTi instruments produced less apical extruded debris than the reciprocating instruments.16 These conflicting results may be due to differences in study design, setup, or type of teeth.\n\nRoot canal preparation techniques cause apical extrusion of dentine debris, pulp tissue, microorganisms, and irrigation solutions through apical foramen, leading to inflammation, resulting in postoperative pain.17 The instrument’s designs or modes of movement (continuous or reciprocating rotary) are considerable factors that influence the apical extrusion of debris and therefore, postoperative pain of the patient.18-21 Instruments with the reciprocating movement induce more debris through apical foramen when compared with instruments with continuous rotary movement.16,22 This affects the choice of instruments among a great array of nickel-titanium root canal instruments.\n\nSodium hypochlorite concentration of 3% was used for the present study, that is similar to that of a previous study.11 A lower concentration of sodium hypochlorite has been considered to reduce the postoperative pain in one study,23 however, that result was different from another study.24 Although the standard concentration of 5.25% was used in other studies,23,24 there was still one study that used a higher concentration of 8.25% with no significant differences of postoperative pain among other lower concentration groups.25\n\nBecause the first 48 hour after endodontic therapy is the most common period when postoperative pain is felt by patient, five time-points (right after treatment, after 6, 12, 24, 48 hours) were used for evaluation.23 Longer periods are also selected to further collect the data after 72 hours and 7 days.23\n\nPostoperative pain related to rotary NiTi instruments was reported by many previous studies using the randomized clinical trial design.5,11,21,26 Two of these studies performed single appointment endodontic therapy with separate EAL, and the results revealed that there was no difference in postoperative pain between the reciprocating and continuous instruments.21,26 These studies enrolled the asymptomatic patients and evaluated only the postoperative pain levels with different VAS instruments. However, postoperative pain in the single-visit endodontic treatments with NiTi instruments was at low levels in these two studies.21,26 Another study also recruited asymptomatic patients with postoperative pain evaluation but used multiple-visit treatment and WL determination during the root canal preparation.11 There were no differences in postoperative pain among the experimental NiTi instruments with both modes of movement in the above studies. The remaining study used the same concept as the present study with the different modalities.5 The result of the previous study revealed that postoperative pain levels on only day 1 of the group using the traditional endodontic motor with separate WL determination were significantly higher than that of the other groups.5 On the other days of the study, the postoperative pain levels were not significantly different between two groups using different modalities.5 This result agreed with that of the present study.\n\nThere are many various scales used to record the pain levels for evaluation of the effectiveness of many endodontic treatments.5,6,27-29 Although the 4- and 5-point rating scales of pain are used commonly and successfully in a clinical setting because of easy instructions for use, these scales did not have enough sensitivity to record the pain experience of patients.6 The Numerical Rating Scale for pain evaluation has low sensitivity when compared with the VAS, and in some previous studies, the VAS proved the high sensitivity and positive correlation with treatment effectiveness. The most important advantage of the VAS among the other pain scales was the difference in pain intensity at the two different times showed the actual difference in pain level.30-32 The Heft-Parker VAS is a line with the dimension of 170 mm with different distances on the scales to describe the pain of the patient.6 The VAS is used commonly in oral-facial pain studies; however, this scale confuses patients in selection of right position on the scale because there are no guides for ratings other than the two extremities.6 Using category word designations on the line of a VAS, the graphic rating scale of Heft and Parker offers more sensitivity than a category scale and is easier to use than a VAS.6\n\nThe result of the present study revealed that although the postoperative pain of patients in the instrumentation with connected EAL group was lower than that of the instrumentation with unconnected EAL group, there was no significant difference in postoperative pain levels at all points in time between the two experimental groups. Therefore, the null hypothesis was accepted.\n\nThe limitations of the present study were the small sample size, that the operator was not blinded to the applications of the two different modalities.\n\nWithin the limitations of the present study, the result revealed that the preoperative pain levels of the subjects in both groups were above the “moderate” level and those reduced after single-visit endodontic treatment with the postoperative pain levels less than the “faint” level. There was just one patient that used anti-inflammation drugs after treatment. Along with many other advantages of single-visit endodontic treatment such as reduction of appointments, exclusion of leakage through temporary restorations and removal risk of additional missing of tooth structure in previously severe structure missing tooth, this mode of treatment is tolerated and preferred better by patients and becomes common practice in many situations.26 Within the limitations of the present study, the endodontic therapy with the single-visit treatment brings the benefit to the patients without increasing the pain.\n\n\nConclusions\n\nWithin the limitations of the present study, endodontic therapy with the single-visit treatment brings the benefit to the patients without increasing the pain. Both groups using the endodontic motors with unconnected or connected electronic apex locator have a similar effect on reduction of the postoperative pain for endodontic patients.\n\n\nData availability\n\nMendeley Data: Khoa Cuong PO Pain, https://doi.org/10.17632/48ytd79w39.1.33\n\nMendeley Data: CONSORT checklist for ‘Comparison of the effect on postoperative pain between instrumentation with and without connected electronic apex locator: a randomized clinical trial’, https://doi.org/10.17632/48ytd79w39.1.33\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nPham KV, Khuc NK: The Accuracy of Endodontic Length Measurement Using Cone-beam Computed Tomography in Comparison with Electronic Apex Locators. Iran Endod J. 2020; 15(1): 12–17. Publisher Full Text\n\nVasconcelos BC, Bastos LM, Oliveira AS, et al.: Changes in Root Canal Length Determined during Mechanical Preparation Stages and Their Relationship with the Accuracy of Root ZX II. J Endod. 2016; 42(11): 1683–1686. eng. PubMed Abstract | Publisher Full Text\n\nPham K, Nguyen N: Cutting efficiency and dentinal defects using two single-file continuous rotary nickel-titanium instruments [Original Article]. Saudi Endod J. 2020; 10(1): 56–60. Publisher Full Text\n\nPham K, Phan T: Evaluation of root canal preparation using two nickel-titanium instrument systems via cone-beam computed tomography [Original Article]. Saudi Endod J. 2019; 9(3): 210–215. Publisher Full Text\n\nArslan H, Güven Y, Karataş E, et al.: Effect of the Simultaneous Working Length Control during Root Canal Preparation on Postoperative Pain. J Endod. 2017; 43(9): 1422–1427. eng. PubMed Abstract | Publisher Full Text\n\nHeft MW, Parker SR: An experimental basis for revising the graphic rating scale for pain. Pain. 1984; 19(2): 153–161. PubMed Abstract | Publisher Full Text\n\nNusstein J, Steinkruger G, Reader A, et al.: The effects of a 2-stage injection technique on inferior alveolar nerve block injection pain. Anesth Prog. 2006; 53(4): 126–130. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Pham K: Endodontic length measurements using 3D Endo, cone-beam computed tomography, and electronic apex locator. BMC Oral Health. 2021; 21(1): 271. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Pham K: Endodontic length measurements using cone beam computed tomography with dedicated or conventional software at different voxel sizes. Sci Rep. 2021; 11(1): 9432. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen P, Pham K: Endodontic length measurements using different modalities: An in vitro study [Original Article]. J Int Soc Prev Community Dent. 2020; 10(6): 752–758. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOliveira PS, da Costa KNB, Carvalho CN, et al.: Impact of root canal preparation performed by ProTaper Next or Reciproc on the quality of life of patients: a randomized clinical trial. Int Endod J. 2019; 52(2): 139–148. eng. PubMed Abstract | Publisher Full Text\n\nPham KV: A Comparison of Cone Beam Computed Tomography and Periapical Digital Radiography for Evaluation of Root Canal Preparation. Applied Sciences. 2021; 11(14). Publisher Full Text\n\nOzsu D, Karatas E, Arslan H, et al.: Quantitative evaluation of apically extruded debris during root canal instrumentation with ProTaper Universal, ProTaper Next, WaveOne, and self-adjusting file systems. Eur J Dent. 2014; 8(4): 504–508. eng. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoçak MM, Çiçek E, Koçak S, et al.: Comparison of ProTaper Next and HyFlex instruments on apical debris extrusion in curved canals. Int Endod J. 2016; 49(10): 996–1000. eng. PubMed Abstract | Publisher Full Text\n\nSilva EJNL, Carapiá MF, Lopes RM, et al.: Comparison of apically extruded debris after large apical preparations by full-sequence rotary and single-file reciprocating systems. Int Endod J. 2016; 49(7): 700–705. eng. PubMed Abstract | Publisher Full Text\n\nBürklein S, Schäfer E: Apically extruded debris with reciprocating single-file and full-sequence rotary instrumentation systems. J Endod. 2012; 38(6): 850–852. eng. PubMed Abstract | Publisher Full Text\n\nRelvas JBF, Bastos MMB, Marques AAF, et al.: Assessment of postoperative pain after reciprocating or rotary NiTi instrumentation of root canals: a randomized, controlled clinical trial. Clin Oral Investig. 2016; 20(8): 1987–1993. PubMed Abstract | Publisher Full Text\n\nPasqualini D, Corbella S, Alovisi M, et al.: Postoperative quality of life following single-visit root canal treatment performed by rotary or reciprocating instrumentation: a randomized clinical trial. Int Endod J. 2016; 49(11): 1030–1039. PubMed Abstract | Publisher Full Text\n\nNekoofar MH, Sheykhrezae MS, Meraji N, et al.: Comparison of the Effect of Root Canal Preparation by Using WaveOne and ProTaper on Postoperative Pain: A Randomized Clinical Trial. J Endod. 2015; 41(5): 575–578. PubMed Abstract | Publisher Full Text\n\nNeelakantan P, Sharma S: Pain after single-visit root canal treatment with two single-file systems based on different kinematics—a prospective randomized multicenter clinical study. Clin Oral Investig. 2015; 19(9): 2211–2217. PubMed Abstract | Publisher Full Text\n\nKherlakian D, Cunha RS, Ehrhardt IC, et al.: Comparison of the Incidence of Postoperative Pain after Using 2 Reciprocating Systems and a Continuous Rotary System: A Prospective Randomized Clinical Trial. J Endod. 2016; 42(2): 171–176. PubMed Abstract | Publisher Full Text\n\nCaviedes-Bucheli J, Castellanos F, Vasquez N, et al.: The influence of two reciprocating single-file and two rotary-file systems on the apical extrusion of debris and its biological relationship with symptomatic apical periodontitis. A systematic review and meta-analysis. Int Endod J. 2016; 49(3): 255–270. PubMed Abstract | Publisher Full Text\n\nMostafa M, El-Shrief YAI, Anous WIO, et al.: Postoperative pain following endodontic irrigation using 1.3% versus 5.25% sodium hypochlorite in mandibular molars with necrotic pulps: a randomized double-blind clinical trial. Int Endod J. 2020 Feb; 53(2): 154–166. eng. PubMed Abstract | Publisher Full Text\n\nFarzaneh S, Parirokh M, Nakhaee N, et al.: Effect of two different concentrations of sodium hypochlorite on postoperative pain following single-visit root canal treatment: a triple-blind randomized clinical trial. Int Endod J. 2018; 51(S1): e2–e11. PubMed Abstract | Publisher Full Text\n\nDemenech LS, de Freitas JV, Tomazinho FSF, et al.: Postoperative Pain after Endodontic Treatment under Irrigation with 8.25% Sodium Hypochlorite and Other Solutions: A Randomized Clinical Trial. J Endod. 2021 May; 47(5): 696–704. eng. PubMed Abstract | Publisher Full Text\n\nÇiçek E, Koçak MM, Koçak S, et al.: Postoperative pain intensity after using different instrumentation techniques: a randomized clinical study [Original Article]. J Appl Oral Sci. 2017; 25(1): 20–26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamamoorthi S, Nivedhitha MS, Divyanand MJ: Comparative evaluation of postoperative pain after using endodontic needle and EndoActivator during root canal irrigation: A randomised controlled trial. Aust Endod J. 2015; 41(2): 78–87. PubMed Abstract | Publisher Full Text\n\nPasqualini D, Mollo L, Scotti N, et al.: Postoperative Pain after Manual and Mechanical Glide Path: A Randomized Clinical Trial. J Endod. 2012; 38(1): 32–36. PubMed Abstract | Publisher Full Text\n\nElMubarak AHH, Abu-bakr NH, Ibrahim YE: Postoperative Pain in Multiple-visit and Single-visit Root Canal Treatment. J Endod. 2010 2010/01/01/; 36(1): 36–39. PubMed Abstract | Publisher Full Text\n\nPrice DD, Bush FM, Long S, et al.: A comparison of pain measurement characteristics of mechanical visual analogue and simple numerical rating scales. Pain. 1994; 56(2): 217–226. PubMed Abstract | Publisher Full Text\n\nKremer E, Atkinson HJ, Ignelzi RJ: Measurement of pain: Patient preference does not confound pain measurement. Pain. 1981; 10(2): 241–248. PubMed Abstract | Publisher Full Text\n\nJensen MP, Karoly P, Braver S: The measurement of clinical pain intensity: a comparison of six methods. Pain. 1986; 27(1): 117–126. PubMed Abstract | Publisher Full Text\n\nPham K: Khoa Cuong PO Pain and Consort Checklist. Mendeley Data, V1. 2021. Publisher Full Text"
}
|
[
{
"id": "122430",
"date": "02 Mar 2022",
"name": "Filipe Colombo Vitali",
"expertise": [
"Reviewer Expertise Postoperative pain",
"randomized clinical trial."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe present study evaluated the occurrence of postoperative pain between instrumentation with and without connected electronic apex locator through a randomized clinical trial. In general, the article is well written with appropriate language use. However, important methodological flaws are not only a bias, but completely invalidates the results of the manuscript:\nthe sample size calculation is not adequate;\n\nthere was no standardization in the sampling of patients, pulp status (vital and necrotic were included) or teeth (maxillary and mandibular molars);\n\nthe methodology applied for the chemical-mechanical preparation of root canals is weak and can lead to several biases in addition to the pain-causing factor evaluated;\n\nthe statistical analysis of the data is incomplete and could be better explored;\n\nThe conclusion is not supported by the results.\n\nMy recommendation for this current version is 'not approved'.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "271593",
"date": "24 May 2024",
"name": "Gabriel Pereira Nunes",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is interesting, but there are points to be explained, improved and/or changed: *Abstract Write a little background before the objective. Enter the Trial registration number.\n*Introduction This section could have more quotes to support the statements made. In addition, report the prevalence of pain during endodontic treatment, as this is the main outcome of the study.\n*Material and Methods The inclusion and exclusion criteria need to be written down. The fact, for example, of including patients without systemic diseases already implies that they would be excluded if they had systemic diseases. The VAS scale is considered the gold standard, so why has another scale been adopted as a method of evaluation?\nDid the prescription of analgesics as reported exclude the patient from the evaluations? It is not clear and the results table does not describe whether the patient took this medication (ibuprofen).\n*Results Assign an acronym/abbreviation to groups 1 and 2; the reading will be more attractive and clearer for readers\n*Discussion The discussion section is well written. However, the authors could comment on the subjective assessment of the pain outcome. In addition, endodontic treatment has several stages that can cause pain and are confounding factors for this outcome, such as: coronal opening/anesthesia, biomechanical preparation, root canal irrigation, obturation process, extrusion or not of the material.\nSeveral systematic reviews have confirmed this in the literature and should be cited.\n- Xiqian L et al (2024 [ref - 1])\n-- Seron MA et al (2023 [ref - 2])\n- Sabino-Silva R et al (2023 [ref - 3])\n- Rossi-Fedele G et al (2023 [ref - 4])\n- Chalub LO et al (2022 [ref - 5])\n\nReferences: In addition to the cited systematic reviews that can be incorporated into the text, I recommend a detailed review of the references (when possible) so that the majority of them are among the articles published in the last 5 years.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-868
|
https://f1000research.com/articles/9-1455/v1
|
14 Dec 20
|
{
"type": "Study Protocol",
"title": "What are the long-term symptoms and complications of COVID-19: a protocol for a living systematic review",
"authors": [
"Melina Michelen",
"Louise Sigfrid",
"Lakshmi Manoharan",
"Natalie Elkheir",
"Claire Hastie",
"Margaret O'Hara",
"Jake C. Suett",
"Vincent Cheng",
"Amanda Burls",
"Carol Foote",
"Charitini Stavropoulou",
"Melina Michelen",
"Louise Sigfrid",
"Lakshmi Manoharan",
"Natalie Elkheir",
"Claire Hastie",
"Margaret O'Hara",
"Jake C. Suett",
"Vincent Cheng",
"Amanda Burls",
"Carol Foote"
],
"abstract": "Although the majority of patients with COVID-19 will experience mild to moderate symptoms and will recover fully, there is now increasing evidence that a significant proportion will experience persistent symptoms for weeks or months after the acute phase of the illness. These symptoms include, among others, fatigue, problems in breathing, lack of smell and taste, headaches, and also depression and anxiety. It has also become clear that the virus has lasting effects not only on the respiratory system but also on other parts of the body, including the heart, liver, and the nervous system. In this paper we present a protocol for a living systematic review that aims to synthesize the evidence on the prevalence and duration of symptoms and clinical features of post-acute COVID-19 and its long-term complications. The living systematic review will be updated regularly, initially monthly with update cycles under continuous review as the pace of new evidence generated develops through the pandemic. We will include studies that follow up with COVID-19 patients who have experienced persistent mild, moderate or severe symptoms, with no restrictions regarding country, setting, or language. We will use descriptive statistics to analyse the data and our findings will be presented as infographics to facilitate transcription to lay audiences. Ultimately, we aim to support the work of policy makers, practitioners, and patients when planning rehabilitation for those recovering from COVID-19. The protocol has been registered with PROSPERO (CRD42020211131, 25/09/2020).",
"keywords": [
"Living systematic review",
"COVID-19",
"long covid",
"lasting effects"
],
"content": "Background\n\nMore than six months into the pandemic, our knowledge around COVID-19 continues to develop rapidly. The range of documented COVID-19 infections vary from asymptomatic to severe, but the vast majority of patients experience mild to moderate symptoms and do not require hospitalisation1. We have previously conducted a rapid review of the literature to identify which symptoms and signs might differentiate mild and moderate from severe COVID-192. Since then, and as more data are being gathered, there is increasing evidence of a “long-tail” of COVID-19 illness, but limited information about the range and duration of symptoms experienced3 or longer term health complications. A community app developed at King’s College London, which tracks self-reported symptoms, has shown that about one in ten will be sick for three weeks or more (https://covid.joinzoe.com/post/covid-long-term). Some individuals with COVID-19 have reported “fatigue, headaches and tingling nerves” that lasted months after symptom onset4. A recent longitudinal cohort of 143 patients followed after hospitalisation from COVID-19 in Italy reported that 87% had at least one ongoing symptom, most (55%) reporting three or more, at 60 day follow up. Fatigue (53%), dyspnoea (43%), joint pain (27%) and chest pain (22%) were the most common ongoing symptoms5, but there is a variety of other symptoms and complications that have been reported including neurocognitive difficulties, muscle pains and weakness, gastrointestinal upset, rashes, metabolic disruption, thromboembolic conditions and mental health conditions6. A prolonged course of illness has also been reported among people with mild COVID-19 who did not require hospitalisation3,7,8.\n\nThe evidence to date remains fragmented as to the onset of symptoms and clinical features, how long symptoms may last, how this relates to the severity of the initial illness, and further lasting impacts to health. A better understanding of patients’ projected recovery from COVID-19 is helpful to patients, healthcare professionals, policymakers and commissioners. The clinical management of persisting symptoms of COVID-19 has started to be addressed in the clinical literature6 and NHS England has issued guidance for the multisystem needs of patients recovering from COVID-199. Our findings could help identify people requiring additional rehabilitation services and, where necessary, specialist referral to establish a secondary cause of their symptoms. Our findings will also be relevant to organisations such as NHS England, which have recently launched an online COVID-19 rehab service supporting patients suffering long-term effects of the disease (https://www.yourcovidrecovery.nhs.uk/) or the British Society of Immunologists, which recently released a briefing note recommending research into the long-term immunological health consequences of COVID-1910.\n\nThe aim of this review is to synthesize the evidence on the prevalence and duration of symptoms and clinical features of post-acute COVID-19 and its long-term complications. This will inform clinical and public health management, prevention and rehabilitation policies.\n\n\nMethods\n\nTo address the aim of this study we will conduct a living systematic review (LSR). LSRs are used in areas where research evidence is emerging rapidly, current evidence is uncertain, and new research may influence policy or practice decisions11. These are all features of COVID-19 research, where much about the long-term effects of the disease are still unknown and policy makers are calling for more evidence. The review will be initially updated monthly, with update cycles under continuous review as the pace of new evidence generated develops through the pandemic. We aim to continue to update the review for up to two years. Our study methodology has been developed and strengthened through consultation with Long Covid Support (a patient support network).\n\nWe will include studies that meet the follow criteria:\n\n- Studies of patients with COVID-19 who have persistent mild, moderate or severe symptoms as defined by the article authors\n\n- Studies following up with COVID-19 patients\n\n- Peer reviewed articles published since 1st January 2020\n\n- No restriction regarding country, setting or language\n\nWe will exclude:\n\n- Studies that focus only on acute COVID-19\n\n- Editorials and opinion papers\n\nA search of the following databases will be conducted: Pubmed and CINAHL through the EBSCO database host for general health peer-reviewed articles and Global Health for global peer-reviewed articles through the Ovid database host. In addition, we will search Cochrane for relevant systematic reviews and Google Scholar for grey literature including pre-prints. We will also look at the WHO Global Research Database on COVID-19 and LitCOVID as two databases that bring together evidence on COVID-19 from a worldwide dataset. Finally, we will contact experts in the field and use social media to identify relevant studies.\n\nData will be managed using the review software Rayyan12.\n\nWe will search using controlled subject headings and keywords of the following concepts: Terms related to 1) COVID-19 OR COVID OR SARS-CoV-2; 2) symptoms OR clinical features OR signs OR characteristics OR sequelae OR complications; 3) long-term OR post-acute OR long-tail OR persistent OR chronic COVID OR long COVID OR post discharge OR prolonged symptoms OR long haul. The search terms were piloted on Pubmed and CINAHL through the EBSCO database host the week starting 14th September 2020 to ensure that recent high profile research articles on long covid were included. No important studies were missed.\n\nAn example is shown below:\n\nInitial screening of titles and abstracts as well as full text screening against the inclusion criteria will be done by two reviewers. Disagreements for inclusion will be resolved by consensus. Where disagreements cannot be resolved, a third researcher will review the papers to make the final decision.\n\nWe will be using the Hoy et al. checklist13 to critically appraise the studies included in the review.\n\nThe following information will be extracted from each study based on the extraction form used for our initial review2: study aim, country of study, setting, method, study design and population size and characteristics, types and frequency of symptoms reported, onset and duration of symptoms. Data extraction will be performed by one reviewer and checked by a second reviewer. Disagreements will be resolved through discussion and consensus.\n\nWe will use descriptive statistics to summarise the types of symptoms, their frequency and duration. We will perform subgroup analysis on the basis of age, sex, comorbidities and severity of the disease. The data will be presented as infographics to facilitate transcription to lay audiences.\n\nThis protocol report is structured according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) statement guidelines14, was registered with PROSPERO (CRD42020211131, 25 September 2020). The protocol will be updated as we progress with the living review as and if needed. CS is the guarantor for this study.\n\n\nData availability\n\nNo underlying data are associated with this article.\n\nFigshare: PRISMA-P checklist for “What are the long-term symptoms and complications of COVID-19: a protocol for a living systematic review”. https://doi.org/10.25383/city.13187456.v115.",
"appendix": "References\n\nCDC: Coronavirus Disease 2019 (COVID-19). Cent Dis Control Prev. 2020; (accessed 6 Aug 2020). Reference Source\n\nMichelen M, Jones N, Stavropoulou C: In patients of COVID-19, what are the symptoms and clinical features of mild and moderate cases? (accessed 6 Aug 2020). Reference Source\n\nRayner C, Lokugamage AU, Molokhia M: Covid-19: Prolonged and relapsing course of illness has implications for returning workers. 2020; (accessed 6 Aug 2020). Reference Source\n\nGarner P: Paul Garner: Covid-19 at 14 weeks—phantom speed cameras, unknown limits, and harsh penalties. The BMJ. (accessed 6 Aug 2020). Reference Source\n\nCarfì A, Bernabei R, Landi F, et al.: Persistent Symptoms in Patients After Acute COVID-19. JAMA. 2020; 324(6): 603–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGreenhalgh T, Knight M, A’Court C, et al.: Management of post-acute covid-19 in primary care. BMJ. 2020; 370: m3026. PubMed Abstract | Publisher Full Text\n\nTenforde MW: Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020. MMWR Morb Mortal Wkly Rep. 2020; 69: 993–998. Publisher Full Text\n\nSigfrid L, Cevik M, Jesudason E, et al.: What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19? - A harmonised, global longitudinal observational study. medRxiv. 2020. Publisher Full Text\n\nNHS England and NHS Improvement: After-care needs of inpatients recovering from COVID-19. 2020; (accessed 24 Sep 2020). Reference Source\n\nBritish Society for Immunology: COVID-19 immunology briefing note: What we know about long-term health consequences and priorities for research. Immunology. 2020. Reference Source\n\nElliott JH, Synnot A, Turner T, et al.: Living systematic review: 1. Introduction-the why, what, when, and how. J Clin Epidemiol. 2017; 91: 23–30. PubMed Abstract | Publisher Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan-a web and mobile app for systematic reviews. Syst Rev. 2016; 5(1): 210. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoy D, Brooks P, Woolf A, et al.: Assessing risk of bias in prevalence studies: modification of an existing tool and evidence of interrater agreement. J Clin Epidemiol. 2012; 65(9): 934–9. PubMed Abstract | Publisher Full Text\n\nMoher D, Shamseer L, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015; 4(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMichelen M, Sigfrid L, Manoharan L, et al.: What are the long-term symptoms and complications of COVID-19: a protocol for a living systematic review. City, University of London. Journal contribution. 2020. http://www.doi.org/10.25383/city.13187456.v1"
}
|
[
{
"id": "78755",
"date": "12 Feb 2021",
"name": "Johannes Siegrist",
"expertise": [
"Reviewer Expertise Social epidemiology systematic reviews"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol paper describes the aims and methods of conducting a living systematic review (LSR) on findings from studies following COVID-19 patients with long-terms symptoms. The LSR is planned to be updated at 2-months intervals up to 2 years. The paper offers information on search strategy with key terms, data management procedure, screening with critical appraisal, data extraction, and strategies of data analysis. Overall, the approach is in line with the PRISMA guidelines of performing systematic reviews and meta-analyses. Moreover, the protocol was registered in PROSPERO. Critical appraisal was proposed according to Hoy et al. 2012, and authors are expected to ensure that relevant criteria of risk of bias can be assessed by this tool.\nIn summary, while the indexing of the paper is endorsed, several minor queries still need to be addressed, as detailed below.\n\nSearch strategy: Authors claim that their search will not be restricted by country and language. However, it is unrealistic to identify and analyse written materials in more than 3 or 4 main languages, and these languages (English plus…) should be explicitly mentioned in the study protocol.\n\nData extraction: I wonder why no data on treatment (therapy of COVID-19 symptoms) are included in the data extraction matrix. This information is crucial if aspects such as symptom severity and duration are being evaluated.\n\nData analysis: This section is not well elaborated. Basic descriptive statistics only are mentioned. However, systematized data from respective publications will probably allow additional, more informative ways of synthesizing the data.\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": "6873",
"date": "27 Aug 2021",
"name": "Charitini Stavropoulou",
"role": "Author Response",
"response": "Thank you for your thorough review of our protocol, please find the response to the comments made outlined below. Search strategy: Authors claim that their search will not be restricted by country and language. However, it is unrealistic to identify and analyse written materials in more than 3 or 4 main languages, and these languages (English plus…) should be explicitly mentioned in the study protocol. Response: The main search will be performed in English, articles identified in non-English languages will be translated using Google translate and assessed by a reviewer with good knowledge of the language. This is now stated on page 7 of the revised protocol. Data extraction: I wonder why no data on treatment (therapy of COVID-19 symptoms) are included in the data extraction matrix. This information is crucial if aspects such as symptom severity and duration are being evaluated. Response: Thank you for the comment. This is part of the information included in the characteristics of population and is now explicitly mentioned in the protocol. Where data is available and synthesizable, we plan to assess the association between acute treatment and symptom severity and duration. Data analysis: This section is not well elaborated. Basic descriptive statistics only are mentioned. However, systematized data from respective publications will probably allow additional, more informative ways of synthesizing the data. Response: Thank you for your comments. We have amended the data analysis section to clarify that the analysis will go beyond descriptive statistics and, when possible, we will perform a meta-analysis. Please see pages 7 and 8 of the revised protocol."
}
]
},
{
"id": "80913",
"date": "22 Mar 2021",
"name": "Madelon van Wely",
"expertise": [
"Reviewer Expertise Epidemiology",
"meta-analyses",
"Obstetrics and Gynaecology"
],
"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\nNo doubt this is an important LSR that needs to be performed. I am in favor of getting this protocol published, however, at present many details are lacking. In my view in LSRs it is crucial to decide beforehand what the authors plan to do. Though it may seem annoying now, it will be helpful in the end.\n\nThe outcomes. You performed a rapid review so you will know what main outcomes you are looking for. The outcomes are not stated in the Prospero protocol either.\n\nIt would also be advisable to have list of inclusion criteria and data you want to extract like risk factors and demographics. You could combine these with outcomes and present them in one table.\n\nData analysis: descriptive analysis sub grouped by age, sex, comorbidities? As the idea is to provide proportions from different studies I think you will be able to pool these, stratified by age etc. You could for instance summarise proportions (maybe use Freeman-Tukey transformation to stabilise variances in case of studies with zero events?), provide 95% CIs and predictive intervals to report on the precision of estimates. (meta-analysis of proportions)\n\nAbout the subgrouping. How are you planning to do so? Are the age groups pre-specified or will they be dichotomised of subgrouped on basis of distribution of the data?\n\nThe duration is very important, how do you intend to present time? As grouped or continuous variable? When you have adequate data you could present the prevalence estimates over time.\n\nBesides prevalence studies you might also include cohorts in which case you may want to assess the risk of bias using the Newcastle Ottawa Scale for comparative cohorts or another such checklist.\n\nSearch: I would also search specifically for the expected outcomes\n\nI do advise to clarify when you consider a symptom to be persistent? You write: persistent mild, moderate or severe symptoms as defined by the article authors. I suppose post-discharge is T0.\n\nHow often do you at this moment intend to update and publish the results?\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "6874",
"date": "27 Aug 2021",
"name": "Charitini Stavropoulou",
"role": "Author Response",
"response": "Thank you for your thorough review, please find an outline of the response to the comments raised. The outcomes. You performed a rapid review so you will know what main outcomes you are looking for. The outcomes are not stated in the Prospero protocol either. Response: Thanks for highlighting, we have updated the text in the methodology section to highlight that the primary outcome is to characterise the prevalence of symptoms and complications of long term Covid-19 in different populations. Secondary outcomes include diagnostics and risk factors for developing different sequelae. This is now stated on page 7 of the revised protocol. It would also be advisable to have list of inclusion criteria and data you want to extract like risk factors and demographics. You could combine these with outcomes and present them in one table. Response: We have provided further details in the methods, regarding the inclusion/exclusion criteria. We have also expanded on the data extraction section to show the clarify the data we will be extracting. Please see page 7 of the revised protocol. Data analysis: descriptive analysis sub grouped by age, sex, comorbidities? As the idea is to provide proportions from different studies I think you will be able to pool these, stratified by age etc. You could for instance summarise proportions (maybe use Freeman-Tukey transformation to stabilise variances in case of studies with zero events?), provide 95% CIs and predictive intervals to report on the precision of estimates. (meta-analysis of proportions) Response We have provided further information in our analysis section to clarify that the analysis will go beyond descriptive statistics and that we will perform meta-analysis wherever this is possible, i.e. when there are more than two studies providing information on a symptom. Please see pages 7 and 8 of the revised protocol. About the subgrouping. How are you planning to do so? Are the age groups pre-specified or will they be dichotomised of subgrouped on basis of distribution of the data? Response: We plan to conduct subgroup analysis to explore the influence of key factors, e.g. age, on the estimates of prevalence. We will identify these key factors by discussing with our clinical experts, patient advocates and by reviewing the literature. We will try to align the division for subgroups with the literature to help inform the analysis and results. However, the methods will heavily depend on the availability and distribution of data. We have updated the methodology section accordingly. The duration is very important, how do you intend to present time? As grouped or continuous variable? When you have adequate data you could present the prevalence estimates over time. Response: We now clarify in the methods section that a subgroup analysis will be performed on follow up timing as indeed this is an important parameter as a group variable. Besides prevalence studies you might also include cohorts in which case you may want to assess the risk of bias using the Newcastle Ottawa Scale for comparative cohorts or another such checklist. Response: We will include any study design including cohort studies with symptom prevalence. We have chosen to use the Hoy et al risk of bias assessment checklist, a validated tool for assessing risk of bias in prevalence studies, which does not prevent us from using it with cohort studies. Search: I would also search specifically for the expected outcomes Thank you for your suggestion. We have conducted pilot searches and noticed considerable diversity in the reported outcomes. The inclusion of key terms for the expected outcomes in search strings generated excessive hits and contributed to low precision, aka a low percentage of useful publications found in the search results. It also limits searches by “expected” outcomes and loses the opportunities finding new types of long covid symptoms and risk factors. Therefore, we used a search strategy using simple search strings focusing on describing long covid and complement the searches by backwards snowball searches in the references of relevant publications and consulting experts. I do advise to clarify when you consider a symptom to be persistent? You write: persistent mild, moderate or severe symptoms as defined by the article authors. I suppose post-discharge is T0. Response. Thanks for highlighting. We have provided further clarification in the inclusion criteria (page 5). In light of the new definitions issued by the Office for National Statistics (ONS), we clarify we will be including studies assessing symptoms or outcomes at 12 or more weeks post Covid-19 onset. How often do you at this moment intend to update and publish the results? Response: We will update the review every 6 months, as now clarified on page 5 of the methods section."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1455
|
https://f1000research.com/articles/10-865/v1
|
27 Aug 21
|
{
"type": "Research Article",
"title": "Limitations of care and comorbidities are associated with increased mortality in patients treated with non-invasive ventilation: A retrospective observational study in a single-center ICU.",
"authors": [
"Erik Svensk",
"Jonas Tydén",
"Jakob Walldén",
"Erik Svensk",
"Jonas Tydén"
],
"abstract": "Background: Non-invasive ventilation (NIV) is a common treatment for acute respiratory failure in intensive care units (ICU). While there is increasing data on outcomes after NIV treatment, there are large variations in staffing and monitoring where NIV is provided, making results hard to generalize. The aim of this study was to characterize patients treated with NIV, describe outcomes, and identify factors associated with outcome in an ICU at a Swedish county hospital.\nMethods: A single-centre retrospective observational study during 2018 of patients treated with NIV in a six-bed ICU at a Swedish county hospital. Patient characteristics, including comorbidities, details of ICU stay, simplified acute physiology score (SAPS-3), details of NIV treatment and 30-day mortality were collected, and the Charlson co-morbidity index (CCI) was calculated. Primary outcomes were 30-day mortality and associated factors.\nResults: 92 patients with mean age (71,3, SD 12,1) were treated with NIV during the study period. 42 (46%) were women. Median CCI was 3 (25th-75th percentiles 1.4)) and median SAPS-3 score was 66 (25th-75th percentiles 58). The 30-day mortality was 37% and in the univariate analysis, SAPS-3 score >66, Charlson comorbidity index, CCI>=3, pCO2 <5.5 and limitation of care were factors associated with increased 30-day mortality. pH <7.35 and pO2<8 at admission showed no associations with 30-day mortality.\nConclusions: We found that patients treated with NIV in ICU were a diverse population where comorbidities and presence of limitations of care might be considered as better predictors of 30-day mortality, rather than physiological parameters.",
"keywords": [
"Critical Care",
"Noninvasive Ventilation",
"Mortality",
"Withholding treatment"
],
"content": "Introduction\n\nNon-invasive ventilation (NIV), i.e. respiratory support through a non-invasive interface such as a facemask or nasal prongs, is an evolving therapy with a broad application in intensive care units (ICU)1–3. NIV reduces the risks related to invasive mechanical ventilation in patients with acute respiratory failure in e.g. chronic obstructive pulmonary disease (COPD) and pneumonia4. Further, NIV improves survival after pulmonary oedema and respiratory failure of different aetiologies5–8.\n\nA delayed start of NIV increases mortality9. Improper selection of patients and continuing treatment when NIV is not sufficient leads to unnecessary harm to the patients and delayed intubation and invasive mechanical ventilation, which is associated with increased mortality10.\n\nThe selection of patients who would benefit from an ICU-admission with NIV-treatment is often difficult, as the patients often present with a complex clinical picture11. For decision support, there are several models that predict ICU outcome, such as the Simplified Acute Physiology Score (SAPS-3)12 and the Acute Physiology and Chronic Health Evaluations (APACHE II)13. Further, the Charlson comorbidity index (CCI)14, a frequently used measure of comorbidity, is also able to predict mortality15,16 Patients treated with NIV frequently have “do not intubate” (DNI) orders17,18. It has been shown that the patients with DNI orders treated with NIV for acute respiratory failure who survive have similar life quality after three months compared to patients without limitations of care19.\n\nThe settings in which NIV is utilized differs between hospitals and countries where NIV is being increasingly used outside of the ICU4,20. The outcome for patients treated with NIV in the acute care setting for specific diagnoses has been extensively studied7. However, there is limited knowledge of the outcomes in a mixed population receiving non-invasive ventilation at an ICU.\n\nThe aim of this study was to describe mortality after NIV at a Swedish county hospital and to identify factors associated with mortality.\n\n\nMethods\n\nA retrospective observational single-centre study conducted in a six-bed ICU at a county hospital (250-bed, Sundsvall, Sweden). Patients >18 years who received NIV in the ICU from January 2018 to December 2018 were included in the study. The study was approved by the Swedish Ethical Review Authority, Uppsala, Sweden (2019-04564, 2019-09-27) and patient consent was waived. The study protocol was performed in accordance with relevant guidelines and the study was registered in clinicaltrials.gov (NCT04115969).\n\nOut of the 547 ICU-admissions during 2018, eligible patients were identified in the local ICU-registry. If a patient had more than one ICU-admission during 2018, only the first admission was included. Data sources were medical records, laboratory records, the local ICU-registry and ICU-charts. Variables collected were patient characteristics, admission status (diagnosis, laboratory findings and risk-scoring), details of ventilatory support, arterial blood-gases, limitation-of-care decisions, and 30-day mortality. Further, overall 30-day mortality and the number of patients with limitations of care was retrieved for all patients admitted to the ICU during 2018.\n\nThe SAPS-3 and APACHE-II-scores were retrieved from the local ICU-registry. The scores were validated for each patient by a review of the records.\n\nCharlson comorbidity index (CCI) was used to quantify comorbidities and the CCI was calculated with weighting (according to the original study), with a maximum score of 3314.\n\nAll variables were registered in an anonymized spreadsheet (Excel, version 1902; Microsoft Excel, RRID:SCR_016137. A free alternative software is Google sheets). Data are presented as numbers (rates), mean (standard deviation, SD) or medians (25th-75th percentiles) as appropriate.\n\nThe dichotomisation of continuous variables was based on deviations from the normal values (pH<7.35, pO2=<8 kPa, pCO2>5.5 kPa), clinically relevant cut-off points (CCI>=3, RLS (Reaction level scale) >3) or if no data for the decision was available, the median value (SAPS-3).\n\nUnivariate analysis was performed using the Chi-2 test to analyse factors associated with 30-day mortality and presented as unadjusted odds-ratios with a corresponding 95% confidence interval. P-values lower than 0.05 were considered statistically significant.\n\nThe statistical analyses were performed using SPSS version 25.0 (IBM SPSS Statistics, RRID:SCR_019096). An open-source alternative software is R, which can perform equivalent functions (R Project for Statistical Computing, RRID:SCR_001905).\n\n\nResults\n\nThe inclusion of patients is presented in Figure 1. 92 patients were treated with NIV during the study period. The mean age was 71 years (SD 12) and 42 (46%) patients were females. Reason for admission to the ICU included respiratory (n=82; 87%) and/or cardiac causes (n=36; 38%). 30 patients (32%) were admitted from the emergency department, 56 (60%) from a hospital ward, 6 (6%) from the operating theatre and 2 (2%) from other ICUs. Further patient characteristics are presented in Table 1.\n\nData are presented as numbers (%) or median (25th–75th percentile). The Mann-Whitney-U test and the Chi-2 test was used for continuous and categorical variables, respectively, to evaluate statistical differences between the groups. ICU=Intensive Care Unit, BMI=Body mass index, CCI=Charlson comorbidity index, ∙SAPS 3=Simplified Acute Physiology Score, RLS=Reaction Level Scale, N.A=not applicable\n\nThe main comorbidities were chronic heart failure (n=44; 48%), chronic obstructive pulmonary disease (COPD) (n=42; 46%), diabetes mellitus (n=35; 38%), previous myocardial infarction (n=27; 29%), and cerebrovascular disease (n=15; 16%). 11 patients (12%) had a CCI of 0, 33 patients (35%) a CCI of 1 or 2, and 50 patients (54%) a CCI>=3.\n\nThe median time spent in the ICU was 1.8 (0.8–5.0) days and the median duration of NIV-treatment was 17 (6–34) hours. 24 patients (26%) were also treated with invasive ventilation during the ICU stay. A total of 38 patients (41%) had limitations of care. 34 (36%) with 'no intubation' and 37 (39%) 'no CPR'. Further details of the ICU stay are presented in Table 2.\n\nData presented as number (%) or median (25th–75th percentiles). The Mann-Whitney-U test and the Chi-2 test was used for continuous and categorical variables, respectively, to evaluate statistical differences between the groups. ICU-Intensive Care unit; CPR-Cardiopulmonary resuscitation; NIV-Non-invasive ventilation; IPAP-Inspiratory positive airway pressure; EPAP Expiratory positive airway pressure\n\nThe 30-day mortality in the study cohort was 37% (n=34). In the univariate analysis, SAPS-3 score >66, CCI >=3, pCO2 <5.5 kPa and limitations of care were factors associated with an increased 30-day mortality, see Table 3.\n\nSAPS 3, Simplified acute physiology score; CI, Confidence interval; CCI, Charlson comorbidity index; BMI, body mass index; RLS, Reaction level scale. For the univariate analysis, the Chi-2 test was used.\n\n30-day mortality for all patients admitted to the ICU during the study period was 21% (n=547). Further, 12% of all patients had limitations of care.\n\n\nDiscussion\n\nOur retrospective study included all patients treated with NIV at a county hospital ICU during one year. We found that one third of these patients had died within 30 days, and the mortality was almost double compared to all patients admitted to the ICU. Further, 30-day mortality was associated with the presence of co-morbidities and limitations of care.\n\nA recent meta-analysis evaluating noninvasive ventilation and survival in acute care settings showed a hospital mortality of 11%7, a much lower mortality than in our cohort. However, there were great variabilities in the studies included in the meta-analysis, regarding the severity and type of conditions treated. A French study evaluating outcome after acute respiratory failure in 14 different ICUs showed a hospital mortality of 30% in patients treated with NIV, which is comparable to our results4. The high mortality in our cohort might also be explained by advanced age, severity of disease, and a high number of patients with limitations of care.\n\nNIV was used in every fifth patient in our ICU, a higher amount number compared to a study of more than thirteen thousand ICU patients, where 4% received NIV21. This might reflect different practices of NIV globally, where NIV more often is used at wards and intermediary units outside the ICU compared to our study setting.\n\nWe found that a high SAPS3-score, a high Charlson Comorbidity Index (CCI), limitation of care and a low pCO2 on admission were associated with an increased mortality. SAPS-3 is a validated score to predict ICU mortality, but when used for patients undergoing NIV in intermediate care units, the prediction accuracy could be lower, but by combining SAPS-3 with patient-risk factors, the mortality prediction can be improved22. This is in line with our results, as we found an association between mortality and co-morbidities.\n\nFurther, several studies identify CCI as a predictor of ICU mortality15,16,23. A study of 347 patients outside an ICU undergoing NIV due to pneumonia concluded that in-hospital mortality was mainly associated with patients' co-morbidities and limitations of care, rather than the degree of acute respiratory failure24. The evidence is conflicting however, as others have not found CCI to be a good predictor for short and medium-term outcomes in patients submitted for NIV due to acute respiratory failure25. However, our data indicates that CCI might be considered as a predictor of mortality in NIV patients in an ICU setting.\n\npCO2 on admission is not included in SAPS3 or APACHE II scoring systems. pCO2 has been studied as a prognostic indicator for patients admitted with pneumonia, but no significant association has been found with mortality26. We found that patients with a high pCO2 had a lower mortality. This might either be explained by a suggested mortality benefit with NIV treatment in hypercapnic COPD patients6 or that patients with normal or low pCO2 had conditions causing respiratory failure with a higher mortality.\n\n41% of our patients had limitations of care, in contrast to all our ICU patients where only 12% hade limitations of care. The observations are in line with a recent meta-analysis which concluded that 27% of patients with acute respiratory failure had a do-not-intubate order27.\n\nIt is a difficult clinical task to identify patients that would benefit from NIV treatment, and several factors might influence the selection of patients admitted to an ICU28. Since limitations of care are common among these patients, it is important to set clear goals with the NIV treatment29. An older age, ARDS or pneumonia, or failure to improve after one hour of treatment is associated with higher risk of NIV failure in hypoxemic patients30. Better prediction tools that can be used clinically, before the ICU admission, are needed31.\n\nExcept for details of comorbidities, pCO2 and NIV-parameters, our data included the same variables that is sent to/included in the Swedish intensive care registry and this makes it possible to perform similar studies on a national level. However, variables are usually collected during the ICU-stay and many of the variables are not known to the clinician when the decision to start NIV treatment is made. Therefore, a strength with the CCI is that it can be calculated at the time of admission to the ICU, in contrast to physiology-based scores that are dependent on laboratory and bedside clinical data. CCI as a predictor of outcome in the population treated with NIV in ICU has not previously been studied and our study indicates that it might be a usable tool.\n\nOur study has limitations and strengths. Patients treated with NIV are a heterogenous group and NIV was used in many different clinical conditions making it hard to generalize results and our single study setting further decreases external validity. However, even though our study was retrospective, our review of patient records added more variable than included in national intensive care registries. Further, we included almost all patients admitted to our ICU for one year. This is a strength as it reflects a general cohort of patients in the need of NIV treatment.\n\n\nConclusions\n\nWe conclude that patients treated with NIV in ICU are a diverse population where comorbidities and presence of limitations of care might be considered as better predictors of 30-day mortality, rather than physiological parameters.\n\n\nList of abbreviations\n\nAPACHE II, Acute Physiology and Chronic Health Evaluations II\n\nARDS, Acute respiratory distress syndrome\n\nCCI, Charlsons co-morbidity index\n\nCI, Confidence Interval\n\nCOPD, Chronic obstructive pulmonary disease\n\nCPR, Cardiopulmonary resuscitation\n\nDNI, 'do-not-intubate'\n\nICU, Intensive care unit\n\nNIV, Non-invasive ventilation\n\nRLS, Reaction level scale\n\nSAPS 3, Simplified Acute Physiology Score 3\n\nSD, Standard deviation\n\n\nDeclarations\n\nThe study was approved by the Swedish Ethical Review Authority (2019-04564, 2019-09-27) and patient consent was waived.\n\n(Swedish Ethical Review Authority, Box 2110, 750 02 Uppsala, Sweden. registrator@etikprovningsmyndigheten.se)\n\nNot applicable\n\nData in the study could not be fully de-identified, and according to the General Data Protection Regulation (GDPR), they cannot be publicly shared. Further, the Ethical Review Authority only permitted us to publicly share data on a group level. However, the dataset generated and analysed during the current study are available from the corresponding author (jakob.wallden@umu.se) upon reasonable request. The dataset will be edited to comply with regulations to preserve privacy before being released for a limited use.\n\nHarvard dataverse: \"STROBE checklist for 'Limitations of care and comorbidities are associated with increased mortality in patients treated with non-invasive ventilation: A retrospective observational study in a single-center ICU.' https://doi.org/10.7910/DVN/BMQDZ0\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Author contributions\n\n\n\nES and JW are the main contributions to the concept and design of the study. ES is the main author working with the review of patient charts, collection of data and analysis. ES drafted the manuscript, including the tables, with substantial revisions and feedback from JW and JT. All authors have read and approved the final version of the manuscript.\n\n\nAuthors' information\n\nErik Svensk is a consultant physician in Anaesthesia and Intensive Care at the Department of Anaesthesia and Intensive Care at Sundsvall Hospital, Region Västernorrland, Sundsvall, Sweden.\n\nJonas Tydén, Ph.D., is a consultant physician in Anaesthesia and Intensive Care at the Department of Anaesthesia and Intensive Care at Östersund Hospital, Region Jämtland Härjedalen, Östersund Sweden, Sweden.\n\nJakob Walldén, is a senior lecturer at Umeå University, Sweden and a consultant physician in Anaesthesia and Intensive Care at the Department of Anaesthesia and Intensive Care at Sundsvall Hospital, Region Västernorrland, Sundsvall, Sweden.\n\nThe clinical departments in Sundsvall and Östersund are affiliated to Umeå University, Department of Surgical and Perioperative Sciences, Anaesthesiology and Intensive Care Medicine.\n\n\nReferences\n\nRochwerg B, Brochard L, Elliott MW, et al.: Official ERS/ATS clinical practice guidelines: noninvasive ventilation for acute respiratory failure. Eur Respir J. 2017; 50(2): 1602426. PubMed Abstract | Publisher Full Text\n\nDemoule A, Chevret S, Carlucci A, et al.: Changing use of noninvasive ventilation in critically ill patients: trends over 15 years in francophone countries. Intensive Care Med. 2016; 42(1): 82–92. PubMed Abstract | Publisher Full Text\n\nNava S, Navalesi P, Gregoretti C: Interfaces and humidification for noninvasive mechanical ventilation. Respir Care. 2009; 54(1): 71–84. PubMed Abstract\n\nSchnell D, Timsit JF, Darmon M, et al.: Noninvasive mechanical ventilation in acute respiratory failure: trends in use and outcomes. Intensive Care Med. 2014; 40(4): 582–91. PubMed Abstract | Publisher Full Text\n\nBerbenetz N, Wang Y, Brown J, et al.: Non-invasive positive pressure ventilation (CPAP or bilevel NPPV) for cardiogenic pulmonary oedema. Cochrane Database Syst Rev. 2019; 4(4): CD005351. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOsadnik CR, Tee VS, Carson-Chahhoud KV, et al.: Non-invasive ventilation for the management of acute hypercapnic respiratory failure due to exacerbation of chronic obstructive pulmonary disease. Cochrane Database Syst Rev. 2017; 7(7): CD004104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCabrini L, Landoni G, Oriani A, et al.: Noninvasive ventilation and survival in acute care settings: a comprehensive systematic review and metaanalysis of randomized controlled trials. Crit Care Med. 2015; 43(4): 880–8. PubMed Abstract | Publisher Full Text\n\nChiumello D, Chevallard G, Gregoretti C: Non-invasive ventilation in postoperative patients: a systematic review. Intensive Care Med. 2011; 37(6): 918–29. PubMed Abstract | Publisher Full Text\n\nJayadev A, Stone R, Steiner MC, et al.: Time to NIV and mortality in AECOPD hospital admissions: an observational study into real world insights from National COPD Audits. BMJ Open Respir Res. 2019; 6(1): e000444. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsquinas AM: Noninvasive mechanical ventilation: theory, equipment, and clinical applications. 2nd ed. 2016. Publisher Full Text\n\nMehta AB, Douglas IS, Walkey AJ: Evidence-based Utilization of Noninvasive Ventilation and Patient Outcomes. Ann Am Thorac Soc. 2017; 14(11): 1667–73. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMetnitz PGH, Moreno RP, Almeida E, et al.: SAPS 3--From evaluation of the patient to evaluation of the intensive care unit. Part 1: Objectives, methods and cohort description. Intensive Care Med. 2005; 31(10): 1336–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKnaus WA, Draper EA, Wagner DP, et al.: APACHE II: a severity of disease classification system. Crit Care Med. 1985; 13(10): 818–29. PubMed Abstract\n\nCharlson ME, Pompei P, Ales KL, et al.: A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. J Chronic Dis. 1987; 40(5): 373–83. PubMed Abstract | Publisher Full Text\n\nChristensen S, Johansen MB, Christiansen CF, et al.: Comparison of Charlson comorbidity index with SAPS and APACHE scores for prediction of mortality following intensive care. Clin Epidemiol. 2011; 3: 203–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStavem K, Hoel H, Skjaker SA, et al.: Charlson comorbidity index derived from chart review or administrative data: agreement and prediction of mortality in intensive care patients. Clin Epidemiol. 2017; 9: 311–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFernandez R, Baigorri F, Artigas A: Noninvasive ventilation in patients with \"do-not-intubate\" orders: medium-term efficacy depends critically on patient selection. Intensive Care Med. 2007; 33(2): 350–4. PubMed Abstract | Publisher Full Text\n\nWilson ME, Majzoub AM, Dobler CC, et al.: Noninvasive Ventilation in Patients With Do-Not-Intubate and Comfort-Measures-Only Orders: A Systematic Review and Meta-Analysis. Crit Care Med. 2018; 46(8): 1209–16. PubMed Abstract | Publisher Full Text\n\nAzoulay E, Kouatchet A, Jaber S, et al.: Noninvasive mechanical ventilation in patients having declined tracheal intubation. Intensive Care Med. 2013; 39(2): 292–301. PubMed Abstract | Publisher Full Text\n\nCabrini L, Moizo E, Nicelli E, et al.: Noninvasive ventilation outside the intensive care unit from the patient point of view: a pilot study. Respir Care. 2012; 57(5): 704–9. PubMed Abstract\n\nMetnitz PG, Metnitz B, Moreno RP, et al.: Epidemiology of mechanical ventilation: analysis of the SAPS 3 database. Intensive Care Med. 2009; 35(5): 816–25. PubMed Abstract | Publisher Full Text\n\nMartinez-Urbistondo D, Alegre F, Carmona-Torre F, et al.: Mortality Prediction in Patients Undergoing Non-Invasive Ventilation in Intermediate Care. PLoS One. 2015; 10(10): e0139702. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYıldız A, Yiğit A, Benli AR: The prognostic role of Charlson comorbidity index for critically ill elderly patients. Eur Res J. 2020; 6(1): 67–72. Publisher Full Text\n\nBrambilla AM, Prina E, Ferrari G, et al.: Non-invasive positive pressure ventilation in pneumonia outside Intensive Care Unit: An Italian multicenter observational study. Eur J Intern Med. 2019; 59: 21–6. PubMed Abstract | Publisher Full Text\n\nMeireles M, Machado A, Lopes J, et al.: Age-adjusted Charlson Comorbidity Index Does Not Predict Outcomes in Patients Submitted to Noninvasive Ventilation. Arch Bronconeumol (Engl Ed). 2018; 54(10): 503–9. PubMed Abstract | Publisher Full Text\n\nYassin Z, Saadat M, Abtahi H, et al.: Prognostic value of on admission arterial PCO 2 in hospitalized patients with community-acquired pneumonia. J Thorac Dis. 2016; 8(10): 2765–71. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilson ME, Mittal A, Karki B, et al.: Do-not-intubate orders in patients with acute respiratory failure: a systematic review and meta-analysis. Intensive Care Med. 2020; 46(1): 36–45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOrsini J, Butala A, Ahmad N, et al.: Factors influencing triage decisions in patients referred for ICU admission. J Clin Med Res. 2013; 5(5): 343–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCurtis JR, Cook DJ, Sinuff T, et al.: Noninvasive positive pressure ventilation in critical and palliative care settings: understanding the goals of therapy. Crit Care Med. 2007; 35(3): 932–9. PubMed Abstract | Publisher Full Text\n\nAntonelli M, Conti G, Moro ML, et al.: Predictors of failure of noninvasive positive pressure ventilation in patients with acute hypoxemic respiratory failure: a multi-center study. Intensive Care Med. 2001; 27(11): 1718–28. PubMed Abstract | Publisher Full Text\n\nBlanch L, Abillama FF, Amin P, et al.: Triage decisions for ICU admission: Report from the Task Force of the World Federation of Societies of Intensive and Critical Care Medicine. J Crit Care. 2016; 36: 301–305. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "92977",
"date": "24 Sep 2021",
"name": "John Botha",
"expertise": [
"Reviewer Expertise 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 has all the limitations of a single centre retrospective study. The conclusions that can be drawn are limited and unlikely to provide assistance to clinicians in critical care.\nIn this, centre NIV ventilation appears to be the default mode of ventilatory support for patients who will not have their level of care escalated. The mortality of patients in the study was over 30% and this indicates a cohort of patients that were critically ill. The study would be more informative if only patients destined for active care were included in the study.\nI would suggest that the sample size be increased over time and that only patients that did not have limitations of care be included.\nThe hours of NIV in the non survivors was minimal suggesting they were pre terminal prior to the initiation of ventilation.\nIf the study were to be indexed in its current form the reasons as to why so many patients were NFR would strengthen the study. I consider the study able to be indexed if these changes were made.\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? Yes",
"responses": []
},
{
"id": "93878",
"date": "18 Oct 2021",
"name": "Hans-Henrik Bülow",
"expertise": [
"Reviewer Expertise non-invasive ventilation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper describes data of one year (2018) of treatment with non-invasive ventilation (NIV) in a single center ICU. The paper is well written with sufficient data to get an impression of the results and conclusions that the authors draw, but there are a number of reservations.\nThe first reviewer has pointed out the general problem with a single center retrospective study like this one, and I agree. I also agree with the first reviewer that it would be interesting to describe why so many patients had limitations.\nThere are 3 issues that, in my opinion, are lacking in this paper, before it can be indexed.\nI do not understand why only the first admission during the data sampling period is included. COPD patients so ill that they need admittance to an ICU are generally in the last period of their disease before death – and their 2nd and any other following admissions is also part of the picture of non-invasive ventilation in an ICU.\n\nThree patients below 18 years are not included in the dataset. As this is just a description of treatment already done in the ICU, I see no reservations with regard to ethics concerning treatment of children/adolescents – and data on NIV and children are not as well described as with adults – something might be learned here.\n\nUnfortunately, the authors only note that 26% of the patients were also treated with invasive ventilation – but this information is of very little value as it is not noted if it was before or after NIV or perhaps both before and after? Different outcomes are often seen whether NIV has to be changed into invasive ventilation because of insufficient ventilation of the patient – or whether NIV is used as “a bridge” to spontaneous breathing after a course of invasive ventilation.\n\nThe authors have one interesting finding which I think they should elaborate on: Patients with a pCO2 below 5.5 had higher mortality than those with higher pCO2s. Most likely these patients suffered from pneumonia (and not COPD) and pneumonia is very difficult to treat with NIV.\nIf these patients did not have limitations, they should probably have been changed to invasive ventilation earlier. If these patients had limitations in the form of “do-not-intubate”, then NIV was their last possibility for treatment, and it is not surprising that they died. These data are worth looking into.\nThe authors write in the discussion section: “Older age, ARDS, pneumonia or failure to improve after one hour of NIV treatment is associated with higher risk of NIV failure ---- better prediction tools are needed” I do not agree with this conclusion. I believe that with the reservations towards NIV that the authors do note, then we have the tools to predict fairly well if NIV treatment has a chance of being successful. But CCI may be an interesting tool to do further research on.\nI am not too happy about the conclusion: “limitation of care is associated with higher mortality”.. e.g., the Ethicus-II study with data from 2016 from a number of European ICU’s has just shown, that an increase in number of limitations in 2016 did not lead to higher mortality compared to data from the same ICU’s in 1999. (Please see Reference 1).\nWith regard to references I would not refer to papers from acute care, as this is often a very different setting and different patient cases compared to the ICU setting.\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? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-865
|
https://f1000research.com/articles/10-863/v1
|
27 Aug 21
|
{
"type": "Research Article",
"title": "Technology readiness and UTAUT2 in e-wallet adoption in a developing country",
"authors": [
"Min Yee Leong",
"Jing Hui Kwan",
"Lai Ming Ming",
"Min Yee Leong",
"Jing Hui Kwan"
],
"abstract": "Background: An e-wallet is a digital equivalent of a physical wallet which plays an essential role in payment system transformation. To embrace the concept of a cashless society, the Malaysian Government and central bank have taken various steps to encourage the adoption of e-wallets. Despite the seamless services offered by the e-wallet, it is yet to reach high-scale adoption in Malaysia. This study aims to investigate Malaysians’ readiness towards the e-wallet and their perceptions of it by employing the UTAUT2 model. Methods: A total of 309 valid data were gathered and analysed with partial least squares structural equation modelling (PLS-SEM). Results: The findings revealed that the respondents were confident about the new technology and tended to believe that e-wallet was somehow useful for them. The results also disclosed that e-wallet adoption intention was significantly influenced by performance expectancy, price value, facilitating conditions, and followed closely by social influence. Nonetheless, insecurity did not present significant impact on both performance expectancy and effort expectancy of e-wallet. Conclusions: This study provides a substantial contribution to the knowledge domain by combining system-specific and individual-specific models in an e-wallet context. The outcomes of this study would also benefit e-wallet service providers and policymakers by delivering holistic insight into Malaysians’ readiness and adoption behaviour of the e-wallet.",
"keywords": [
"e-wallet",
"UTAUT2",
"cashless payment",
"technology readiness",
"Malaysia"
],
"content": "Introduction\n\nThe evolution of payment system is always in the spotlight and making the impossible come true such as cashless, card-less, and even contactless. Electronic wallets (e-wallets) appeared to be one of the famous examples of technology innovation in payment solutions. Back in 2011, the central bank, Bank Negara Malaysia proposed a ten-year masterplan called the Financial Sector Blueprint (FSBP) to provide a roadmap to further advance the country’s financial system (Bank Negara Malaysia, 2011). One of the agenda items is to increase the offering and adoption of electronic payments (e-payments). As part of e-payments, the use of the e-wallet is welcomed in Malaysia as the country aims to move towards a cashless society. Bank Negara Malaysia has put various efforts in place such as guidelines on Interoperable Credit Transfer Framework (ICTF) and Electronic Money (E-Money) to encourage the adoption of e-wallets. In the year 2019, the government provided a one-off RM30 incentive for all eligible Malaysians in Budget 2020 and RM100 incentive for the youths in Budget 2021 to accelerate e-wallet adoption in the year 2020 (Bank Negara Malaysia, 2019; Goverment of Malaysia, 2020).\n\nNevertheless, as reported by Nielsen Malaysia (2019), the e-wallet adoption rate in Malaysia is as low as 8%. It seems like Malaysians are not ready for a transformation despite the high financial literacy (95% of Malaysians are banked), high smartphone usage (91%) and Internet penetration (90.1%) in 2019 (Department of Statistics Malaysia, 2019; Touch’N Go eWallet, 2019).\n\nGiven these facts, the Government and e-wallet service providers are facing challenges in attracting Malaysians to adopt e-wallets as a daily payment tool. Convincing people to use new technology is not a simple process as human thinking and behaviour are a complex process. Along this line, this study comprehensively integrated two models, namely technology readiness with Unified Theory of Acceptance and Use of Technology (UTAUT2), to understand Malaysian users’ readiness and perceptions towards the e-wallet.\n\nTechnology readiness is defined as a person’s propensity to embrace and use specific new technology for accomplishing life and work-related goals (Parasuraman, 2000, p. 308). It consists of four dimensions which can be categorized into two scopes, namely: positive enablers (optimism and innovativeness) and negative inhibitors (discomfort and insecurity) to measure human reactions (Parasuraman, 2000a). Parasuraman (2000, p. 311) describes optimism as “a positive view of technology”; innovativeness as “A tendency to be a technology pioneer and thought leader”; discomfort as “a perceived lack of control over technology and a feeling of being overwhelmed by it”; lastly, insecurity as “distrust of technology and skepticism about its ability to work properly”.\n\nBack in 2005, a new model named “TRAM” which is an integrated model of Technology Acceptance Model (TAM) and technology readiness was presented by Lin, Shih, Sher, & Wang (2005) to carry out a research regarding e-service adoption in Taiwan. The reason that led the authors to the combination is that TAM is system-specific whereas technology readiness is individual-specific, and therefore, they believed that they are interrelated. Extant research has incorporated technology readiness and technology adoption model to explain users’ readiness and perceptions toward financial technology (Walczuch, Lemmink, & Streukens, 2007), electronic human resource management (Erdoǧmu & Esen, 2011), electronic health record system (Godoe & Johansen, 2012; Kuo, Liu, & Ma, 2013), web-based attendance management system (Nugroho & Fajar, 2017) and mobile payment system (Rahman, Taghizadeh, Ramayah, & Alam, 2017).\n\nUTAUT2 developed by Venkatesh, Thong, & Xu (2012), is the extension of UTAUT (Venkatesh, Morris, Davis, & Davis, 2003). UTAUT2 consists of seven core constructs namely performance expectancy, effort expectancy, facilitating conditions, social influence, and three additional constructs: price value, habit, and hedonic motivation to explain one’s perceptions toward technology from the consumer view (Venkatesh et al., 2012). Performance expectancy is defined as “the degree to which a person believes that using the system will help him or her to attain gains in job performance” (Venkatesh et al., 2003, p. 447); effort expectancy is defined as “the degree of ease associated with the use of the system which reflects user perception of the difficulty when using a specific technology (Venkatesh et al., 2003, p. 405); facilitating conditions is defined as “the degree to which a person believes that an organisational and technical infrastructure exists to support the use of the system” (Venkatesh et al., 2003, p. 453); social influence is defined as “the degree to which a person perceives that important others believe he or she should use the new system” (Venkatesh et al., 2003, p. 451); hedonic motivation is defined as “the pleasure or fun derived from technology use” (Brown & Venkatesh, 2005; Venkatesh et al., 2012, p. 161); lastly, price value is defined as “the trade-offs between the perceived benefits and cost of using a specific technology” (Venkatesh et al., 2012, p.161).\n\nCompared to UTAUT, the improvements made in UTAUT2 have established a significant enhancement in describing the variability of behavioural intention (18% increase) and use behaviour (12% increase) (Venkatesh et al., 2012). It can be said that UTAUT2 consists of the essences of the recognized theories. UTAUT3 is not considered in this study as the additional construct of UTAUT3: personal innovativeness is already involved in the technology readiness model.\n\nThe proposed research framework is portrayed in Figure 1. The research framework proposed that the personality traits of technology readiness are interrelated with performance expectancy and effort expectancy from UTAUT2. Building on the literature of the TRAM model, this study postulated the following hypotheses:\n\nH1: Optimism positively influences performance expectancy (a) and effort expectancy (b) of e-wallets among Malaysians.\n\nH2: Innovativeness positively influences performance expectancy (a) and effort expectancy (b) of e-wallets among Malaysians.\n\nH3: Discomfort negatively influences performance expectancy (a) and effort expectancy (b) of e-wallets among Malaysians.\n\nH4: Insecurity negatively influences performance expectancy (a) and effort expectancy (b) of e-wallets among Malaysians.\n\nExtant research has applied UTAUT2 to explain user adoption of e-wallets (Tang, Lai, Law, Liew, & Phua, 2014), mobile payments (Hussain, Mollik, Johns, & Rahman, 2019; Kalinic, Marinkovic, Molinillo, & Liébana-Cabanillas, 2019; Liébana-Cabanillas, Molinillo, & Ruiz-Montañez, 2019; Morosan & DeFranco, 2016; Oliveira et al., 2016; Sivathanu, 2019), mobile banking (Alalwan et al., 2017), and mobile financial services (Rahman et al., 2017). The construct “habit” was eliminated as one should have rich experience in using such technology in order to allow examination of the “habit” role (Alalwan, Dwivedi, & Rana, 2017; Oliveira, Thomas, Baptista, & Campos, 2016). Therefore, the following hypotheses were derived:\n\nH5-H10: Performance expectancy (H5), effort expectancy (H6), facilitating conditions (H7), social influence (H8), hedonic motivation (H9) and price value (H10) positively influences behavioural intention to adopt e-wallets among Malaysians.\n\nH11: Behavioral intention to adopt positively influences e-wallet adoption among Malaysians.\n\n\nMethods\n\nThe sample of this study is Malaysian e-wallet users. To acquire the empirical data needed to verify the research model, a structured questionnaire was adopted. The questionnaire consisted of three sections. Section A consisted of five screening questions related to the respondents’ e-wallet usage status to ensure that they were e-wallet users. The questions included have they ever used an e-wallet, what types of e-wallet are they using, when are they using e-wallets, how long have they been using e-wallets, and how frequently do they use e-wallets per month. Section B consisted of a 16-item Technology Readiness Index 2.0 scale adapted from Parasuraman & Colby (2014) to measure technology readiness and the last section consisted of a 26-item UTAUT2 scale adapted from Venkatesh et al. (2003, 2012). A seven-point Likert scale ranging from 1 (strongly disagree) to 7 (strongly agree) was considered.\n\nPrior to the actual questionnaire distribution, a pilot study was carried out in the Multimedia Super Corridor (MSC) area to explore issues pertaining to the quality of the questions that could arise. A total of 49 valid responses were gathered and analysed using partial least squares structural equation modelling (PLS-SEM). The results reveal that one item from innovativeness construct need to be omitted because of low outer loadings. Hence, it was not considered in the actual questionnaire to ensure the consistency and accuracy of the items in measuring the constructs.\n\nThe actual data collection was conducted in Kuala Lumpur, Penang, Ipoh, Johor Bahru, and Melaka as they are the fastest-growing cities in the country, indicating high merchant acceptance of e-wallet payment which would allow the desired respondents to be precisely reached (Gregory, 2018). The data collection involved conducting face-to-face communication with the respondents in 2019. To ensure the respondents were actual users of e-wallets, the targeted respondents for this study were practically reached by monitoring from afar their payment methods at the cashiers in the shopping malls whether e-wallet payments were used or not. Then, the researcher approached and invited these respondents to participate in this study. Written and verbal consent were sought from participants prior to conducting the survey. This survey had obtained approval number of EA1852021 from Research Ethics Committee of Multimedia University. The respondents were politely requested to answer the questions from a Google Form on a tablet. Within a two-month period (June and July 2019), 309 valid responses were gathered and used for further analysis. The data analysis was carried out using two software, namely IBM SPSS Statistics Version 22.0 and SmartPLS. IBM SPSS Statistics Version 22.0 was mainly employed for data screening and descriptive analysis of the profile of respondents usage frequency and percentage while SmartPLS was used for Partial Least Squares Structural Equation Modelling (PLS-SEM) evaluation.\n\n\nResults\n\nIBM SPSS Statistics Version 22.0 was utilized to assess the demographic details such as gender, age, employment status and highest level of academic qualification of the sample respondents and their e-wallet usage status. It was found that the responses were made up of 120 male respondents and 189 female respondents. 74.4% of the respondents are from 18 – 34 years old range. With respect to employment status, 70.9% of them were employed full time. Among all the valid responses, 27.5% of them are degree holders and 21.7% of them qualified at “Sijil Pelajaran Malaysia or also known as SPM or below. It is worth noting that ‘Sijil Pelajaran Malaysia’ is equivalent to O-level certificate.\n\nBased on the responses on the e-wallet usage status, Touch n’ Go e-wallet was found to be the most popular e-wallet with nearly 29.4% reporting using it. Majority of the respondents use e-wallet for transportation transaction (24.4%) and food and beverage transaction (21.4%). 35.9% of the respondents reported having one to six months usage experience. In terms of the frequency of e-wallet usage, 17.5% of the respondents were light users while 17.5% of the respondents were heavy users who used e-wallet more than eight times a month.\n\nTo estimate and test the causal relations, partial least squares structural equation modelling (PLS-SEM) was considered because of its appropriateness in prediction purpose, exploratory study, and complex structural models (Hair, Ringle, & Sarstedt, 2011).\n\nThe reliability and validity of the constructs were first assessed. Based on the evaluation using SmartPLS, the outer loadings of all items above 0.708, except for INS1 (0.178), INS2 (0.388), and INS3 (0.553) of insecurity. The Average Variance Extracted (AVE) of insecurity was 0.329 which is under the acceptable value of 0.5. Hence, the indicator with the lowest loading, INS1 was deleted and the analysis was reconducted. The results in Table 1 showed that all the remaining indicators of insecurity achieved a satisfactory level for both outer loadings and AVE after removing INS1. The Composite Reliability (CR) values were also found to be above 0.867, indicating that the recommended CR value of 0.60 for exploratory research by Hair, Hult, Ringle, & Sarstedt (2016) was met.\n\nThe discriminant validity was analysed. It was found that all the Heterotrait-Monotrait ratios (HTMT) were found to be lower than 0.85, indicating the criteria of Kline (011) is fulfilled. Overall, the criteria of reliability and validity had been achieved at this stage of evaluation.\n\nBefore testing the hypotheses, the lateral collinearity issues were examined. All the Variance Inflation Factor (VIF) values were found to be below 2.503, suggesting that the issue of lateral collinearity is not a concern for this study.\n\nIn the path coefficients’ significance testing, bootstrapping was used to calculate the t-values with 5000 subsamples as the higher the number of subsamples, the higher the accuracy of the results (Hair et al., 2016). As shown in Table 2, all the relationships were found to have t-values of at least 1.617, and thus, significant at 0.10 level of significance, except for H4a and H4b. In the coefficient of determination (R2) assessment, it was found that all the R2 values are above the threshold value of 0.26, indicating that the model is substantial.\n\nNote: ***p < 0.01, **p < 0.05, *p < 0.10.\n\nNext, the effect sizes (f2) of the constructs are evaluated. The value of 0.02, 0.15, and 0.35 signify small, medium, and large effects (Cohen, 1988). Based on the results, it was found that optimism had a medium impact on performance expectancy. The effect size values of performance expectancy, facilitating conditions, social influence, and price value indicated small effects on behavioural intention to adopt. The remaining constructs did not exhibit adequate effects on behavioural intention to adopt.\n\nPredictive relevance was also assessed to predict the visible indicator of the constructs in the model which can be evaluated through Q2 value (Stone, 1974). The results showed that all the Q2 values are higher than 0, implying that the model possesses a predictive relevance.\n\n\nDiscussion\n\nThe results revealed that the respondents had strong positive feelings towards new technology, where they are hopeful about the usefulness of e-wallets. Additionally, the results showed that e-wallet adoption intention is strongly influenced by performance expectancy, price value, facilitating conditions followed closely by social influence, meaning that helpfulness, value gained, availability of facilitative assistance, and peer influence in using e-wallets are the decisive factors of usage intention among Malaysian e-wallet users. Nevertheless, the relationships between insecurity and performance expectancy and effort expectancy were found not to be significant. It can be said that even though some users feel anxious about new technology, it would not have any impact on the usefulness and ease of use of e-wallets.\n\nThe outcomes of this study offer valuable insights about the personality of Malaysian e-wallet users and their perceptions about e-wallets. Policymakers and e-wallet service providers could gain from the results of this study by learning and better understanding the way users behave and their needs and wants, and therefore, place necessary effort to enhance the use and adoption of e-wallets.\n\n\nData availability\n\nFigshare: E_wallet_adoption.csv, https://doi.org/10.6084/m9.figshare.14871048.v1 (Leong et al., 2021).\n\nThe project contains the following underlying data:\n\n- E_wallet_adoption.csv\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor contributions\n\nKwan, J. H. and Lai, M. M. were involved in overall direction and planning and supervised the work. Leong, M. Y. developed the research framework, carried out the implementation and analysed the data. Leong, M. Y. wrote the manuscript with input from all authors.",
"appendix": "Acknowledgment\n\nThe authors wish to thank to all participants and Multimedia University for the supports in making this study possible.\n\n\nReferences\n\nAlalwan AA, Dwivedi YK, Rana NP: Factors influencing adoption of mobile banking by Jordanian bank customers: Extending UTAUT2 with trust. Int J Information Management. 2017; 37(3): 99–110. Publisher Full Text\n\nBagla RK, Sancheti V: Gaps in customer satisfaction with digital wallets: challenge for sustainability. J Management Devel. 2018; 37(6): 442–451. Publisher Full Text\n\nBank Negara Malaysia: Financial Sector Blueprint 2011–2020. 2011.\n\nBank Negara Malaysia: Budget. 2019: 2020.\n\nBrown SA, Venkatesh V: Model of Adoption of Technology in Households: A Baseline Model Test and Extensuin Incorporation Household Life Cycle. MIS Quarterly. 2005; 29(3): 399–426. Publisher Full Text\n\nCohen J: The effect size. Statistical Power Analysis for the Behavioral Sciences. 1988: 77–83.\n\nDepartment of Statistics Malaysia: ICT Use and Access By Individuals and Households Survey Report. 2019. Reference Source\n\nErdoǧmu N, Esen M: An investigation of the effects of technology readiness on technology acceptance in e-HRM. 7th International Strategic Management Conference. 2011; Vol. 24, pp. 487–495. Publisher Full Text\n\nGodoe P, Johansen TS: Understanding adoption of new technologies. J Europ Psychol Students. 2012; 3: 38–53. Publisher Full Text\n\nGoverment of Malaysia: Budget 2021 Touchpoints. 2020. Reference Source\n\nGregory S: Biggest Cities In Malaysia.2018. Reference Source\n\nHair JF, Hult GTM, Ringle C, et al.: A primer on partial least squares structural equation modeling (PLS-SEM). Sage; 2016.\n\nHair JF, Ringle CM, Sarstedt M: PLS-SEM: Indeed a silver bullet. J Marketing Theory Practice. 2011; 19(2): 139–152. Publisher Full Text\n\nHussain M, Mollik AT, Johns R, et al.: M-payment adoption for bottom of pyramid segment: an empirical investigation. Int J Bank Marketing. 2019; 37(1): 362–381. Publisher Full Text\n\nKalinic Z, Marinkovic V, Molinillo S, et al.: A multi-analytical approach to peer-to-peer mobile payment acceptance prediction. J Retailing Consumer Services. 2019; 49: 143–153. Publisher Full Text\n\nKline RB: Principles and practice of structural equation modeling. New York: Guilford Publications; 2011.\n\nKuo KM, Liu CF, Ma CC: An investigation of the effect of nurses’ technology readiness on the acceptance of mobile electronic medical record systems. BMC Med Inform Decis Mak. 2013; 13(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeong MY, Kwan JH, Lai M-M: E_wallet_adoption.csv. figshare. Dataset. 2021. Publisher Full Text\n\nLiébana-Cabanillas F, Molinillo S, Ruiz-Montañez M: To use or not to use, that is the question: Analysis of the determining factors for using NFC mobile payment systems in public transportation. Technological Forecasting and Social Change. 2019; 139(August): 266–276. Publisher Full Text\n\nLin CH, Shih HY, Sher PJ, et al.: Consumer adoption of e-Service: Integrating technology readiness with the technology acceptance model. Portland International Conference on Management of Engineering and Technology. 2005; (pp. 483–488). Publisher Full Text\n\nMorosan C, DeFranco A: It’s about time: Revisiting UTAUT2 to examine consumers’ intentions to use NFC mobile payments in hotels. Int J Hospitality Management. 2016; 53: 17–29. Publisher Full Text\n\nNielsen Malaysia: Cash or cashless? Malaysia’s shifting payment landscape. 2019.\n\nNugroho MA, Fajar MA: Effects of Technology Readiness Towards Acceptance of Mandatory Web-Based Attendance System. 4th Information Systems International Conference 2017, ISICO 2017, 6-8 November 2017, Bali, Indonesia. Elsevier B.V.; 2017; (Vol. 124, pp. 319–328). Publisher Full Text\n\nOliveira T, Thomas M, Baptista G, et al.: Mobile payment: Understanding the determinants of customer adoption and intention to recommend the technology. Computers Human Behav. 2016; 61: 404–414. Publisher Full Text\n\nParasuraman A: Technology Readiness Index (TRI). J Service Res. 2000a; 2(4): 307–320. Publisher Full Text\n\nParasuraman A: Technology Readiness Index (TRI) A Multiple-Item Scale to Embrace New Technologies. J Service Res. 2000b; 2(May 2000): 307–320. Publisher Full Text\n\nParasuraman A, Colby CL: An Updated and Streamlined Technology Readiness Index: TRI 2.0. J Service Res. 2014; 18(1), 1–16. Publisher Full Text\n\nRahman SA, Taghizadeh SK, Ramayah T, et al.: Technology acceptance among micro-entrepreneurs in marginalized social strata: The case of social innovation in Bangladesh. Technological Forecasting and Social Change. 2017; 118: 236–245. Publisher Full Text\n\nSivathanu B: Adoption of digital payment systems in the era of demonetization in India: An empirical study. J Science Technology Policy Management. 2019; 10(1): 143–171. Publisher Full Text\n\nStone M: Cross-validatory choice and assessment of statistical predictions. J Royal Statistical Society: Series B (Methodological). 1974; 36(2): 111–133. Publisher Full Text\n\nTang CY, Lai CC, Law CW, et al.: Examining key determinants of mobile wallet adoption intention in Malaysia: an empirical study using the unified theory of acceptance and use of technology 2 model. Int J Modelling Operations Management. 2014; 4(3): 248–265. Reference Source\n\nTouch’N Go eWallet: Touch’N Go eWallet Malaysia Fintect Report. 2019. Publisher Full Text\n\nVenkatesh V, Morris MG, Davis GB, et al.: User Acceptance of Information Technology: Toward a Unified View. J Chemical Information Modeling. 2003; 53(9): 1689–1699. Publisher Full Text\n\nVenkatesh V, Thong JYL, Xu X: Consumer Acceptance and Use of Information Technology: Extending the Unified Theory of Acceptance and Use of Technology. MIS Quarterly. 2012; 36(1): 157–178. Publisher Full Text\n\nWalczuch R, Lemmink J, Streukens S: The effect of service employees’ technology readiness on technology acceptance. Information and Management. 2007; 44(2): 206–215. Publisher Full Text"
}
|
[
{
"id": "93283",
"date": "03 Sep 2021",
"name": "Shaista Wasiuzzaman",
"expertise": [
"Reviewer Expertise Corporate finance",
"financial 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 study investigates Malaysia's readiness and their perception towards the usage of an e-wallet as a payment tool. The paper is clear in that it follows the correct research process and the analysis conducted is suitable for the research objectives that have been formed for this research. Data is collected via a questionnaire distributed by the authors and the authors have provided the underlying data sources to ensure full reproducibility.\nHowever, the literature that the study refers to especially in the Introduction section is not up to date. The last research cited in this section is from the year 2017. It would be good if the researchers updated their literature review.\nFinally, the authors do not get into a detailed discussion of the results which may be due to the requirement of the journal. So to me, it seems lacking and the conclusion section is too short. I would have liked to see a discussion of the results with respect to the results of previous studies and based on the theory that was introduced earlier.\nI would have also liked to see the authors present the implications of the study to theory and practice. And also the limitations of their research with suggestions for future research directions.\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": "93282",
"date": "20 Sep 2021",
"name": "Peik Foong Yeap",
"expertise": [
"Reviewer Expertise Organizational behavior and sustainability",
"strategic management",
"inter-organizational collaboration",
"cross cultural inclusiveness",
"teaching and learning."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article studies Malaysians’ readiness and perceptions towards the adoption of e-wallet using the Unified Theory of Acceptance and Use of Technology (UTAUT2) model. A sample of 309 valid data was collected and analysed with the partial least squares structural equation modelling (PLS-SEM). The results show that the adoption of e-wallet in this study is significantly influenced by performance expectancy, price value, facilitating conditions, and social influence. This study provides practical implications for e-wallet service providers and policymakers to enhance Malaysians’ readiness and adoption behaviour of e-wallet.\nThe method of this study is appropriate and well designed. The data analysis and results have been explained clearly. The hypothesis has been tested and answered. The discussion has sound implications for practitioners and policymakers.\n\nHowever, there are a few points that need to be further explained:\nThe study adopted a structured questionnaire, but it was not mentioned clearly which questionnaire was adopted and the reasons why the questionnaire was adopted. It would be good to provide reasons and justification for the adoption of the structured questionnaire in the methods section and further attach it in the Appendix for reference.\n\nIn addition, it would be good to justify the reason for using the seven-point Likert scale in this study.\n\nThe findings in the discussion section could be further supported and discussed with findings from the previous studies in the literature.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-863
|
https://f1000research.com/articles/10-258/v1
|
30 Mar 21
|
{
"type": "Review",
"title": "Calcium imaging analysis – how far have we come?",
"authors": [
"Miranda Robbins",
"Charles N. Christensen",
"Clemens F. Kaminski",
"Marta Zlatic",
"Miranda Robbins",
"Charles N. Christensen",
"Clemens F. Kaminski"
],
"abstract": "Techniques for calcium imaging were first achieved in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular, alongside our preferred, methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress, and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.",
"keywords": [
"Calcium Imaging",
"Denoising",
"Motion Correction",
"Classification",
"Quantification",
"Machine Learning",
"Neural Networks"
],
"content": "Introduction\n\nThe ability to image calcium ion (Ca2+) dynamics in cells has long been of interest, particularly in the neurosciences, where it can be used as a marker for neuronal excitability. The origins of calcium imaging began in the mid-1970s (Blinks et al., 1976; Moisescu et al., 1975), however the most Ca2+specific BAPTA-based dye was developed in 1980 by Roger Tsien, and its derivatives are still used today (Tsien, 1980). In the past forty years, the methods available for measuring Ca2+ fluxes in cells have expanded to include ratiometric, fluorescence lifetime, or fluorescence intensity, based reporters, and genetically-encoded options (Miyawaki et al., 1997; Ohkura et al., 2005) alongside dyes. The use of microscopy modalities has also advanced to include light-sheet microscopy (Huisken et al., 2004) for long-term imaging, and two-photon microscopy (Denk et al., 1990) for deep tissue and cell specific uncaging techniques.\n\nCalcium imaging is an inherently noisy method due to the high spatiotemporal information desired from a sample often showing low signal-to-noise alongside drift or cell movement, particularly for living organisms. In recent years, a number of software packages have been written for individual aspects of the commonly used pipeline in calcium imaging analysis (Figure 1). This processing pipeline includes image denoising, motion correction, classification for cell identification, and quantification of calcium signals.\n\n\nDenoising\n\nAlthough denoising is not a required step in the pipeline, effective denoising can improve the subsequent steps by artificially enhancing signal-to-noise. Traditionally, image denoising has been based on local averaging approaches, such as the application of a Gaussian smoothing filter (Buades et al., 2005; Lindenbaum et al., 1994). Other local filter methods include least mean squares filter (Haykin & Widrow, 2003), anisotropic filters (Perona & Malik, 1990) and in the frequency domain, Wiener filters (Wiener, 1950) and wavelet thresholding methods (Donoho, 1995).\n\nLocal methods are computationally light but have clear limitations. Firstly, the averaging often involved in local methods introduces blur, rendering features to be less defined. Secondly, they do not perform well for high noise levels, since the correlations between neighbouring pixels deteriorate (Shao et al., 2014).\n\nNon-local filters solve some of these problems by using self-similarity of natural images beyond neighbouring pixels (Shao et al., 2014). The first method to propose this is the non-local means method (Buades et al., 2005), in which patches are restored by weighted averaging of all other patches in an image. Since then, there have been a number of improvements such as invariance to patches that are rotated or mirrored with respect to each other (Grewenig et al., 2011), improved computational efficiency, and automated parameter tuning and extension to 3D image stacks (Coupé et al., 2008). Although non-local filters are better at high noise levels, they will typically lead to artefacts like over-smoothing (Shao et al., 2014). A modern, well-balanced and state-of-the-art non-local method is ND-SAFIR, which is specifically geared towards application in fluorescence microscopy imaging (Boulanger et al., 2010). ND-SAFIR is a powerful method for removing Poisson-Gaussian noise, which is based on non-local means denoising (Buades et al., 2011) to first use a variance stabilisation step, followed by spatial and temporal patch-based weighted averages of intensity values. The method is widely applicable between experimental samples and can be used directly for 2D+t and 3D+t datasets.\n\nIn recent years, deep learning methods have become state-of-the-art for denoising. Methods such as DnCNN (Zhang et al., 2017), FFDNet (Zhang et al., 2018) and CARE (Weigert et al., 2018) rely on convolutional neural networks that are trained in a supervised learning approach. However, this requires ground truths to be available for model training, which may be difficult to obtain in practice. A different approach was developed in noise2noise (Lehtinen et al., 2018), where instead of learning the mapping from noisy images to clean targets, the model is trained with other noisy images as targets. The images must be corresponding pairs displaying the same objects but with independent noise. Assuming the noise sources underlying the images have zero-mean distributions, the weights of the network will then converge during training to the same values as a network trained with clean targets because the noise that manifests in the weights cancels out. A more recent method, noise2void (Krull et al., 2019), aims to resolve this issue of needing ground truths, by using self-supervised learning. Here, the network is optimised to predict the value of each pixel from the values of neighbouring pixels in an image, thus requiring no separate ground truths.\n\n\nMotion correction\n\nMotion correction can be split into two main categories, which may be selected depending on the experimental model. Many samples will face drift during imaging or shift when imaging the same field of view over multiple days. which can be well rectified using standard registration methods (Thévenaz et al., 1998).\n\nMore complex motion such as organism movement can be harder to correct as it is often non-uniform, over a large area, and causes movement in-and-out of the focal plane. These require non-rigid registration methods or motion tracking. A commonly used example available in Python and MATLAB is Non-Rigid Motion Correction, NoRMcorre (Pnevmatikakis & Giovannucci, 2017), which uses patch-based field of view registration whereby separate images are then merged by smooth interpolation. The popularity of NoRMcorre may in part be due to its general applicability.\n\nTwo correction methods have been produced for 2-photon in vivo imaging in awake rodents, one based on the Lucas–Kanade (gradient descent) image registration algorithm using MathWorks® MATLAB platform (Greenberg & Kerr, 2009), the other using a Hidden Markov Model (Dombeck et al., 2007). Although effective, these methods have not been packaged for easy implementation and are reliant in cells remaining in the x- and y- dimensions as it cannot track following movement between z-axes. In cases with z-axis movement, tracking-based methods may be more reliable, and specialist options exist using control theory and machine learning approaches for post-processing (Nguyen et al., 2017), or applied to a motorised stage (Cong et al., 2017; Kim et al., 2017).\n\nTracking methods specifically designed to be more basic to implement and widely available include plug-ins for image processing packages (Abramoff et al., 2004) such as Trackmate (Tinevez et al., 2017), or Time Series Analyzer (Balaji, UCLA).\n\n\nClassification\n\nClassification can be achieved through pixel- or object-based segmentation. Pixel-based methods map each pixel to a class according to the spectral similarities. Popular pixel-based methods for calcium image analysis include Maximum Likelihood Classification (MLC) or Otsu thresholding to separate ‘light’ and ‘dark’ clustered pixels (Otsu, 1979) as used as part of the SIMA Python package ROI pipeline (Kaifosh et al., 2014).\n\nObject-based segmentation is a two-step process using both spectral and spatial/contextual information to group pixels into objects which are then classified. CaImAn is an open-source classification method based on convolutional neural networks (Giovannucci et al., 2019). It was packaged into EZcalcium in an effort to improve usability by providing a GUI in MathWorks® MATLAB (Cantu et al., 2020). However, using limited CaImAn function in EZcalcium does not easily allow for segmentation of more complex structures or large organelles or clusters of cells and is better for somas or smaller, less complex areas. Cellpose is another generalist, deep learning-based segmentation method that uses entirely open source packages in Python with a GUI to aid implementation. There is also a web-based option for testing Cellpose, which makes it very easy to use (Stringer et al., 2020), though it too can be limited at detecting more complex cell shapes such as dendrites and axons.\n\nDenoiSeg is an extension of Noise2Void that offers an end-to-end neural network, which is jointly optimised to denoise and segment images. The denoising capability is learnt by the self-supervised learning principle that noise2void introduced (Krull et al., 2019). By combining this with a supervised learning approach using a few annotated ground truths of segmentation maps, the final segmentation performance ends up performing better than without co-learning, i.e. having two separate networks perform the respective tasks (Buchholz et al., 2020).\n\nCell classification methods have been discussed with the conclusion that ‘learning-based methods score among the best-performing methods, but well-optimized traditional methods can even surpass these approaches in a fraction of the time’ (Vicar et al., 2019).\n\n\nQuantification\n\nThe aim of each step is for signal extraction to allow a quantitative output from the images of calcium signals. The most commonly used measure is the relative fluorescence variation (ΔF/F0) for classified cells. Packages will therefore either provide this data for further analysis, or provide a direct plot. Background subtraction may need to be considered as not all packages will take this into account.\n\nAnother feature commonly needed by researchers is timing of neuronal action potentials or ‘spike detection’. A wide range of algorithms can be used as discussed in the results to the Spikefinder challenge (Berens et al., 2018) as there are multiple methods of varying complexity that can be used. EZcalcium directly shows the raw fluorescence, inferred activity and deconvolved neural ‘spiking’, whereby the data can then be exported into file formats for proprietary (.mat, .xlsx) or open (.csv) software programmes for further analysis (Cantu et al., 2020; Giovannucci et al., 2019).\n\n\nConclusion\n\nA great number of analysis advancements have been made since calcium imaging was first developed. Popular packages for various steps of the pipeline (Figure 1) include CaImAn, SIMA, Suite2P, and EZcalcium (Cantu et al., 2020; Giovannucci et al., 2019; Kaifosh et al., 2014; Pachitariu et al., 2016). Although these packages are great starting tools for the community, many require programming knowledge in Python or commercial packages such as MathWorks® MATLAB. Many of the available options are only semi-automated and the limited automated options available are often designed for a very limited experimental context and are not actively supported when problems are experienced, e.g. other than for cells of a specific size and shape imaged in vitro. Suite2P and EZcalcium both attempt to offer an automated pipeline from raw images to spike extraction (Cantu et al., 2020; Pachitariu et al., 2016). EZcalcium is one of the most intuitive options, which has improved the usability of CaImAn, NoRMCorre, but again seems best suited to analyse cell bodies.\n\nIt therefore seems that perhaps some of the biggest advances could be made by designing packages for detecting neuritic structures or organelles and improving the spatial resolution of the analysis to be intracellular, such as has been used for calcium sparks (Berens et al., 2018). On the other end of the scale, pipelines for functional imaging in organisms such as zebrafish, C. elegans and Drosophila, where motion correction is often required and improved analysis for connectomics purposes are much needed.\n\nAs the application of machine learning in calcium imaging analysis matures, a higher level of automation and throughput for analysis tasks can be expected to follow. This will be enabled by more generalised and robust machine learning models. The barrier to training and deploying these methods will also reduce as more research is made into few-shot learning (using small training datasets) in addition to training approaches such as self-supervised and unsupervised learning.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgments\n\nThis publication was supported by COST Action NEUBIAS (CA15124), funded by COST (European Cooperation in Science and Technology).\n\n\nReferences\n\nAbramoff MD, Magalhaes PJ, Ram SJ: Image Processing with ImageJ. Biophotonics International. 2004; 11(7): 36–42. Reference Source\n\nBerens P, Freeman J, Deneux T, et al.: Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. bioRxiv. 2018; 177956. Publisher Full Text\n\nBlinks JR, Prendergast FG, Allen DG: Photoproteins as biological calcium indicators. Pharmacol Rev. 1976; 28(1): 1–93. PubMed Abstract\n\nBoulanger J, Kervrann C, Bouthemy P, et al.: Patch-based nonlocal functional for denoising fluorescence microscopy image sequences. IEEE Trans Med Imaging. 2010; 29(2): 442–454. PubMed Abstract | Publisher Full Text\n\nBuades A, Coll B, Morel JM: A non-local algorithm for image denoising. 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05). 2005; 2(0): 60–65. Publisher Full Text\n\nBuades A, Coll B, Morel JM: Non-Local Means Denoising. Image Processing On Line. 2011; 1. Publisher Full Text\n\nBuchholz TO, Prakash M, Schmidt D: DenoiSeg: joint denoising and segmentation. European Conference on Computer Vision. 2020; 324–337. Publisher Full Text\n\nCantu DA, Wang B, Gongwer MW, et al.: EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data. Front Neural Circuits. Frontiers Media S.A. 2020; 14: 25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCong L, Wang Z, Chai Y, et al.: Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio). eLife. 2017; 6: e28158. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoupé P, Yger P, Prima S, et al.: An optimized blockwise nonlocal means denoising filter for 3-D magnetic resonance images. IEEE Trans Med Imaging. 2008; 27(4): 425–441. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDenk W, Strickler JH, Webb WW: Two-photon laser scanning fluorescence microscopy. Science. 1990; 248(4951): 73–76. PubMed Abstract | Publisher Full Text\n\nDombeck DA, Khabbaz AN , Collman F, et al.: Imaging Large-Scale Neural Activity with Cellular Resolution in Awake, Mobile Mice. Neuron. Elsevier. 2007; 56(1): 43–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDonoho DL: De-noising by soft-thresholding. IEEE Trans Inf Theory. 1995; 41(3): 613–627. Publisher Full Text\n\nGiovannucci A, Friedrich J, Gunn P, et al.: CaImAn an open source tool for scalable calcium imaging data analysis. eLife. NLM (Medline). 2019; 8: e38173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGreenberg DS, Kerr JND: Automated correction of fast motion artifacts for two-photon imaging of awake animals. J Neurosci Methods. Elsevier. 2009; 176(1): 1–15. PubMed Abstract | Publisher Full Text\n\nGrewenig S, Zimmer S, Weickert J: Rotationally invariant similarity measures for nonlocal image denoising. J Vis Commun Image Represent. 2011; 22(2): 117–130. Publisher Full Text\n\nHaykin S, Widrow B: Least-Mean-Square Adaptive Filters. Wiley Online Library. 2003; 31. Publisher Full Text\n\nHuisken J, Swoger J, Bene FD, et al.: Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science. 2004; 305(5686): 1007–1009. PubMed Abstract | Publisher Full Text\n\nKaifosh P, Zaremba JD, Danielson NB, et al.: SIMA: Python software for analysis of dynamic fluorescence imaging data. Front Neuroinform. Frontiers Research Foundation. 2014; 8: 80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKim DH, Kim J, Marques JC, et al.: Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish. Nat Methods. Nature Publishing Group. 2017; 14(11): 1107–1114. PubMed Abstract | Publisher Full Text\n\nKrull A, Buchholz TO, Jug F: Noise2void - learning denoising from single noisy images. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. 2019; 2129–2137. Publisher Full Text\n\nLehtinen J, Munkberg J, Hasselgren J, et al.: Noise2Noise: Learning Image Restoration without Clean Data. 2018. Reference Source\n\nLindenbaum M, Fischer M, Bruckstein A: On Gabor’s contribution to image enhancement. Pattern Recogn. 1994; 27(1): 1–8. Publisher Full Text\n\nMiyawaki A, Llopis J, Heim R, et al.: Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature. Nature Publishing Group. 1997; 388(6645): 882–887. PubMed Abstract | Publisher Full Text\n\nMoisescu DG, Ashley CC, Campbell AK: Comparative aspects of the calcium-sensitive photoproteins aequorin and obelin. Biochim Biophys Acta. 1975; 396(1): 133–140. PubMed Abstract | Publisher Full Text\n\nNguyen JP, Linder AN, Plummer GS, et al.: Automatically tracking neurons in a moving and deforming brain. PLoS Comput Biol. Edited by E. Dyer. Public Library of Science. 2017; 13(5): e1005517. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOhkura M, Matsuzaki M, Kasai H, et al.: Genetically encoded bright Ca2+ probe applicable for dynamic Ca2+ imaging of dendritic spines. Anal Chem. American Chemical Society. 2005; 77(18): 5861–5869. PubMed Abstract | Publisher Full Text\n\nOtsu N: Threshold Selection Method From Gray-Level Histograms. IEEE Trans Syst Man Cybern. 1979; 9(1): 62–66. Publisher Full Text\n\nPachitariu M, Stringer C, Dipoppa M, et al.: Suite2p: beyond 10,000 neurons with standard two-photon microscopy. bioRxiv. Cold Spring Harbor Laboratory. 2016; 061507. Publisher Full Text\n\nPerona P, Malik J: Scale-space and edge detection using anisotropic diffusion. IEEE Trans Pattern Anal Mach Intell. 1990; 12(7): 629–639. Publisher Full Text\n\nPnevmatikakis EA, Giovannucci A: NoRMCorre: An online algorithm for piecewise rigid motion correction of calcium imaging data. J Neurosci Methods. Elsevier B.V. 2017; 291: 83–94. PubMed Abstract | Publisher Full Text\n\nShao L, Yan R, Li X, et al.: From Heuristic Optimization to Dictionary Learning: A Review and Comprehensive Comparison of Image Denoising Algorithms. IEEE Trans Cybern. 2014; 44(7): 1001–1013. PubMed Abstract | Publisher Full Text\n\nStringer C, Wang T, Michaelos M: Cellpose: A generalist algorithm for cellular segmentation. bioRxiv. 2020; 2020.02.02.931238. Publisher Full Text\n\nThévenaz P, Ruttimann UE, Unser M: A pyramid approach to subpixel registration based on intensity. IEEE Trans Image Process. 1998; 7(1): 27–41. PubMed Abstract | Publisher Full Text\n\nTinevez JY, Perry N, Schindelin J, et al.: TrackMate: An open and extensible platform for single-particle tracking. Methods. Academic Press Inc. 2017; 115: 80–90. PubMed Abstract | Publisher Full Text\n\nTsien RY: New Calcium Indicators and Buffers with High Selectivity Against Magnesium and Protons: Design, Synthesis, and Properties of Prototype Structures. Biochemistry. 1980; 19(11): 2396–2404. PubMed Abstract | Publisher Full Text\n\nVicar T, Balvan J, Jaros J, et al.: Cell segmentation methods for label-free contrast microscopy: Review and comprehensive comparison. BMC Bioinformatics. BioMed Central Ltd. 2019; 20(1): 360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeigert M, Schmidt U, Boothe T, et al.: Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat Methods. 2018; 15(12): 1090–1097. PubMed Abstract | Publisher Full Text\n\nWiener N: Extrapolation, interpolation, and smoothing of stationary time series: with engineering applications. Technology Press. 1950. Reference Source\n\nZhang K, Zuo W, Chen Y, et al.: Beyond a Gaussian denoiser: Residual learning of deep CNN for image denoising. IEEE Trans Image Process. 2017; 26(7): 3142–3155. PubMed Abstract | Publisher Full Text\n\nZhang K, Zuo W, Zhang L: FFDNet: Toward a fast and flexible solution for CNN Based image denoising. IEEE Trans Image Process. 2018; 27(9): 4608–4622. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "83580",
"date": "05 May 2021",
"name": "Christopher Rowlands",
"expertise": [
"Reviewer Expertise Microscopy",
"instrument development",
"automation and data analysis",
"neurophotonics",
"biophotonics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a brief review of processing and analysis methods for calcium imaging data in neuroscience. The article breaks down the processing steps typically required to view calcium signals from neurons, including denoising, motion correction, and classification, and then the quantification of the data. It appears that the primary contribution of the article is to summarize the most recent and up-and-coming methods for the processing of calcium activity in neurons. The abstract describes the intentions of the paper well, bringing the reader up to date on the last 60 years of calcium analysis tools, however several claims are made which are not followed up in the manuscript. For example, the authors do not highlight their preferred methods as they state they will in the abstract, much less provide justification for these choices. The abstract concludes by stating the authors will describe the future needs in the field, and this is successfully done in the conclusion, albeit briefly and without much justification – we would have liked to see some examples of the kinds of groups who might be making progress in these fields, or papers in different fields which might be applicable to calcium activity monitoring.\nOverall we find the contents of this review to be beneficial to users applying calcium imaging to their research, however some additional information or clarification needs to be included or clarified. The following corrections should be made to the review before formal ‘publication’: The description of the purpose and benefits of denoising is well explained at the start of the section. In the following sections of motion correction and classification however, the authors proceed directly to the methods used to perform the task, and while this is comprehensive, they fail to justify why these steps are needed in the calcium processing and analysis pipeline. An ‘introduction’ sentence or paragraph for each section is needed.\nThe acronym BAPTA should be defined before it is used.\nIn the motion-correction section, more distinction should be made between ‘camera-based’ motion correction, where the whole image is captured simultaneously, and ‘scanning-based’ motion correction. There are distinct differences in capabilities and limitations for each approach (for example, scanning-based imaging can suffer from ‘warping’ which affects camera-based imaging much less, but can also sample regions of interest as opposed to the whole image, speeding up imaging to overcome motion artifacts). The authors successfully reference the original papers for the different approaches to denoising, motion correction, and classification, but they should also include the references for when the techniques were first applied and used in calcium image analysis, as this is the focus of the review.\nThe standard of presentation is OK, but should really be improved before ‘publication’. The first sentence of the abstract is difficult to parse and is not a complete statement. Furthermore, throughout the manuscript there are several difficult-to-parse sentences and some that are ungrammatical (e.g. “to include ratiometric, fluorescence lifetime, or fluorescence intensity, based reporters, and genetically-encoded options […] alongside dyes”, “rendering features to be less defined.”, “ND-SAFIR is a powerful method for removing Poisson-Gaussian noise, which is based on non-local means denoising […] to first use a variance stabilisation step, followed by spatial and temporal patch-based weighted averages of intensity values”, “over multiple days. which can be well rectified using standard registration methods” and so on). Finally, the structure could be improved (“Motion correction can be split into two main categories” really should be followed by an explanation of what those two categories are, and background subtraction is alluded to in the “Quantification” section but not elaborated upon).\nFigure captions should generally be self-contained and comprehensive – they should explain what the reader is expected to observe/pay attention to, and what conclusions should be drawn. Some more elaboration in the figure caption would therefore be welcome.\nOther more minor adjustments that are recommended (but not required) include: It would be nice to see a definition of Poisson-Gaussian noise since this is unlikely to be understood by many readers. Similarly clear definition of a ‘patch’ would be helpful, as would explanation of the difference between local and non-local methods.\nAs stated previously, further expansion of the methods used for the analysis of calcium signals, such as calculation of dF/F and spike sorting, that are touched on in the quantification section, would be helpful. This section is very brief but would seem to be the section of most interest to the general reader.\nThe authors state the paper will describe the methods used for calcium imaging analysis however the focus of the paper is more on the pre-processing methods rather than the analysis. It would be nice to elaborate further on what kinds of analyses are performed on the data after pre-processing – how these calcium traces can be used to infer useful neurobiological information.\nIn summary, this is a brief but well-focussed review on a topic that is of interest to several researchers and thus should be formally published after the necessary revisions have been made.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "7030",
"date": "26 Aug 2021",
"name": "Miranda Robbins",
"role": "Author Response",
"response": "The authors present a brief review of processing and analysis methods for calcium imaging data in neuroscience. The article breaks down the processing steps typically required to view calcium signals from neurons, including denoising, motion correction, and classification, and then the quantification of the data. It appears that the primary contribution of the article is to summarize the most recent and up-and-coming methods for the processing of calcium activity in neurons. We thank the reviewers for highlighting areas of improvement in our review article. The abstract describes the intentions of the paper well, bringing the reader up to date on the last 60 years of calcium analysis tools, however several claims are made which are not followed up in the manuscript. For example, the authors do not highlight their preferred methods as they state they will in the abstract, much less provide justification for these choices. We acknowledge this inconsistency between the abstract and the content of the manuscript. On closer inspection, we have decided that we do not want to explicitly emphasise our personal preferences and justify them, but rather objectively discuss the strengths of the respective methods and leave it to the reader – particularly as the “best” methods will often be dependent upon the experimental methods used by individual researchers. We have therefore removed the mentioning of “our preferred [methods]” in the relevant sentence in the abstract from: “We will discuss some of the most popular, alongside our preferred, methods for calcium imaging” The abstract concludes by stating the authors will describe the future needs in the field, and this is successfully done in the conclusion, albeit briefly and without much justification – we would have liked to see some examples of the kinds of groups who might be making progress in these fields, or papers in different fields which might be applicable to calcium activity monitoring. We have extended the discussion on future challenges to include: “Longitudinal tracking of specific cells across imaging sessions also remains a challenge so that individual cells can be identified between multiple imaging sessions. A MathWorks® MATLAB toolkit has been made with reported error rates of < 5 % (Sheintuch et al., 2017); an alternative approach is also available using CaImAn (Giovannucci et al., 2019) though direct comparisons between these methods is difficult without knowing ground truths. Calcium imaging for population activity has also been highlighted as an area that requires further research, particularly when imaging over larger fields of view. Using models specific for neuron types imaged may improve detection of APs, which are commonly under-represented in population activity measurements (Huang et al., 2021). Recent toolboxes with large datasets containing ground-truths may reduce false negatives during analysis (Rupprecht et al., 2021).” Overall we find the contents of this review to be beneficial to users applying calcium imaging to their research, however some additional information or clarification needs to be included or clarified. The following corrections should be made to the review before formal ‘publication’: The description of the purpose and benefits of denoising is well explained at the start of the section. In the following sections of motion correction and classification however, the authors proceed directly to the methods used to perform the task, and while this is comprehensive, they fail to justify why these steps are needed in the calcium processing and analysis pipeline. An ‘introduction’ sentence or paragraph for each section is needed. We have added introductory sentences as follows: “Motion correction is often required for samples due to drift during imaging, or organism movement.” “Classification is required to ensure that the quantification can be performed over specific regions of interest, such as for subcellular area, specific cells, or tissue regions.” The acronym BAPTA should be defined before it is used. We have now included this. In the motion-correction section, more distinction should be made between ‘camera-based’ motion correction, where the whole image is captured simultaneously, and ‘scanning-based’ motion correction. There are distinct differences in capabilities and limitations for each approach (for example, scanning-based imaging can suffer from ‘warping’ which affects camera-based imaging much less, but can also sample regions of interest as opposed to the whole image, speeding up imaging to overcome motion artifacts). We agree with this suggestion to more clearly outline the types of motion correction described. Most importantly, we want to distinguish between motion that occurs in the imaging system (such as the camera-based and scanning-based motion effects mentioned here) and the more complex motion effects that are due to specimen movement. We have added the following to the “Motion correction” section: “Motion correction is often required to ensure consistent image processing across a time stack. We distinguish between two types of motion: (a) drift occurring in the imaging system itself caused by thermal gradients in the microscope, vibrations and mechanical instability (Kreft et al., 2005); (b) subject motion such as fluctuations in the immersion media or the movement of organisms (Jenkinson et al., 2002).” The authors successfully reference the original papers for the different approaches to denoising, motion correction, and classification, but they should also include the references for when the techniques were first applied and used in calcium image analysis, as this is the focus of the review. We thank the reviewer for this comment. We can appreciate the point that references describing applications of processing methods specific to calcium imaging should be more plentiful. These references are often difficult to find from the existing reviews on calcium imaging and we have therefore tried to add relevant references to this review where possible: For anisotropic filters we have added the references: (Broser et al., 2004; Kitamura and Häusser, 2011). For wavelet thresholding methods we have included: (Besbeas, Feis and Sapatinas, 2004; Wegner, Both and Fink, 2006). We have added: “In the context of calcium imaging, local methods have been shown to perform well (Malik et al., 2011).”. For motion correction using rigid methods we have added (Dubbs, Guevara and Yuste, 2016). In ‘Classification’ we have added (Malik et al., 2011) as an example of Maximum Likelihood Classification. While the calcium imaging literature does not have a lot of examples of non-trivial image processing applications, we have augmented the section with a new reference that indeed does: “Malik, Wasim Q., et al. \"Denoising two-photon calcium imaging data.\" PloS one 6.6 (2011)”. The standard of presentation is OK, but should really be improved before ‘publication’. The first sentence of the abstract is difficult to parse and is not a complete statement. Furthermore, throughout the manuscript there are several difficult-to-parse sentences and some that are ungrammatical (e.g. “to include ratiometric, fluorescence lifetime, or fluorescence intensity, based reporters, and genetically-encoded options […] alongside dyes”, “rendering features to be less defined.”, “ND-SAFIR is a powerful method for removing Poisson-Gaussian noise, which is based on non-local means denoising […] to first use a variance stabilisation step, followed by spatial and temporal patch-based weighted averages of intensity values”, “over multiple days. which can be well rectified using standard registration methods” and so on). Finally, the structure could be improved (“Motion correction can be split into two main categories” really should be followed by an explanation of what those two categories are, and background subtraction is alluded to in the “Quantification” section but not elaborated upon). Thank you for highlighting these errors. We have edited the sentences as follows: “Techniques for calcium imaging were first demonstrated in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved today” “In the past forty years, the methods available for measuring Ca 2+ fluxes in cells have expanded to include ratiometric, fluorescence lifetime, or fluorescence intensity-based dyes, and genetically-encoded calcium indicators (GECIs) ( Miyawaki et al., 1997; Ohkura et al., 2005).” “… causing features to appear less well defined.” “ND-SAFIR is a powerful method for removing Poisson-Gaussian noise. It is based on non-local means denoising using a variance stabilisation step, followed by calculating the spatial and temporal patch-based weighted averages for intensity values.” “…view over multiple days, which can be rectified by using standard registration methods.” We have deleted the sentence “Motion correction can be split into two main categories” which has been replaced with the introductory sentence on motion correction. We have expanded the sentence on background subtraction to say: “Multiple methods can be used, including subtracting the intensity values from a region of the image that does not contain Ca2+ indicator from the intensity values in regions of interest. However, care should be taken using background subtraction with ratiometric indicators (Shkryl, 2020). F0 baseline values can be calculated by averaging the values before the onset of stimulation in the same region (Galizia, Menzel and Holldobler, 1999), or by low-pass filtering the signal (Balkenius, Bisch-Knaden and Hansson, 2009)(For review Balkenius, Johansson and Balkenius, 2015). “ Figure captions should generally be self-contained and comprehensive – they should explain what the reader is expected to observe/pay attention to, and what conclusions should be drawn. Some more elaboration in the figure caption would therefore be welcome. We have adapted the Figure caption as follows: “Figure 1. The steps of a common pipeline for calcium imaging analysis can be subdivided into three areas before quantitative analysis is performed. Denoising is an optional step that can help to improve signal-to-noise and enhance features. Motion correction may be necessary in cases of drift or movement. Classification can select regions of interest for which quantitative analysis is performed. “ Other more minor adjustments that are recommended (but not required) include: It would be nice to see a definition of Poisson-Gaussian noise since this is unlikely to be understood by many readers. Similarly clear definition of a ‘patch’ would be helpful, as would explanation of the difference between local and non-local methods. Thank you for these suggestions. We agree that these things were not necessarily clear to the general reader, so we have incorporated various changes to address these points. First of all, definitions of the noise sources in fluorescence microscopy and a reference that deals more thoroughly with the subject: “Live-cell imaging generally requires short exposure times and low excitation power to limit the effects of photo-toxicity and photo-bleaching. This leads to image degradation in the form of noise. In fluorescence microscopy the two prevalent noise sources are Poisson noise and Gaussian noise. Poisson noise is caused by the stochastic and discrete nature of photon emission and tends to be dominant at low light levels, whereas Gaussian noise describes the intrinsic thermal and electronic fluctuation in the image sensor (Luisier et al., 2011). “ Secondly, non-local methods are now described as using global information, a distinction to local methods that we believe should now make the difference clear. Lastly, we have included a definition of patch as a block of pixels representing a subregion of an image. As stated previously, further expansion of the methods used for the analysis of calcium signals, such as calculation of dF/F and spike sorting, that are touched on in the quantification section, would be helpful. This section is very brief but would seem to be the section of most interest to the general reader. The authors state the paper will describe the methods used for calcium imaging analysis however the focus of the paper is more on the pre-processing methods rather than the analysis. It would be nice to elaborate further on what kinds of analyses are performed on the data after pre-processing – how these calcium traces can be used to infer useful neurobiological information. We have included the following in the ‘quantification’ section: “Packages will therefore either provide this data of the baseline fluorescence (F0) and deviations from baseline (ΔF), for further analysis, or provide a direct plot.” “Signal extraction from single cells can be particularly difficult for in vivo recordings due to large background fluxes and high spatial overlaps of cells outside of the focus plane which is further increased in 1-photon compared to 2-photon imaging. Semi-automated ROI analysis (Barbera et al., 2016; Klaus et al., 2017; Pinto & Dan, 2015), principal component analysis independent components analysis (PCA/ICA) (Mukamel et al., 2009), clustering based approaches (like Suite2P; Pachitariu et al., 2016), and constrained nonnegative matrix factorization (CNMF) (Pnevmatikakis et al., 2016) approaches are techniques that have been explored with different strengths for detecting background and spatial overlap. An ‘extended’ CNMF method (CNMF-E) has been developed with an adjusted spatiotemporal background model that outperformed PCA/ICA for the simulated and experimental datasets that were tested (Zhou et al., 2018). For a package method, the toolbox MIN1PIPE combines a CNMF (Pnevmatikakis et al., 2016) with additional steps to remove false positives (Lu et al., 2018). CaImAn also builds upon the CNMF algorithm (Pnevmatikakis et al., 2016) to allow it to be fully automated, and CNMF-E for 1-photon endoscopic data (Zhou et al., 2018).” “The ability to accurately detect spikes requires knowledge of ground truth, usually from electrophysiological recordings. Calcium imaging can be susceptible to variation between neuron type, calcium indicator and its concentration used, the optical resolution, the sampling rate and the noise level. Therefore, it is fundamental to understand how specific indicators react under the given imaging conditions, which cannot be readily generalized across protocols. To try and improve the accuracy of spike detection, a toolkit using a supervised algorithm of spike inference has been developed using a ‘ground truth database’ from a large number of sets of calcium imaging with corresponding electrophysiological measurements (Rupprecht et al., 2021).” In summary, this is a brief but well-focussed review on a topic that is of interest to several researchers and thus should be formally published after the necessary revisions have been made. We thank you for your positive comments and helpful additions to our article."
}
]
},
{
"id": "84794",
"date": "24 May 2021",
"name": "William Zeiger",
"expertise": [
"Reviewer Expertise Stroke",
"neural circuits",
"two-photon calcium imaging"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 their review “Calcium imaging analysis – how far have we come?”, Robbins et al. present a concise overview of the basic steps involved in transforming raw microscopy images from calcium imaging experiments to quantifiable data. This is an extremely important topic with broad relevance to many fields. As such, the review should draw considerable interest. The review is well written. It is logically organized, with the analysis pipeline broken down into 4 distinct steps, each of which is discussed separately. The language is easy to follow for a broad audience of varying degrees of expertise. Many of the most popular software implementations are covered at least to some degree. Overall, I think this will be a useful and important review with significant impact.\nHowever, I do have some suggestions that I believe could strengthen the manuscript. My main concern is that the target audience for the review is not clear. Calcium imaging is broadly used in many areas of the life sciences, including both in vitro and in vivo preparations, across multiple species, multiple tissues, and widely varying spatial scales (sub-cellular, cellular, bulk tissue signals). Given that much of the review is devoted to denoising and motion correction (problems which are relatively minor in in vitro preparations with no organismal movement and relatively high signal-to-noise), and that quantification focuses on spike detection, the review feels most well suited to in vivo two-photon imaging applications in the brain. If this was the intention, it would benefit the review to make this more explicit and provide more discussion tailored to this technique, particularly in the quantification section. If this assumption is not correct and the review is meant to be targeted at a more general audience, I would suggest the introduction be expanded to include at least a brief discussion of the types of calcium indicators available (ratiometric, FRET, fluo, GCaMP, etc) and imaging techniques in use (widefield fluorescence, confocal, 2P, miniscopes, etc). This is important for a beginner/generalist audience as the indicator and imaging technique used will strongly influence the subsequent processing pipeline needs.\nIn addition to this primary concern I have a few other suggestions that would improve the scope of the review:\nThe quantification section should be significantly expanded. This step is the shortest in description, yet arguably can be fraught with the most pitfalls to which investigators fall prey.\n\nCaImAn is included under the “classification” section, but includes modules to do more than just classify, including motion correction and registration across imaging sessions\n\nSpike detection is mentioned, but it should be made explicit that spike detection is completely dependent on knowledge of ground truth about how specific indicators under specific imaging conditions relate and cannot be readily generalized across labs/indicators/preparations. See this recent preprint (Rupprecht et. al https://www.biorxiv.org/content/10.1101/2020.08.31.272450v21)\n\nOn a related point about spike detection, the authors may want to include information about the relative sensitivity (or in some cases lack thereof) of calcium indicators for spike detection (see Hunag et. al https://elifesciences.org/articles/516752).\n\nIt would be interesting for the authors to comment on 1P miniscope calcium imaging, as this technique is rapidly disseminating and poses specific challenges for imaging analysis. See Lu et. al (https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30826-X3)\n\nLongitudinal tracking of cells across imaging sessions remains a challenge for the field – I am not aware of many algorithms that are widely available to tackle this problem. It could be included in the future directions.\n\nThe Allen institute recently published a preprint on a new denoising technique which looks promising (See Lecoq et. al https://www.biorxiv.org/content/10.1101/2020.10.15.341602v24)\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "7031",
"date": "26 Aug 2021",
"name": "Miranda Robbins",
"role": "Author Response",
"response": "In their review “Calcium imaging analysis – how far have we come?”, Robbins et al. present a concise overview of the basic steps involved in transforming raw microscopy images from calcium imaging experiments to quantifiable data. This is an extremely important topic with broad relevance to many fields. As such, the review should draw considerable interest. The review is well written. It is logically organized, with the analysis pipeline broken down into 4 distinct steps, each of which is discussed separately. The language is easy to follow for a broad audience of varying degrees of expertise. Many of the most popular software implementations are covered at least to some degree. Overall, I think this will be a useful and important review with significant impact. We thank Dr. Zeiger for his positive comments about our review and interesting literature references that he has provided. However, I do have some suggestions that I believe could strengthen the manuscript. My main concern is that the target audience for the review is not clear. Calcium imaging is broadly used in many areas of the life sciences, including both in vitro and in vivo preparations, across multiple species, multiple tissues, and widely varying spatial scales (sub-cellular, cellular, bulk tissue signals). Given that much of the review is devoted to denoising and motion correction (problems which are relatively minor in in vitro preparations with no organismal movement and relatively high signal-to-noise), and that quantification focuses on spike detection, the review feels most well suited to in vivo two-photon imaging applications in the brain. If this was the intention, it would benefit the review to make this more explicit and provide more discussion tailored to this technique, particularly in the quantification section. If this assumption is not correct and the review is meant to be targeted at a more general audience, I would suggest the introduction be expanded to include at least a brief discussion of the types of calcium indicators available (ratiometric, FRET, fluo, GCaMP, etc) and imaging techniques in use (widefield fluorescence, confocal, 2P, miniscopes, etc). This is important for a beginner/generalist audience as the indicator and imaging technique used will strongly influence the subsequent processing pipeline needs. We were indeed targeting the review at a more general reader. We have therefore expanded the regions of the introduction where we mention calcium indicators and imaging techniques as well as including a sentence to discuss differences between in vivo and in vitro samples as follows: “The combination of Ca 2+ indicator and imaging modality used will reflect the properties of the sample and the scientific question, as well as the methodologies available to the researcher. For example, in vitro imaging, or in vivo invertebrate imaging, may use exogenous or GECIs, imaged using LSM, epifluorescence, 2PM or other fluorescence microscopes depending on the temporal-resolution, timescale of imaging, and thickness of the sample being taken into consideration. Other specialist options for in vivo imaging of GECIs are available for imaging in awake and behaving animals including miniaturized forms of 1- or 2- photon fluorescence microscopes (miniscopes) for single-cell in vivo recordings (Chen et al., 2013; Cai et al., 2016; Silva, 2017). As calcium imaging is used across a broad range of samples, from sub-cellular, cellular, networks, bulk tissue dynamics to whole organisms and behaving animals, aspects of this pipeline can vary substantially with no ‘one size fits all’ approach.” In addition to this primary concern I have a few other suggestions that would improve the scope of the review: The quantification section should be significantly expanded. This step is the shortest in description, yet arguably can be fraught with the most pitfalls to which investigators fall prey. We have expanded the quantification section: “Signal extraction from single cells can be particularly difficult for in vivo recordings due to large background fluxes and high spatial overlaps of cells outside of the focus plane. Semi-automated ROI analysis (Barbera et al., 2016; Klaus et al., 2017; Pinto & Dan, 2015), principal component analysis independent components analysis (PCA/ICA) (Mukamel, Nimmerjahn, & Schnitzer, 2009), and constrained nonnegative matrix factorization (CNMF) (Pnevmatikakis et al., 2016; Zhou et al., 2018) approaches are techniques that have been explored with different strengths for detecting background and spatial overlap. An ‘extended’ CNMF method has been developed with an adjusted spatiotemporal background model that outperformed PCA/ICA for the simulated and experimental datasets that were tested (Zhou et al., 2018). For a package method, the toolbox MIN1PIPE combines a CNMF (Pnevmatikakis et al., 2016) with additional steps to remove false positives (Lu et al., 2018).” CaImAn is included under the “classification” section, but includes modules to do more than just classify, including motion correction and registration across imaging sessions We have clarified this by adding the sentence: “CaImAn is an open-source package with modules for classification, motion correction, source extraction, and spike deconvolution. The classification method is based on convolutional neural networks( Giovannucci et al., 2019).” Spike detection is mentioned, but it should be made explicit that spike detection is completely dependent on knowledge of ground truth about how specific indicators under specific imaging conditions relate and cannot be readily generalized across labs/indicators/preparations. See this recent preprint (Rupprecht et. al https://www.biorxiv.org/content/10.1101/2020.08.31.272450v21) Thank you for bringing this very interesting preprint to our attention. We appreciate this point and we have included the addition: “The ability to accurately detect spikes requires knowledge of ground truth, usually from electrophysiological recordings. Calcium imaging can be susceptible to variation between neuron type, calcium indicator and its concentration used, the optical resolution, the sampling rate and the noise level. Therefore, it is fundamental to understand how specific indicators react under the given imaging conditions, which cannot be readily generalized across protocols. To try and improve the accuracy of spike detection, a toolkit using a supervised algorithm of spike inference has been developed using a ‘ground truth database’ from a large number of sets of calcium imaging with corresponding electrophysiological measurements (Rupprecht et al., 2021).” On a related point about spike detection, the authors may want to include information about the relative sensitivity (or in some cases lack thereof) of calcium indicators for spike detection (see Hunag et. al https://elifesciences.org/articles/516752). We have included a discussion in the conclusion about the sensitivity of spike detection: “Calcium imaging for population activity has also been highlighted as an area that requires further research, particularly when imaging over larger fields of view. Using models specific for neuron types imaged may improve detection of Aps, which are commonly under-represented in population activity measurements (Huang et al., 2021). Recent toolboxes with large datasets containing ground-truths may reduce false negatives during analysis (Rupprecht et al., 2021).” It would be interesting for the authors to comment on 1P miniscope calcium imaging, as this technique is rapidly disseminating and poses specific challenges for imaging analysis. See Lu et. al (https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30826-X3) We have added discussion of miniscopes to Introduction: “Other specialist options for in vivo imaging of GECIs are available for imaging in awake and behaving animals including miniaturized forms of 1- or 2- photon fluorescence microscopes (miniscopes) for single-cell in vivo recordings (Chen et al., 2013; Cai et al., 2016; Silva, 2017).” to the Motion correction section: “A MathWorks® MATLAB toolbox, miniscope 1-photon imaging pipeline (MIN1PIPE), has been developed to include denoising, motion correction and signal extraction (Lu et al., 2018). MIN1PIPE motion correction includes several steps including the Lucas-Kanade and Kanade-Lucas-Tomasi (Lucas and Kanade, 1981; Shi and Tomasi, 1994) trackers, and Log-Demons registration (Vercauteren et al., 2009), and outperforms the Lucas-Kanade, Kanade-Lucas-Tomasi, and NoRMcorre for using sample 2-photon videos (Lu et al., 2018).” to the Quantification section: “For a package method, the toolbox MIN1PIPE combines a CNMF (Pnevmatikakis et al., 2016) with additional steps to remove false positives (Lu et al., 2018).” Longitudinal tracking of cells across imaging sessions remains a challenge for the field – I am not aware of many algorithms that are widely available to tackle this problem. It could be included in the future directions. We have added to the discussion on future challenges: “Longitudinal tracking of specific cells across imaging sessions also remains a challenge so that individual cells can be identified between multiple imaging sessions. A MathWorks® MATLAB toolkit has been made with reported error rates of < 5 % (Sheintuch et al., 2017); an alternative approach is also available using CaImAn (Giovannucci et al., 2019) though direct comparisons between these methods is difficult without knowing ground truths.” The Allen institute recently published a preprint on a new denoising technique which looks promising (See Lecoq et. al https://www.biorxiv.org/content/10.1101/2020.10.15.341602v24) This is an interesting preprint that does indeed seem promising. It can be seen as an extension of the Noise2void method, which we already touch on. We have added the following sentence to the manuscript: “In another recent method, DeepInterpolation (Lecoq et al., 2020), the need for ground truth training data is avoided by treating the denoising task as a nonlinear interpolation problem. This assumes the data have a sequential component, such that spatiotemporally overlapping features can be exploited.”"
}
]
},
{
"id": "84795",
"date": "07 Jun 2021",
"name": "Anubhuti Goel",
"expertise": [
"Reviewer Expertise Systems neuroscience",
"Calcium imaging",
"mouse behavior",
"electrophysiology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe review by Miranda et al provides an overview of the calcium imaging pipeline and the open source resources available to the scientific community. Overall the review is a helpful resource to anyone aiming to analyze their calcium imaging data. However a clearer understanding of which resource is better suited to which model system or type of analysis will be a helpful addition (maybe some examples will be particularly insightful). The authors mention Suite2P and EZCalcium as the top analysis tools available however it is not clear which one the reader should pick. Furthermore both Suite2P and EZCalcium come with a user interface which means other than downloading either python or MATLAB no programming knowledge is needed. This fact is not clear in the review.\nOne reference is mentioned as \"Balaji, UCLA\". The authors should specify if indeed that is a personal communication or perhaps an unpublished tool.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": [
{
"c_id": "7032",
"date": "26 Aug 2021",
"name": "Miranda Robbins",
"role": "Author Response",
"response": "The review by Miranda et al provides an overview of the calcium imaging pipeline and the open source resources available to the scientific community. Overall the review is a helpful resource to anyone aiming to analyze their calcium imaging data. We thank the reviewer for their helpful suggestions for our article. However a clearer understanding of which resource is better suited to which model system or type of analysis will be a helpful addition (maybe some examples will be particularly insightful). We have included in the introduction information about the methods that may better suit in vitro, versus in vivo imaging methods: “The combination of Ca 2+ indicator and imaging modality used will reflect the properties of the sample and the scientific question, as well as the methodologies available to the researcher. For example, in vitro imaging, or in vivo invertebrate imaging, may use exogenous or GECIs, imaged using LSM, epifluorescence, 2PM or other fluorescence microscopes depending on the temporal-resolution, timescale of imaging, and thickness of the sample being taken into consideration. Other specialist options for in vivo imaging of GECIs are available for imaging in awake and behaving animals including miniaturized forms of 1- or 2- photon endoscopic fluorescence microscopes (miniscopes) for single-cell in vivo recordings (Cai et al., 2016; Chen et al., 2013; Silva, 2017).” We have added more information for 1 photon in vivo imaging paragraph in ‘motion correction’ section. We have added more information to the in vivo quantification section: “Signal extraction from single cells can be particularly difficult for in vivo recordings due to large background fluxes and high spatial overlaps of cells outside of the focus plane. Semi-automated ROI analysis (Pinto and Dan, 2015; Barbera et al., 2016; Klaus et al., 2017), principal component analysis independent components analysis (PCA/ICA) (Mukamel, Nimmerjahn and Schnitzer, 2009), and constrained nonnegative matrix factorization (CNMF) (Pnevmatikakis et al., 2016; Zhou et al., 2018) approaches are techniques that have been explored with different strengths for detecting background and spatial overlap. An ‘extended’ CNMF method has been developed with an adjusted spatiotemporal background model that outperformed PCA/ICA for the simulated and experimental datasets that were tested (Zhou et al., 2018). For a package method, the toolbox MIN1PIPE combines a CNMF (Pnevmatikakis et al., 2016) with additional steps to remove false positives (Lu et al., 2018).” The authors mention Suite2P and EZCalcium as the top analysis tools available however it is not clear which one the reader should pick. Furthermore both Suite2P and EZCalcium come with a user interface which means other than downloading either python or MATLAB no programming knowledge is needed. This fact is not clear in the review. We have added the following in the conclusion: “Suite2P and EZcalcium both attempt to offer an automated pipeline from raw images to spike extraction with no prior programming knowledge required by the user ( Cantu et al., 2020; Pachitariu et al., 2016). As both packages are suited to similar experimental data, the choice may be based upon personal preference.” One reference is mentioned as \"Balaji, UCLA\". The authors should specify if indeed that is a personal communication or perhaps an unpublished tool. We understand that this may cause confusion; as this plug-in is not published and we have now added the ImageJ webpage as a reference."
}
]
}
] | 1
|
https://f1000research.com/articles/10-258
|
https://f1000research.com/articles/10-857/v1
|
26 Aug 21
|
{
"type": "Systematic Review",
"title": "High-intensity interval training effects on ultra-processed food consumption in adolescents: a systematic review",
"authors": [
"Matias Noll",
"Ana Paula dos Santos Rodrigues",
"Alexandre Aparecido de Almeida",
"Carolina Rodrigues de Mendonça",
"Priscilla Rayanne e Silva Noll",
"Ana Paula dos Santos Rodrigues",
"Alexandre Aparecido de Almeida",
"Carolina Rodrigues de Mendonça",
"Priscilla Rayanne e Silva Noll"
],
"abstract": "Nowadays, within the vigorous intensity activities, there is a huge interest in high-intensity interval training (HIIT), in both research and clinical perspectives. Although HIIT has shown several benefits (e.g. increase in VO2 peak; improving cardiorespiratory fitness and body composition; beneficial effects on cognition and mental health), as far as we know, no systematic review has focused on the HIIT effects on ultra-processed food (UPF) consumption and the relationship between the two remains inconclusive. To fill this gap in the current literature, our review aimed to answer the following question: is HIIT associated with UPF consumption in adolescents? We executed a systematic review that aimed to investigate how HIIT affects UPF consumption. After conducting the search strategy, no articles fitted our inclusion criteria and our systematic review was therefore classified as an empty review. This absence in the literature highlights shows that is an urgent need for additional epidemiological studies focusing on this issue, for example longitudinal studies and controlled trials, in order to show if there is a relationship between HIIT performance and UPF consumption.",
"keywords": [
"ultra-processed food",
"diet",
"adolescent",
"interval training"
],
"content": "Introduction\n\nOverweight is an important risk factor for chronic non-communicable diseases.1–3 The global prevalence of overweight in adolescents is approximately 20–25%, and is related with high consumption of ultra-processed food (UPF).4–8 Generally, UPF are industrially manufactured foods that contain large amounts of calories, trans fats, sugars, sodium, and chemical additives.9–11 Overweight is also associated with lower intake of vitamins, minerals, fiber and protein.7,8 In this context, reducing the consumption of UPF, as well as improving the amount of physical activity and exercise practice are essential to decreasing the prevalence of overweight in children and adolescents.\n\nExercise is associated with food consumption and energy intake.12,13 Drenowatz et al.14 reported in their review that longitudinal analyses indicate that habitual exercise is beneficial on dietary intake and intake of specific foods. In addition, exercise has been shown to lead to several health benefits in school-aged children and adolescents.15–17 To reach wide health benefits, increasing moderate and vigorous activities are indicated, the highest advantage given when exercise is at vigorous intensity.18,19 In accordance with the current recommendation for children and young people (5–17 years old), vigorous-intensity activities are critical “including those that strengthen muscle and bone, at least three times per week”.20 Cardiorespiratory fitness and muscular strength are central indicators of health in infants and youth. High cardiorespiratory fitness and muscular strength are related to healthy outcomes and a lower risk of developing diseases in the next decades.19,21–23\n\nCurrently, within vigorous intensity activities, there is a surge of interest in high-intensity interval training (HIIT), in both research and clinical perspectives views. In this regard, a recent review24 compared the effects between moderate-intensity continuous training and interval training and showed that interval training provided greater reductions in total absolute fat mass. HIIT refers to alternating short bursts of high intensity activities with recovery periods or light exercise25 and ‘near maximal’ efforts performed at ≥80% of the maximal heart rate or the equivalent as expressed in the function of the maximal oxygen consumption.24 Although HIIT has shown several benefits (e.g. increase in VO2 peak26; improving cardiorespiratory fitness and body composition27; beneficial effects on cognitive performance28,29 and mental health29), to the best of our knowledge, no systematic review has focused on HIIT effects on UPF consumption and the relationship between the two remains inconclusive. To fill this gap in the current literature, our study objectives aimed to answer the following question: is HIIT associated with UPF consumption in adolescents? We executed a systematic review that aimed to investigate the influence of HIIT on UPF consumption in adolescents.\n\n\nMethods\n\nThe eligibility criteria were specified according to the Population, Intervention, Comparison, Outcome (PICO) framework: “P”, adolescent; “I”, the practice of high-intensity training; “C”, the use of other therapies or placebo; and “O”, UPF.\n\nThe eligibility criteria were articles with the following features: (a) adolescent samples (10–19 years old, as defined by the World Health Organization30); (b) assessment of high-intensity interval training; (c) assessment of UPF consumption; (d) studies with observational and clinical trials designs. No language and year of publication restrictions were applied. Articles with incomplete results and systematic reviews were excluded.\n\nWe used three databases (SCOPUS, PubMed, and Embase) for our searches. The search strategy pattern of three blocks of keywords used in PubMed are provided in Box 1. Identical keyword patterns were searched in SCOPUS and Embase. We ran the search for each database in June 2020. The search was performed by two independent researchers (MN and CRM), who also evaluated all references of included articles to find additional sources. Moreover, we also searched in Google Scholar for potential additional articles\n\n(“adolescent”[MeSH Terms] OR “minors”[MeSH Terms] OR “adolescent”[Title/Abstract] OR “minors”[Title/Abstract] OR “Youth”[Title/Abstract] OR “juvenile”[Title/Abstract] OR “teen”[Title/Abstract] OR “teenager”[Title/Abstract] OR “Childhood”[Title/Abstract] OR “adolescence”[Title/Abstract] OR “schoolchild”[Title/Abstract] OR “Schoolchildren”[Title/Abstract] OR “young”[Title/Abstract])\n\nAND\n\n(Ultra-processed[Title/Abstract]) OR “ultra processed”[Title/Abstract]) OR ultraprocessed[Title/Abstract]) OR food processing[MeSH Terms]) OR ready-to-eat[Title/Abstract]) OR “ready to eat”[Title/Abstract]) OR “ready-to-consume”[Title/Abstract]) OR fast food[MeSH Terms]) OR “fast-food”[Title/Abstract]) OR “fast food”[Title/Abstract]) OR fastfood[Title/Abstract]) OR “junk food”[Title/Abstract]) OR “Ready Prepared Food”[Title/Abstract]) OR “Convenience Food”[Title/Abstract])\n\nAND\n\n(“High-intensity training”[Title/Abstract] OR “High-intensity interval training”[Title/Abstract] OR “high-intensity interval training”[MeSH Terms] OR “high intensity intermittent training”[Title/Abstract] OR “Repeated sprint training”[Title/Abstract] OR “interval training”[Title/Abstract] OR “intermittent training”[Title/Abstract] OR “high intensity sprint”[Title/Abstract] OR “aerobic interval training”[Title/Abstract] OR “High-intensity interval training”[Title/Abstract] OR “high-intensity interval exercise”[Title/Abstract] OR “high-intensity interval exercise”[Title/Abstract] OR “high-intensity intermittent exercise”[Title/Abstract] OR “high-intensity intermittent exercise”[Title/Abstract] OR “high intensity intermittent training”[Title/Abstract] OR “high intensity intermittent training”[Title/Abstract] OR “HIIE”[Title/Abstract] OR “HIIT”[Title/Abstract]).\n\nAfter executing the search strategy, articles from all databases were organized, and duplicates eliminated with Mendeley software (Desktop version - 2021). Two reviewers (MN and CRM) separately screened the titles and abstracts of all studies identified in the literature search to see if they met the eligibility criteria. Disagreements were resolved by a third reviewer (PN). All three reviewers have backgrounds in systematic reviews and were trained on the eligibility criteria.\n\n\nResults\n\nEleven suitable articles were recognized (PubMed, 2 studies; SCOPUS, 4 studies; Embase, 5 studies) (Figure 1). After removal of duplicates, five articles remained.31–35 None of the five articles met our eligibility criteria; elimination reasons included that the population was adults and not adolescent, or UPF consumption was not included as an outcome.\n\n\nConclusions\n\nIn accordance with Yaffe et al.,36 if no study meets the eligibility criteria, the review is referred to as an ‘empty review’; empty reviews are known to contribute to inspiring future research.36 Despite the empty review, we believe that it is pertinent to publish our results as our study identifies a gap in the literature concerning HIIT, adolescents and UPF consumption, and may motivate new investigations on this topic and contribute to progress in this research. The present lack of evidence highlights how essential additional epidemiological research will be, especially those with high quality methods and longitudinal and controlled trial designs.\n\nIn adults under a fast food diet, HIIT seems to prevent weight gain and cardiometabolic deterioration.32 These initial findings demand more investigation, as they show promising results against the negative effects of fast foods. Most ready-to-consume foods that are present in fast foods can be considered UPF in the novel classification according to the processing level.10,11 In adolescents with obesity, a single HIIT session is associated with reduced energy intake and subsequent food reward.37 Thus, investigating strategies to counteract the deleterious effects of UPF in health is required and HIIT may have a role to play.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA checklist for ‘High-intensity interval training effects on ultraprocessed food consumption in adolescents: a systematic review’, https://doi.org/10.6084/m9.figshare.15111792.v1.38\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\nTo the Instituto Federal Goiano [ifgoiano.edu.br] for the support.\n\n\nReferences\n\nNg M, Fleming T, Robinson M, et al.: Global, regional, and national prevalence of overweight and obesity in children and adults during 1980–2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2014; 384: 66–81. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgden CL, Carroll MD, Lawman HG, et al.: Trends in Obesity Prevalence Among Children and Adolescents in the United States, 1988-1994 Through 2013-2014. Jama. 2016; 315: 2292–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Global health risks: mortality and burden of disease attributable to selected major risks. Geneva: WHO Press; 2009.\n\nCosta CS, Del-Ponte B, Assunção MCF, et al.: Consumption of ultra-processed foods and body fat during childhood and adolescence: a systematic review. Public Health Nutr. 2018; 21: 148–59. PubMed Abstract | Publisher Full Text\n\nJiang Y, Wang J, Wu S, et al.: Association between Take-Out Food Consumption and Obesity among Chinese University Students: A Cross-Sectional Study. Int J Environ Res Public Health. 2019; 16: 1071. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTripicchio GL, Kachurak A, Davey A, et al.: Associations between Snacking and Weight Status among Adolescents 12–19 Years in the United States. Nutrients. 2019; 11: 1486. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElizabeth L, Machado P, Zinöcker M, et al.: Ultra-Processed Foods and Health Outcomes: A Narrative Review. Nutrients. 2020; 12: 1955. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHall KD, Ayuketah A, Brychta R, et al.: Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain: An Inpatient Randomized Controlled Trial of Ad Libitum Food Intake. Cell Metab. 2019; 30: 67–77.e3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFardet A, Rock E, Bassama J, et al.: Current food classifications in epidemiological studies do not enable solid nutritional recommendations for preventing diet-related chronic diseases: the impact of food processing. Adv Nutr. 2015; 6: 629–38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoubarac J, Claro RM, Baraldi LG, et al.: International differences in cost and consumption of ready-to-consume food and drink products: United Kingdom and Brazil, 2008–2009. Glob Public Health. 2013; 8: 845–56. PubMed Abstract | Publisher Full Text\n\nMonteiro CA, Cannon G: The impact of transnational “big food” companies on the south: a view from Brazil. PLoS Med. 2012; 9: 1–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBeaulieu K, Hopkins M, Blundell J, et al.: Homeostatic and non-homeostatic appetite control along the spectrum of physical activity levels: An updated perspective. Physiol Behav. 2018; 192: 23–9. 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PubMed Abstract | Publisher Full Text\n\nWeston KS, Wisløff U, Coombes JS: High-intensity interval training in patients with lifestyle-induced cardiometabolic disease: a systematic review and meta-analysis. Br J Sports Med. 2014; 48: 1227–34. PubMed Abstract | Publisher Full Text\n\nBaquet G, Berthoin S, Dupont G, et al.: Effects of High Intensity Intermittent Training on Peak VO2 in Prepubertal Children. Int J Sports Med. 2002; 23: 439–44. PubMed Abstract | Publisher Full Text\n\nCostigan SA, Eather N, Plotnikoff RC, et al.: High-intensity interval training for improving health-related fitness in adolescents: a systematic review and meta-analysis. Br J Sports Med. 2015; 49: 1253–61. PubMed Abstract | Publisher Full Text\n\nHwang J, Brothers RM, Castelli DM, et al.: Acute high-intensity exercise-induced cognitive enhancement and brain-derived neurotrophic factor in young, healthy adults. Neurosci Lett. 2016; 630: 247–53. PubMed Abstract | Publisher Full Text\n\nLeahy AA, Mavilidi MF, Smith JJ, et al.: Review of High-Intensity Interval Training for Cognitive and Mental Health in Youth. Med Sci Sport Exerc. 2020; Publish Ah. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: World Health Report. Genebra: WHO; 2001.\n\nTucker WJ, Sawyer BJ, Jarrett CL, et al.: High-intensity interval exercise attenuates but does not eliminate endothelial dysfunction after a fast food meal. Am J Physiol Circ Physiol. 2018; 314: H188–94. PubMed Abstract | Publisher Full Text\n\nDuval C, Rouillier M-A, Rabasa-Lhoret R, et al.: High Intensity Exercise: Can It Protect You from A Fast Food Diet? Nutrients. 2017; 9: 943. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLittle JP, Langley J, Lee M, et al.: Sprint exercise snacks: a novel approach to increase aerobic fitness. Eur J Appl Physiol. 2019; 119: 1203–12. PubMed Abstract | Publisher Full Text\n\nSîrbu E, Buzaș R, Mihăescu R, et al.: Influence of exercise training and eating behavior on arterial stiffness in young healthy students. Wien Klin Wochenschr. 2015; 127: 555–60. PubMed Abstract | Publisher Full Text\n\nJenkins EM, Nairn LN, Skelly LE, et al.: Do stair climbing exercise “snacks” improve cardiorespiratory fitness? Appl Physiol Nutr Metab. 2019; 44: 681–4. PubMed Abstract | Publisher Full Text\n\nYaffe J, Montgomery P, Hopewell S, et al.: Empty Reviews: A Description and Consideration of Cochrane Systematic Reviews with No Included Studies. PLoS One. 2012; 7: e36626. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMiguet M, Fillon A, Khammassi M, et al.: Appetite, energy intake and food reward responses to an acute High Intensity Interval Exercise in adolescents with obesity. Physiol Behav. 2018; 195: 90–7. PubMed Abstract | Publisher Full Text\n\nNoll M: PRISMA checklist. figshare. Figure. 2021. Publisher Full Text"
}
|
[
{
"id": "100347",
"date": "15 Dec 2021",
"name": "Glauber Menezes Lopim",
"expertise": [
"Reviewer Expertise Molecular biology",
"Genetics",
"Liver tumor",
"Neuroscience",
"stress",
"HPA axis",
"Epilepsy",
"Temporal Lobe Epilepsy",
"distress."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 article that proposed to do a meta-analysis review looking at the effects of HIIT exercise on adolescents consuming ultra-processed food. The search methodology for article selection was well done, using the correct Boolean terms in three databases. We realized in our evaluation that other databases could be used, such as Scielo and Lilacs, since the 3 databases selected did not find any paper that related to the theme. For this reason, we believe that it is not possible to replicate the study if other researchers want to use these other two databases.\nFinally, the conclusions presented by the authors are valid; however, the question remains, if the search were expanded to other databases, would it find papers related to the proposed theme.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-857
|
https://f1000research.com/articles/10-476/v1
|
16 Jun 21
|
{
"type": "Research Article",
"title": "Factors influencing COVID-19 vaccine acceptance in Indonesia: an adoption of Technology Acceptance Model",
"authors": [
"Taufik Faturohman",
"Giofella Adesta Navaky Kengsiswoyo",
"Harapan Harapan",
"Suhaiza Zailani",
"R. Aswin Rahadi",
"Neneng Nurlaela Arief",
"Giofella Adesta Navaky Kengsiswoyo",
"Harapan Harapan",
"Suhaiza Zailani",
"R. Aswin Rahadi",
"Neneng Nurlaela Arief"
],
"abstract": "Background: It is critical to understand the factors that could affect the acceptance of the coronavirus disease 2019 (COVID-19) vaccine in the community. The aim of this study was to determine factors that could possibly affect the acceptance of Indonesian citizens of COVID-19 vaccination. Methods: An online survey was conducted between the first and fifth of November, 2020. Participants were asked to respond to questions on acceptance, perceived usefulness, perceived ease of use, perceived religiosity towards, and amount of information about COVID-19. This study used the Technology Acceptance Model (TAM) as the framework to decide factors that affect vaccine acceptance. Structural Equation Model was employed to assess the correlation between all explanatory variables and vaccine acceptance. Mann-Whitney test and Kruskal-Wallis rank were employed to assess demographic factors associated with acceptance. Results: In total, 311 responses were included for analysis. Our TAM model suggested that high perceived usefulness significantly increased COVID-19 vaccine acceptance and high perceived ease of use significantly increased the perceived usefulness. Perceived religiosity did not substantially affect vaccine acceptance. The amount of information on COVID-19 also did not significantly affect vaccine acceptance. Our data suggested that vaccine acceptance was associated with age, type of occupation, marital status and monthly income to some degree. Conclusion: Since perceived usefulness affects vaccine acceptance, the government should focus on the usefulness of the vaccine when promoting the COVID-19 vaccine to Indonesian citizens. In addition, since perceived ease of use significantly affects users’ acceptance to COVID-19 vaccine, the easier to acquire the vaccine in the community, the higher chance that the citizens are willing to be vaccinated.",
"keywords": [
"COVID-19 vaccine",
"acceptance",
"technology acceptance model",
"Indonesia"
],
"content": "Introduction\n\nIn December 2019, unknown pneumonia cases in Wuhan were reported to the World Health Organization (WHO) and later named as coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The outbreak was officially declared a Public Health Emergency of International Concern on January 30, 2020 by the WHO and announced as a pandemic on March 11, 2020.1–2 The pandemic has affected human welfare globally, including in Asia-Oceania countries such as Indonesia.3 Several COVID-19 vaccine candidates have been or are being clinically evaluated and more than a hundred vaccine candidates are in preclinical study.4–6 COVID-19 vaccines produced by Pfizer, BioNTech, and Moderna have been reported to have good efficacy.7 However, vaccine hesitancy does exist among potential vaccine receivers. Vaccine hesitancy could delay the implementation of vaccination and increase refusal in community.8 There is strong evidence that vaccine hesitancy could decrease vaccine coverage and increase the risk of vaccine-preventable disease outbreaks and epidemics.9 In addition, it is critical to understand the factors that could possibly affect the acceptance level since the vaccination is voluntary. Governments need to plan the best approaches to promoting vaccines when they become available for the citizens.\n\nMany factors could affect vaccine acceptance. Studies have assessed the role of perceived risk, vaccine efficacy, amount of information, and types of job on vaccine acceptance.10–12 However, due to culture diversity, each country might have different level of acceptance and associated determinants. A previous study integrated religiosity into the Technology Acceptance Model (TAM) in Indonesian citizens,13 and another study revealed that religiosity emerged as an essential determinant influencing parents’ approach on health management issues.14 Religious aspects on vaccination are important for Indonesians such as the controversy regarding halal certification of a rubella vaccine in 2018.15 Data from the Pew Research Center survey showed that Indonesia is one of most religious counties in the world.16 Therefore, perceived religiosity could be an important factor that affects vaccine acceptance.\n\nThis study was conducted to assess determinants that could affect the acceptance of the COVID-19 vaccine in Indonesia. This study used TAM model as an approach to assess the possible determinants associated with vaccine acceptance, as TAM is more applicable compared to the Theory of Planned Behavior (TPB) or the Theory of Reasoned Action (TRA).17 TPB is a theory that explains how human behavior is formed and why individuals act the way they act, and the study factors include attitude toward an act of behavior, subjective norm, and perceived behavioral control.18 TRA model modifies the TPB model by adding several factors that influence the attitude and subjective norm.19 Since the vaccine is considered to be technology, TAM is therefore adopted. This is the first study that uses the TAM model in assessing COVID-19 vaccine acceptance in Indonesia. The findings of this study could help the policymaker to choose the most suitable campaign strategy or plan to promoting the COVID-19 vaccine.\n\n\nMethods\n\nThe study was conducted according to the guidelines of the Declaration of Helsinki, and ap-proved by the Institutional Review Board of Institut Teknologi Bandung (2475/IT1.C09.1/DL/2021). Prior to participating in the survey, the participants were provided with a brief explanation of the aims and benefits of the study. Participants read an informed consent form and confirmed their consent by clicking “I agree to participate in the study” prior to any data collection occurring.\n\nThere was no COVID-19 vaccine available in Indonesia when the study was conducted. Therefore, a hypothetical COVID-19 vaccine was used as described in previous studies.12,20–22 An online survey using Google Forms was conducted between the first and the fifth of November 2020. The target population was Indonesians who were 18 years old or older and able to read and understand Bahasa Indonesia. We employed a snowball sampling technique where the survey was distributed through online platforms such as WhatsApp, Line, Instagram and Twitter. It took approximately 10 minutes to finish the survey. The minimum sample needed to conduct the Structural Equation Model (SEM) was 300 respondents since it had less than seven constructs.23 The population in Indonesia reached 265 million24 and this study received 311 responses. A total sample of 311 from a population greater than 100.000 has an error rate of ±7%.25\n\nA questionnaire was developed based on information and questions from a previous study.10 The questionnaire consisted of several sections: sociodemographic, COVID-19 vaccine acceptance, and some explanatory variables. The response variable of the present study was COVID-19 acceptance. To access the acceptance, respondents were provided some hypothetical information, adopted from a previous study:10 (a) a COVID-19 vaccine is not available and respondents were asked to think if the vaccine is available; (b) a COVID-19 vaccine has been developed and clinically tested on humans; (c) the results of the clinic trial indicated that the vaccine has a chance to generate some side effects such as fever, skin rash and pain at injection area. The acceptance on COVID-19 was measured using four statements: (1) I am willing to be vaccinated; (2) I am willing to be vaccinated if the government give it for free; (3) I am willing to be vaccinated if the vaccine efficacy is more than 70%; and (4) I am willing to be vaccinated if the vaccine efficacy is more than 50%. The possible responses were provided in a Likert scale from strongly disagree (scored as one) to strongly agree (scored as five).\n\nThe explanatory variables and the number of questions to assess each explanatory variable were: perceived usefulness (four questions); perceived ease of use (three questions); perceived religiosity (four questions); and amount of information on COVID-19 (five questions). The possible responses were also provided in a Likert scale from strongly disagree (scored as one) to strongly agree (scored as five). The detailed questions used to assess each domain are presented in Table 1. The questionnaire also collected information on age, gender, marital status, religion, educational attainment, type of occupation, and monthly income.\n\nTo assess the validity and reliability of the questionnaire, average variance extracted (AVE), composite reliability, factor loading and Cronbach’s alpha were measured for each domain of variable. Our data suggested that each item within each domain had standard loadings value higher than 0.5 and AVE higher than 0.5, suggesting that the question within the domain had acceptable convergence and all items used within domain are valid (Table 1). In addition, both composite reliability and Cronbach’s alpha were greater than 0.7 indicating that items within the domain were reliable (Table 1).\n\nA previous study modified the TAM model to assess the customers’ acceptance26 where perceived religiosity, amount of information, perceived usefulness, and perceived ease of use were used to evaluate customers’ acceptance.26 In our proposed TAM model, we included four explanatory variables: (1) perceived usefulness; (2) perceived ease of use; (3) perceived religiosity; and (4) amount of information that might affect the acceptance on COVID-19 vaccine. This study also sought to assess whether perceived ease of use influenced the perceived usefulness. The constructs of the proposed TAM model are presented in Figure 1. The proposed model consisted of five hypotheses: (1) perceived usefulness influences the vaccine acceptance (H1); (2) perceived ease of use influences perceived usefulness (H2); (3) perceived religiosity influences the vaccine acceptance (H3); (4) amount of information on COVID-19 influences perceived usefulness (H4); and (5) perceived ease of use influences the perceived usefulness (H5). SEM modeling was used to assess the relationship between the variables. The goodness of fit of the model was measured using: (1) absolute best fit (degree of freedom (df) and root mean square error of approximation (RMSEA)) and (2) incremental goodness of fit (goodness of fit index (GFI); adjusted goodness of fit index (AGFI); minimum discrepancy per degree of freedom (CMIN/DF); Tucker-Lewis index (TLI); and comparative fit index (CFI)). The relationship between the variables in the hypotheses were interpreted based on the value of regression weights. A significant relationship was indicated as p < 0.05 and the critical ratio of each relation should be higher than 2.00.\n\nIn addition, to assess the demographic factors associated with acceptance of COVID-19 vaccine, Mann-Whitney test was employed. For variables that had more than two sub-groups, Kruskal-Wallis rank was used first to assess the difference among sub-groups.27 The analyses were conducted using SPSS Amos version 24 and STATA version 13.\n\n\nResults\n\nWe received 311 completed responses and included all of them in the analysis. Of the total respondents, the vast majority (219/311, 70.4%) were female and more than half (52.7%) aged between 18-24 years-old (Table 2). Of total respondents, 58.5% were un-married and vast majority (73.9%) were Muslim. More than half (50.8%) of respondents had no university degree and 52.4% respondents earned less than 2.5 million Indonesian Rupiah each month (equivalent to approximately USD 172). Less than 15% of them had monthly income more than 10 million Indonesian Rupiah (USD 690).\n\nInitial analysis of our proposed TAM model suggested that the model did not meet some parameters based on goodness of fit test (Table 3). The proposed model only passed the df, and CMIN/DF indicating that the goodness of fit of proposed model was unsatisfactory. Therefore, the model should be modified to ensure that the model was acceptable. Figure 2A shows the modified model. In the modified model, a variable that was not significant to vaccine acceptance, perceived religiosity, was eliminated. The modified model's three hypotheses were tested: (1) perceived usefulness influences the vaccine acceptance (H1); (2) perceived religiosity influences the vaccine acceptance (H2); and (3) perceived ease of use influences perceived usefulness (H3).\n\nThe results of the goodness of fit of the modified model are presented in Table 4. We used two types of goodness of fit model analysis: absolute best fit and incremental goodness of fit. The indicators used for absolute best fit analysis were df and RMSEA. The value of df and RMSEA were acceptable since it met the requirement of the cut-off value. Five indicators were used for the incremental goodness of fit analysis: GFI, AGFI, CMIN/DF, TLI, and CFI. Our data suggested that all indicators met the requirements suggesting that the model was fit and acceptable (Table 3 and Figure 2B).\n\nThe results of SEM analysis of the modified model are shown in Table 4. Our data suggested that perceived usefulness significantly affected the acceptance for a COVID-19 vaccine (p < 0.001). Data revealed that perceived religiosity did not significantly affect the vaccine acceptance (p = 0.217). Lastly, SEM analysis indicated that perceived ease of use significantly affected the perceived usefulness (p < 0.001).\n\nOur data suggested that the acceptance score was associated with age group, types of occupation, marital status and monthly income to some degree (Table 5). Our data suggested that respondents who were single had higher acceptance compared to married respondents (p = 0.001). Respondents who were between 18-24 years old had higher vaccine acceptance compared to those between 25-44 years old (p = 0.017) or to those who were older than 44 years (p < 0.001).\n\na Analyzed with Mann-Whitney test.\n\nb Analyzed with Kruskal-Wallis rank test.\n\nWe also found a significant difference of COVID-19 vaccine acceptance between three categories of monthly incomes (p < 0.043) (Table 5). The vaccine acceptance score was significantly different between respondents who earned less than 2.5 million rupiahs in a month and those who earned 2.5 to 10 million Indonesia Rupiah in a month (p < 0.001). Interestingly, no significant difference on acceptance score was observed between the poorest group compared to the wealthiest group (mean score 3.71 vs 3.51 with p = 0.531). Our data suggested that gender (p = 0.132), educational attainment (p = 0.060), and religion (p=0.140) had no association with acceptance of a COVID-19 vaccine.\n\n\nDiscussion\n\nPositive behavior and high end-user’s acceptance are important to increase the customer's chance to accept, buy, or use a product. Marketing campaigns are required not only for commercial products but also for public products and facilities such as vaccination. Therefore, it is critical to understand the factors associated with vaccine acceptance in order to be able to use the right campaign strategy to promote the vaccine to the correct community groups. The objective of our study was to assess the associated determinants of COVID-19 vaccine acceptance using a TAM model in Indonesia. There are several studies that have used the TAM in assessing vaccine acceptance; however, to the best of our knowledge, this is the first study that used TAM model to assess COVID-19 vaccine acceptance in Indonesia. Our TAM model suggested that perceived usefulness influenced the vaccine acceptance, suggesting that the more useful a vaccine is perceived to be by a respondent, the more likely the respondent is willing to be vaccinated. This indicates that the usefulness is an essential factor for communities to accept a vaccine and to be willing to be vaccinated.\n\nA study suggested that perceived ease of use is where a person believes that using a system will be free from effort.28 In this study, perceived ease of use refers to the ease and convenience of acquiring the COVID-19 vaccine in Indonesia. Our data demonstrated that perceived ease of use did not directly influence the COVID-19 vaccine acceptance. However, it did influence the perceived usefulness, which in turn influenced vaccine acceptance. These suggest that the ease and convenience in acquiring the COVID-19 vaccine influences the respondents’ perspective on vaccination.\n\nOur study also reported some findings that could help government to identify which demographic groups had low COVID-19 vaccine acceptance. Our data suggested that the older community and those who were working as employees and entrepreneurs had lower COVID-19 vaccine acceptance compared to younger citizens and students, respectively. Taking these findings into account, the government could consider targeting those groups for a mass vaccine campaign to increase the vaccine coverage.\n\nWe recommend that the government create a strategy that focuses on the usefulness and ease of using the vaccine to the citizens. The perceived usefulness of this vaccine can be shown by using the word “useful”, “helpful”, “protect”, or any other terms indicating that the vaccine is beneficial for the community if they are vaccinated as soon as possible. Also, since perceived ease of use affects the perceived usefulness, the government needs to ensure that it will be easy for Indonesian citizens to acquire the vaccine. An even distribution of the COVID-19 vaccine for Indonesian citizens could increase their perceived ease of use.\n\nThere are however some limitations of this study. The sample size was relatively small due to limited amount of time in conducting the study. Nevertheless, the number of samples used met the minimal sample size for TAM model. In addition, since this study was meant to provide the recommendation to the Indonesian government, time was the main concern during conducting the study. There were only four factors that were analyzed using the TAM model and some other important factors such as perceived risk, perceived severity, and perceived barriers might need to be determined and analyzed in future.\n\n\nConclusions\n\nOur data indicate that perceived usefulness affects the COVID-19 vaccine acceptance, while the perceived usefulness is influenced by perceived ease of use. Therefore, during the mass vaccination campaign, we recommend the Indonesian government or other related organizations focus on providing information on the benefit of vaccination to the community and to ensure that the vaccines are easy to be accessed.\n\n\nData availability\n\nFigshare: Factors influencing COVID-19 vaccine acceptance in Indonesia: an adoption of Technology Acceptance Model (TAM). https://doi.org/10.6084/m9.figshare.14741508.29\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Questionnaire Factors influencing COVID-19 vaccine acceptance in Indonesia: An adoption of Technology Acceptance Model (TAM). https://doi.org/10.6084/m9.figshare.14741424.30\n\nThis project contains the following extended data:\n\n• Full questionnaire with English translation\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nWe would like to thank Narra Studio Jurnal for assistance.\n\n\nReferences\n\nWorld Health Organization: Statement on the Second Meeting of the International Health Regulations (2005) Emergency Committee Regarding the Outbreak of Novel Coronavirus (2019-nCoV) (2020). [Accessed December 13, 2020]. Reference Source\n\nWorld Health Organization: WHO Director-General’s Opening Remarks at the Media Briefing on COVID-19 (2020). [Accessed December 13, 2020]. Reference Source\n\nChhetri JK, Chan P, Arai H, et al.: Prevention of COVID-19 in older adults: a brief guidance from the international association for gerontology and geriatrics (IAGG) Asia/Oceania region. J Nutr Health Aging. 2020; 24: 471–472. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Draft Landscape of COVID-19 Candidate Vaccines.2020. [Accessed December 13, 2020]. Reference Source\n\nZhu FC, Li YH, Guan XH, et al.: Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet. 2020; 395: 1845–1854. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu FC, Guan XH, Li YH, et al.: Immunogenicity and safety of a recombinant adenovirus type-5-vectored COVID-19 vaccine in healthy adults aged 18 years or older: a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet. 2020; 396: 479–488. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnson CY, Steckelberg A: What you need to know about the Pfizer, Moderna and AstraZeneca vaccines.2020. [Accessed December 13, 2020]. Reference Source\n\nYufika A, Wagner AL, Nawawi Y, et al.: Parents’ hesitancy towards vaccination in Indonesia: A cross-sectional study in Indonesia. Vaccine. 2020; 38(11): 2592–2599. PubMed Abstract | Publisher Full Text\n\nDubé E, Laberge C, Guay M, et al.: Vaccine Hesitancy. Hum Vaccin Immunother. 2013; 9: 1763–1773. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarapan H, Wagner AL, Yufika A, et al.: Acceptance of a COVID-19 vaccine in southeast Asia: a cross-sectional study in Indonesia. Front Public Health. 2020; 8: 381. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLazarus JV, Ratzan SC, Palayew A, et al.: A global survey of potential acceptance of a COVID-19 vaccine. Nat Med. 2020; 27: 225–228. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHarapan H, Anwar S, Setiawan AM, et al.: Dengue vaccine acceptance and associated factors in Indonesia: A community-based cross-sectional survey in Aceh. Vaccine. 2016; 34: 3670–3675. PubMed Abstract | Publisher Full Text\n\nUsman H, Mulia D, Chairy C, et al.: Integrating trust, religiosity and image into technology acceptance model: the case of the Islamic philanthropy in Indonesia. J Islam Mark. 2020. Publisher Full Text\n\nThomas T, Blumling A, Delaney A: The influence of religiosity and spirituality on rural parents’ health decision making and human papillomavirus vaccine choices. ANS Adv Nurs Sci. 2015; 38: E1–E12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNovitasari Y: Imunisasi Menurut Agama, Bagaimana Hukumnya? kumparan. 2020. [Accessed December 17, 2020] Reference Source\n\nIswara MA: Indonesia ranks among most religious countries in Pew study.2020. [Accessed December 17, 2020] Reference Source\n\nVenkatesh V, Davis FD: A Theoretical Extension of the Technology Acceptance Model: Four Longitudinal Field Studies. Manage Sci. 2000; 46: 186–204. Publisher Full Text\n\nAjzen I: The Theory of Planned Behavior. Organ Behav Hum Decis Process. 1991; 50: 179–211. Publisher Full Text\n\nFishbein M: A theory of reasoned action: Some applications and implications. Nebr Symp Motiv. 1979; 27: 65–116. PubMed Abstract\n\nHarapan H, Mudatsir M, Yufika A, et al.: Community acceptance and willingness-to-pay for a hypothetical Zika vaccine: A cross-sectional study in Indonesia. Vaccine. 2019; 37: 1398–1406. PubMed Abstract | Publisher Full Text\n\nHarapan H, Anwar S, Bustamam A, et al.: Willingness to pay for a dengue vaccine and its associated determinants in Indonesia: A community-based, cross-sectional survey in Aceh. Acta Trop. 2017; 166: 249–256. PubMed Abstract | Publisher Full Text\n\nRajamoorthy Y, Radam A, Taib NM, et al.: Willingness to pay for hepatitis B vaccination in Selangor, Malaysia: A cross-sectional household survey. PLoS One. 2019; 14: 1–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHair JF: Multivariate Data Analysis. Edinburg: Pearson; 2014.\n\nBadan Pusat Statistik: Statistical yearbook of indonesia 2018. indonesia: Badan Pusat Statistik; 2018.\n\nIsrael GD: Determining Sample Size. Florida: University of Florida; 2012.\n\nAmin H, Abdul-Rahman AR, Ramayah T, et al.: Determinants of Online Waqf Acceptance: An Empirical Investigation. Electron J Inf Syst Dev Ctries. 2014; 60: 1–18. Publisher Full Text\n\nMcKnight PE, Najab J: Mann-Whitney U test. The corsini encyclopedia of psychology. 2010. Publisher Full Text\n\nDavis F: Perceived usefulness, perceived ease of use, and user acceptance of information technology. MIS Q. 1989; 13: 319–340. Publisher Full Text\n\nFaturohman F, Kengsiswoyo GAN, Harapan H, et al.: Factors influencing COVID-19 vaccine acceptance in Indonesia: An adoption of Technology Acceptance Model (TAM). Figshare. Dataset. 2021. Publisher Full Text\n\nFaturohman F, Kengsiswoyo GAN, Harapan H, et al.: Questionnaire_Factors influencing COVID-19 vaccine acceptance in Indonesia: An adoption of Technology Acceptance Model (TAM). Figshare. Journal contribution. 2021. Publisher Full Text"
}
|
[
{
"id": "89126",
"date": "08 Jul 2021",
"name": "Ching Sin Siau",
"expertise": [
"Reviewer Expertise health psychology",
"public health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an important study on the factors influencing COVID-19 vaccine acceptance, with a unique take from a TAM Model point of view.\nAbstract\nI suggest that the TAM Model should be mentioned in the Background of the Abstract, as it is the unique approach and is foundational to the placement and analysis of the paper.\n\nIntroduction\nI would like to suggest that the authors consider improving the first sentence, as it is rather long and difficult to read.\n\nThe authors cited another study that had used the TAM Model. Could the authors consider elaborating more on the results, so that we know what has already been done in this aspect? Otherwise, readers may misunderstand that the TAM model had already been used in vaccine acceptance studies in Indonesia.\n\nThe rationale of the study: Is there currently a problem in vaccine uptake in the country? It would be interesting to know the vaccination status and any problems encountered which gave rise to the study.\n\nAim of the study: Please incorporate the religious component into the aim, as it is one of the important variables that was investigated.\n\nMethods Study design and setting:\nPlease correct the spelling of \"ap-proved\".\n\nHad the vaccination programme begun in Indonesia on 1-5 November 2021? If not, it is useful to mention that the vaccination programme had not been rolled out. This will provide an important context to the study.\n\nAnother context that can be provided (perhaps in the Introduction) is the number of confirmed cases and deaths in early November 2020 in Indonesia. This can be retrieved from WHO COVID-19 Dashboard.\n\nStudy instrument and variables:\nI wonder if it would be more accurate to use the term \"vaccine effectiveness\"? As this is a public perception study and not a controlled experiment or clinical trial, I think \"effectiveness\" would be more appropriate. Please consider revising.\n\nPlease mention somewhere in the study instrument section that the questionnaire was in Bahasa Indonesia.\n\nResults\nRespondents' characteristics - since Indonesia is a large country, is the locality involved in the respondents' place of origin?\n\nDiscussion\nRather than \"Marketing campaigns\" - in which a product is being promoted - I think \"public health awareness campaign\" would be more appropriate. I understand that there are similarities, but marketing a vaccine is unethical in a developing country, and especially so since the vaccine is provided for free in most countries. Therefore, I strongly recommend removing this allusion.\n\nThere is a lack of comparison to other studies conducted in the Discussion, therefore the section lacks depth and context. Please try to relate the findings to the existing literature on vaccination, and more specifically (if available) other countries that had used the TAM model in evaluating vaccine acceptance.\n\nOlder individuals had low vaccine acceptance. Why do you think so? Please discuss this in more depth and with reference to other studies, preferably those conducted in this region (Southeast Asia).\n\nPlease discuss further on the aspect of perceived usefulness. Does this mean that, perhaps, the participants did not believe that the vaccines are not effective? Therefore, the questions on vaccine effectiveness that were utilised in this study should be discussed further (50% vs 70% effectiveness comparisons).\n\nPlease discuss the results pertaining to religion as it was one of the variables in this study.\n\nLimitations\nPlease mention the limitations inherent in a cross-sectional and online survey using convenience sampling.\n\nAlso, the lack of information on the locality of the participants (if applicable) in a large country.\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": "7054",
"date": "26 Aug 2021",
"name": "Taufik Faturohman",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for your suggestions and corrections. We appreciate all of them. Here are our detailed responses: Abstract I suggest that the TAM Model should be mentioned in the Background of the Abstract, as it is the unique approach and is foundational to the placement and analysis of the paper. RESPONSE(S): Thank you. It has been added. Introduction I would like to suggest that the authors consider improving the first sentence, as it is rather long and difficult to read. RESPONSE(S): Thank you, it has been revised. The authors cited another study that had used the TAM Model. Could the authors consider elaborating more on the results, so that we know what has already been done in this aspect? Otherwise, readers may misunderstand that the TAM model had already been used in vaccine acceptance studies in Indonesia. RESPONSE(S): Have been added: “The study used TAM in the use of financial technology (Fintech) in the context of Islamic philanthropy in Indonesia and found that the relationship between perceived usefulness and perceived ease of use was determined by trust and religiosity.” The rationale of the study: Is there currently a problem in vaccine uptake in the country? It would be interesting to know the vaccination status and any problems encountered which gave rise to the study. RESPONSE(S): Thank you for your suggestion. We have added this in the revised manuscript. We added: “Vaccination is one of the strategies to control the current COVID-19 pandemic. The coverage of COVID-19 vaccination in Indonesia is lower compared to countries in the region and a study in Indonesia found that COVID-19 acceptance is influenced by the effectiveness of the vaccine as well as the perceived risk. This study was conducted to assess other determinants that could affect the acceptance of the COVID-19 vaccine in Indonesia.” Aim of the study: Please incorporate the religious component into the aim, as it is one of the important variables that was investigated. RESPONSE(S): Thank you. Religious component has been added. We added: “This study was conducted to assess other determinants that could affect the acceptance of the COVID-19 vaccine in Indonesia including perceived religiosity that is rarely evaluated.” Methods Study design and setting: Please correct the spelling of \"ap-proved\". RESPONSE(S): Corrected. Thank you. Had the vaccination programme begun in Indonesia on 1-5 November 2021? If not, it is useful to mention that the vaccination programme had not been rolled out. This will provide an important context to the study. RESPONSE(S): Thank you. We have added the information. “An online survey using Google Forms was conducted between the first and the fifth of November 2020 when vaccination programme had not been rolled out in the country.” We would like to correct that the study was conducted 1-5 November 2020, not 2021. Another context that can be provided (perhaps in the Introduction) is the number of confirmed cases and deaths in early November 2020 in Indonesia. This can be retrieved from WHO COVID-19 Dashboard. RESPONSE(S): Thank you. We have added this information in the Methods rather than in the Introduction. This is to help readers to have a better understanding of why we provide the number of cases and mortality cases in those periods. We added: “During the study period the daily COVID-19 cases ranged between 2,696-4,065 with case mortality ranged between 74-113 deaths.” Study instrument and variables: I wonder if it would be more accurate to use the term \"vaccine effectiveness\"? As this is a public perception study and not a controlled experiment or clinical trial, I think \"effectiveness\" would be more appropriate. Please consider revising. RESPONSE(S): Thank you. We agree with the reviewer and we have revised as recommended. We revised: “(3) I am willing to be vaccinated if the vaccine effectiveness is more than 70%; and (4) I am willing to be vaccinated if the vaccine effectiveness is more than 50%.” Please mention somewhere in the study instrument section that the questionnaire was in Bahasa Indonesia. RESPONSE(S): Have been added. We added: “A questionnaire in Bahasa Indonesia (national language) was developed based on information and questions from a previous study”. Results Respondents' characteristics - since Indonesia is a large country, is the locality involved in the respondents' place of origin? RESPONSE(S): During the study, we collected the information of the residential of the respondents but we chose not to include them since some places had a limited number of respondents and the places are very diverse. Discussion Rather than \"Marketing campaigns\" - in which a product is being promoted - I think \"public health awareness campaign\" would be more appropriate. I understand that there are similarities, but marketing a vaccine is unethical in a developing country, and especially so since the vaccine is provided for free in most countries. Therefore, I strongly recommend removing this allusion. RESPONSE(S): Thank you for your suggestion. We have deleted the sentence. There is a lack of comparison to other studies conducted in the Discussion, therefore the section lacks depth and context. Please try to relate the findings to the existing literature on vaccination, and more specifically (if available) other countries that had used the TAM model in evaluating vaccine acceptance. RESPONSE(S): Thank you for your suggestion. Studies assessing vaccine acceptance using the TAM model are limited. However, we have added some previous studies with their references. We provided also explained the findings of the previous study on influenza vaccine acceptance. Older individuals had low vaccine acceptance. Why do you think so? Please discuss this in more depth and with reference to other studies, preferably those conducted in this region (Southeast Asia). RESPONSE(S): That statement is based on our data that suggesting people aged ≥45-year group had lower vaccine acceptance compared to those within the 18-24-years group (See Table 5). However, we have elaborated this finding with previous studies. We wrote: “The role of age on vaccine acceptance is conflicting; some studies found the association while some studies found no association. We cited some references: (1) Sallam M. COVID-19 Vaccine Hesitancy Worldwide: A Concise Systematic Review of Vaccine Acceptance Rates. Vaccines 2021, 9, 160 (2) Bono SA, Faria de Moura Villela E, et al. Factors affecting COVID-19 vaccine acceptance: an international survey among low- and middle-income countries. Vaccines 2021, 9, 515 (3) Lazarus JV, Ratzan SC, Palayew A, et al. A global survey of potential acceptance of a COVID-19 vaccine. Nat. Med 2021;27:225-228 Please discuss further on the aspect of perceived usefulness. Does this mean that, perhaps, the participants did not believe that the vaccines are not effective? Therefore, the questions on vaccine effectiveness that were utilised in this study should be discussed further (50% vs 70% effectiveness comparisons). RESPONSE(S): We have included the information of perceived usefulness in the revised manuscript. We added: “Perceived usefulness in the present study refers to the degree to which the individual believes that vaccination could prevent themselves from getting COVID-19.” Please discuss the results pertaining to religion as it was one of the variables in this study. RESPONSE(S): Thank you for your suggestion. Since perceived religiosity has no association with vaccine acceptance, we prefer not to discuss the negative result. Limitations Please mention the limitations inherent in a cross-sectional and online survey using convenience sampling. RESPONSE(S): Thank you for your suggestion. Since we have stated clearly the setting of our study (cross-sectional and online survey using convenience sampling), we believe that readers already acknowledge the limitation of our study. However, we have added: “Since this study used the convenience sampling, the number of respondents was not equally distributed from all parts of Indonesia”. Also, the lack of information on the locality of the participants (if applicable) in a large country. RESPONSE(S): During the study, we collected the information of the residential of the respondents but we chose not to include them since some places had a limited number of respondents and the places are very diverse. We have included this as our limitation: “The sample size was relatively small due to limited amount of time in conducting the study and therefore some regions had limited numbers of respondents.” Thank you."
}
]
},
{
"id": "91709",
"date": "16 Aug 2021",
"name": "Timotius Ivan Hariyanto",
"expertise": [
"Reviewer Expertise COVID-19",
"internal medicine",
"epidemiology",
"public health",
"infectious disease",
"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\nEditorial Note from F1000Research - 31st March 2023: This report has been updated to include a conflict of interest statement which was not declared at the time of publishing of this report.\nThank you for inviting me to review this manuscript.\nThis manuscript provides evidence regarding the COVID-19 vaccine acceptance rate and analyzed the factors which influence COVID-19 vaccine acceptance in Indonesia. Overall, this study has good methodological quality and was presented in a descriptive and informative manner. I only have a few comments/concerns regarding this manuscript:\nThis study was conducted in November 2020 where there was no COVID-19 vaccine available in Indonesia. Of course, this can be a great limitation to this study because, at that time, information regarding the COVID-19 vaccine in Indonesia was relatively low, and not all Indonesian citizens had enough exposure to information regarding the COVID-19 vaccine - including its content, efficacy, and safety profiles. Knowledge and having sufficient information regarding the COVID-19 vaccine surely may influence the vaccine acceptance; however, this study did not assess the participants' information or knowledge regarding the COVID-19 vaccine. Please mention this in the limitations of this study. This study also still needs confirmation from the newer studies about the COVID-19 vaccine which were conducted in February or March 2021 when the COVID-19 vaccine was already available in Indonesia.\n\nThis study only assesses three factors for COVID-19 vaccine acceptance: perceived usefulness, perceived religiosity, and perceived ease of use in the SEM analysis of the modified model. How about the safety profile of the COVID-19 vaccine? Safety profile has also become the main issue among Indonesian citizens which can also influence vaccine acceptance.\n\nThis study was conducted in Indonesia. Indonesia has 34 provinces. Do the authors have data regarding the participant's province or region? The region or province of the participants is also an important factor because each province in Indonesia has different cultures and beliefs which may also affect the COVID-19 vaccine acceptance.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7055",
"date": "26 Aug 2021",
"name": "Taufik Faturohman",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for your suggestions and corrections. We appreciate all of them. Here are our detailed responses: Thank you for inviting me to review this manuscript. This manuscript provides evidence regarding the COVID-19 vaccine acceptance rate and analyzed the factors which influence COVID-19 vaccine acceptance in Indonesia. Overall, this study has good methodological quality and was presented in a descriptive and informative manner. I only have a few comments/concerns regarding this manuscript: This study was conducted in November 2020 where there was no COVID-19 vaccine available in Indonesia. Of course, this can be a great limitation to this study because, at that time, information regarding the COVID-19 vaccine in Indonesia was relatively low, and not all Indonesian citizens had enough exposure to information regarding the COVID-19 vaccine - including its content, efficacy, and safety profiles. Knowledge and having sufficient information regarding the COVID-19 vaccine surely may influence the vaccine acceptance; however, this study did not assess the participants' information or knowledge regarding the COVID-19 vaccine. Please mention this in the limitations of this study. This study also still needs confirmation from the newer studies about the COVID-19 vaccine which were conducted in February or March 2021 when the COVID-19 vaccine was already available in Indonesia. RESPONSE(S): We have added this as one of our limitations. We added: “One of the possible determinant of vaccine acceptance is knowledge and having sufficient information regarding the COVID-19 vaccine and our present study did not assess these domains.” This study only assesses three factors for COVID-19 vaccine acceptance: perceived usefulness, perceived religiosity, and perceived ease of use in the SEM analysis of the modified model. How about the safety profile of the COVID-19 vaccine? Safety profile has also become the main issue among Indonesian citizens which can also influence vaccine acceptance. RESPONSE(S): Thank you for your comment. We have discussed this as one of the main limitations in the original manuscript. Also, we have done the study to assess the effect of vaccine profiles (efficacy and safety) in Indonesia and the manuscript has been submitted to the journal. This study was conducted in Indonesia. Indonesia has 34 provinces. Do the authors have data regarding the participant's province or region? The region or province of the participants is also an important factor because each province in Indonesia has different cultures and beliefs which may also affect the COVID-19 vaccine acceptance. RESPONSE(S): During the study we collected the information of the residential of the respondents but we chose not to included them since some places had limited number of respondents and the places are very diverse. We have included in our limitation: “The sample size was relatively small due to limited amount of time in conducting the study and therefore some regions had limited numbers of respondents.”"
}
]
}
] | 1
|
https://f1000research.com/articles/10-476
|
https://f1000research.com/articles/10-856/v1
|
26 Aug 21
|
{
"type": "Research Article",
"title": "The cost of business restrictions during the COVID-19 pandemic",
"authors": [
"Joshua T. Cohen",
"Samuel B. Weidner",
"Samuel B. Weidner"
],
"abstract": "Background: In addition to reducing mortality and morbidity, COVID-19 therapies confer societal benefits by reducing the disease’s economic impact. Therapies that address COVID hospitalizations mitigate the need for government-imposed economic restrictions to reduce disease spread and hence the risk that hospitals become overwhelmed. We investigated the potential value of such therapies by estimating the cost of government restrictions imposed during late 2020, costs that COVID therapies might make less necessary. Methods: We combined high frequency consumer spending and initial unemployment claims data (outcomes), information about when state governments restricted business activities (explanatory variable of interest), and case incidence and mortality data (proxies for the potential confounding effect of pandemic severity on voluntary economic activity reductions). We developed linear mixed models that account for nesting within US state and correlation across observations close in time. Sensitivity analyses explored the impact of: (1) limiting attention to the 10 U.S. states that “mostly closed” at some point during late 2020; (2) excluding subsets of potential confounding variables; (3) altering our outcome variable definition (i.e., for designating a state as “mostly closed”); and (4) considering alternative model correlation structures.\nResults: Government-imposed restrictions reduced total consumer spending by 2% and spending on restaurants and accommodations by 5%. They increased weekly initial unemployment claims by 0.21% of the 2019 US workforce. We estimate that restrictions in the U.S. during late 2020 reduced consumer spending by $12 billion and increased initial weekly unemployment claims by 114,000. Sensitivity analyses indicated that our findings are robust. Conclusions: Assuming that late 2020 is representative of tendencies for the government to restrict economic activity in response to high hospital utilization, therapies reducing hospital utilization have the potential to confer substantial societal value. Recognizing societal benefits in health technology assessment will help allocate resources to address the most important risks society faces.",
"keywords": [
"COVID-19",
"cost",
"COVID-19 treatments",
"COVID-19 therapies",
"economics",
"business restrictions",
"consumer spending",
"unemployment claims",
"hospital utilization"
],
"content": "Introduction\n\nCOVID’s most notable impact has been illness and the loss of life, but the pandemic has also imposed a substantial societal cost. The economy has grabbed headlines, as cumulative losses during just the first two quarters of 2020 amounted to between 1 and 7% of annual GDP across the globe, and approximately 3% of annual GDP in the United States.1 Other societal costs include reduced care for health conditions other than COVID,2,3 although that impact may have been largely limited to the initial several months of the pandemic.4 Finally, evidence suggests that lost in-person schooling will permanently diminish economic opportunities for today’s students; moreover, the impact is greatest for students from the most disadvantaged backgrounds.5\n\nThe pandemic’s economic costs suggest that COVID-19 medical interventions could confer societal benefits exceeding the value of their health benefits.6 Based on stock market movements in apparent response to positive news about vaccines in development, for example, one analysis estimated a pandemic-ending therapy to be worth between 5 and 15% of total wealth.7 In the United States alone, that result implies a value ranging from $6 to $17 trillion.8\n\nAssessing the societal value of COVID therapies that have a less dramatic impact on the population as a whole, such as antiviral treatments9 and monoclonal antibodies,10 presents a distinct challenge. These therapies do not directly address population disease transmission and therefore have less potential to return life to “normal”. Instead, they aim to prevent progression to severe disease or speed recovery.\n\nWe hypothesize that these clinical benefits, if the data hold up, nonetheless confer a societal benefit by diminishing the need for government-imposed restrictions on economic activity designed to increase social distancing. By “flattening the curve”, economic restrictions and other distancing measures aim in part to prevent the health care system from becoming overwhelmed.11,12 The link between hospital utilization in particular and government-imposed restrictions seems evident in headlines from late 2020. For example, one headline noted, “If NY hospitals get overwhelmed, state could shut down again, Cuomo says”.13 Another stated, “California’s Governor Warns of ‘Drastic Action’ as Hospitals Near Crisis”.14 A December 3 executive order outlined economic restrictions in California when a region’s free intensive care unit capacity dropped below 15% – including a ban on hotel stays for out-of-state guests, suspension of indoor dining at restaurants, and a 20% capacity limit on retail establishments.15 When Massachusetts governor, Charlie Baker, loosened business restrictions toward the end of January 2021, he identified a drop in COVID hospitalizations as a key factor informing his decision.16\n\nBecause high hospital utilization levels trigger restrictions, therapies that reduce hospitalizations or hospital length of stay can also reduce the need for restrictions. This paper’s aim is to estimate the cost of these restrictions and hence the potential value conferred by COVID-19 therapies that help avert hospital admissions by preventing progression to severe disease or that speed recovery.\n\n\nMethods\n\nTo assess the cost of government-imposed economic restrictions, we combined high frequency economic data, information on the pandemic’s progression (case incidence and mortality), and information about when state governments imposed and lifted restrictions on business activities. Rather than including data from spring, 2020, when the pandemic’s initial onslaught increased unemployment claims and reduced consumer spending to an extent unrepresentative of subsequent periods during the pandemic,17,18 we instead focused on the fall and winter of 2020-2021. All of the analysis was conducted in R v4.0.3, utilizing the R nlme package for regression analysis (R package: nlme, RRID:SCR_015655).\n\nDescriptive statistics: We report the number of observations, mean, and standard deviation for all outcome quantities and all explanatory variables. We stratify the data by the level of regulatory measures in place during that week. As described below (see Data), we classify each U.S. state during each week as either “mostly closed” due to government-imposed activity restrictions, or as not “mostly closed.”\n\nBase case analysis: We used regression to predict the influence of restrictions on consumer spending and weekly initial unemployment claims. We controlled for daily COVID case count, COVID mortality, and the change in these two rates over the preceding two weeks. More formally, we developed three sets of models, one set for each of three outcomes:1 percent change since January, 2020 in total seasonally adjusted consumer spending,2 percent change in seasonally adjusted consumer spending on restaurants and accommodations since January, 2020, and3 weekly unemployment claims (not seasonally adjusted) as a percent of the 2019 US workforce.\n\nOur base case regression specification models each outcome as,\n\nOutcomeis=α+β1Restrictedis+β2NewCasesis+β3DeltaNewCasesis+β4NewDeathsis+β5DeltaNewDeathsis,\n\nwhere the subscript i denotes the week and the superscript s denotes one of the 50 U.S. states (and Washington, D.C. for the initial unemployment claims). Explanatory variables included Restrictedis (a binary variable indicating if state s was “mostly closed” during week i; see data sources below); NewCasesis and NewDeathsis, which refer to state-specific, population-normalized daily case incidence and mortality; and DeltaNewCasesis and DeltaNewDeathsis, which refer to state-specific, population-normalized changes in these values over the last two weeks. We included the COVID case and mortality rates, and their rate of change to address the possibility that reduced economic activity may in part be due to voluntary disengagement from the economy in response to reports of higher rates of COVID illness and death.\n\nAll regressions are linear mixed models that account for nesting within state and correlation across observations that are close in time. To account for temporal correlation, the base case model implemented a first-order, autoregressive (lag 1-week) covariance structure. This covariance structure assumes correlation is greatest for observations adjacent in time, with decreasing correlation between observations more distant in time.\n\nSensitivity analysis: We conducted a series of sensitivity analyses to explore how alternative assumptions influence our conclusions.\n\nFirst, we conducted an analysis limited to the 10 states designated “mostly closed” at some point between September 15 through December 27, 2020 (California, Kentucky, Illinois, Michigan, Minnesota, New Mexico, Oregon, Pennsylvania, Rhode Island, and Washington).\n\nSecond, we explored alternative model specifications that omitted some of the explanatory variables in the base case model, including1 the daily COVID mortality rate,2 the daily COVID case rate, or3 both the case rate and the mortality rate. We conducted this sensitivity analysis because inclusion of the case rate and mortality rate in the regression model may lead to “over-control” of phenomena correlated with government restrictions, and that could artificially reduce the estimated impact of government restrictions on economic activity. This set of sensitivity analyses explores the potential magnitude of this type of potential error.\n\nThird, we considered alternative criteria for designating a week as subject to government-imposed restrictions. The first alternative designates a state as subject to restrictions only after restrictions have been in place for at least 14 days. This alternative explores the potential for a lag (of two weeks) between a state’s imposition of restrictions and the impact of those restrictions on economic activity. For example, if a state enacted restrictions from the 1st to the 21st of October, this sensitivity analysis designates the week of October 1st and the week of October 8th as not Restricted, but designates the week of October 15th as Restricted. The second alternative recognizes only those restrictions that remain in place for at least three weeks. For the preceding example, that would mean that all three weeks (starting October 1st, October 8th, and October 15th) would be designated as Restricted. On the other hand, if the state had imposed restrictions from October 1st to October 20th (just under 3 weeks), this sensitivity analysis would designate all three weeks as not Restricted. That is, we treat states imposing only restrictions shorter than three weeks in duration as unrestricted at all times. The third alternative set of criteria recognizes only those restrictions that include a complete ban on indoor dining at restaurants.\n\nFinally, we considered alternative model correlation structures, including 2nd, 3rd, and 4th order autoregressive models (i.e., AR2, AR3, and AR4), 1st and 2nd order moving average (i.e., MA1 and MA2), and a series of autoregressive-moving average models (ARMA) with different combinations of first- and second-order AR and MA components (i.e., AR1MA1, AR1MA2, AR2MA1, and AR2MA2).\n\nWe report the Akaike Information Criterion (AIC) statistic as an indicator of goodness of fit for each model (lower or more negative values indicate better fit).\n\nData: We report our time series data as weekly values. For spending data reported by the original source as daily seven-day moving averages, we retained one value from each seven-day period to represent that week.\n\nOutcomes – Outcomes data come from the Opportunity Insights COVID-19 Economic Tracker project at Harvard University.19,20 The Opportunity Insights Economic Tracker data repository sourced its spending data from Affinity Solutions, and its initial unemployment claims data from the Department of Labor. Selection of these outcomes reflects the expectation that government restrictions affect consumer spending in general and restaurant dining and accommodations in particular. These impacts, in turn, contribute to higher initial unemployment claims.\n\nFor state s and week i, outcomes include percent change in seasonally adjusted spending on restaurants and accommodations compared to January 2020 (SpndRstis), and percent change in seasonally adjusted total consumer spending compared to January 2020 (SpndTtlis). To eliminate weekend and weekday periodicity, the Opportunity Insights Economic Tracker group computed seven-day moving average values for the spending data, as described above. To eliminate effects of state size, they also normalized all spending values by population size. The spending data span the period September 15 to December 27, 2020. Our third outcome, for state s and week i, was initial unemployment claims (reported on Thursday of each week) per 100 people in the 2019 labor force (UEis). This data series spanned the period September 19 to December 19, 2020.\n\nHigh frequency data are well suited to assessing restrictions imposed at moderately different times across states and remaining in effect for durations often measured in weeks during the fall and winter of 2020-2021. Moreover, because states imposed and lifted these restrictions only shortly before we conducted our analysis, frequently updated data best cover salient periods. Conventional economic activity datasets, like government estimates of gross domestic product (GDP) growth, undergo updating too infrequently to assess the impact of short-term restrictions and the recent imposition of restrictive government measures.\n\nExplanatory variables – As with outcomes, we index explanatory variables by state s and week i. Our primary explanatory variable of interest, designated Restrictedis, is binary. We classified state businesses as restricted or not restricted based on narrative descriptions of state-level closures maintained by the New York Times, which reported for each day whether businesses in each state were “mostly closed.”21 Based on review of these narratives, we identified when each state changed from not “mostly closed” to “mostly closed”, or the reverse. Our base case analysis designated business in a state as “restricted” during week i if, according to the New York Times database, businesses were “mostly closed” on Monday (for the consumer spending outcomes) or Thursday (for the initial unemployment claim outcome) of that week.\n\nWe included other explanatory variables in an effort to account for how news about the pandemic might influence voluntary, spontaneous reductions in economic activity. These variables included seven-day average, population-normalized1 daily new COVID cases (NewCasesis),2 daily COVID mortality (NewDeathsis),3 the increase in daily new COVID cases over the last two weeks (DeltaNewCasesis), and4 the increase in daily COVID mortality over the last two weeks (DeltaNewDeathsis). Daily COVID cases and deaths were provided from the New York Times COVID-19 Repository to the Opportunity Insights Economic Tracker data repository.22\n\n\nResults\n\nDescriptive statistics: Table 1 summarizes the data. Outcomes (consumer spending, unemployment claims) are more favorable during weeks without restrictions (first three numeric columns) than during weeks with restrictions (last three numeric columns). Case counts and mortality are lower during weeks without restrictions than during weeks with restrictions. The rate at which case counts grow (increase per two-week period) is higher during weeks without restrictions. On the other hand, the change in mortality is similar across these two sets of weeks.\n\na Percent change in spending compared to January 2020.\n\nb Claims, as a percentage of the 2019 labor force.\n\nc Seven-day moving average, number per 100,000 state population.\n\nd Missing values: The original dataset included 750 observations for total consumer spending and for spending on restaurants and accommodations (50 states, 15 weeks). We removed 12 observations because zero reported deaths during the index week meant we could not compute a percent change in deaths over the following two weeks. The 12 missing observations included 1 observation for ME, 10 for VT, and 1 for WY. For initial unemployment claims, the original dataset included 714 observations (50 states plus DC, 14 weeks). We removed 13 observations for the same reason as described above for spending, including 1 observation for ME, 1 for NH, 10 for VT, and 1 for WY. All removed observations come from weeks without restrictions. These missing values represent less than 2 percent of our original sample, and a substantially smaller fraction of U.S. GNP. We therefore took no action to provide values for these missing observations.\n\nBase case analysis: Table 2 reports regression analysis results for our base case models. The estimated impacts of government-imposed restrictions (row labeled “Restricted”) are statistically significant and in the expected direction for all three outcomes – i.e., a reduction in consumer spending, a reduction in restaurant and accommodations spending, and an increase in initial unemployment claims.\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\nSensitivity analysis: Our first sensitivity analysis (Table 3) explored the impact of restricting attention to the 10 states that all experienced periods during which the government imposed restrictions and other periods during which the government did not impose restrictions. For these 10 states, government restrictions had the same impact on total consumer spending (coefficient of -0.02 for Restricted, i.e., a 2% reduction) as they had for all 50 states (Table 2). The impacts on restaurant and accommodations spending (coefficient of -0.04 in Table 3 vs. coefficient of -0.05 in Table 2) and on initial unemployment claims (coefficient of 0.20 in Table 3 vs. coefficient of 0.21 in Table 2) were slightly smaller than the corresponding impacts in the base case.\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na Data from California, Kentucky, Illinois, Minnesota, Michigan, Oregon, Washington, Rhode Island, New Mexico, and Pennsylvania.\n\nTables 4, 5, and 6 show results for the second set of sensitivity analyses – i.e., for alternative models that do not control for COVID case rate, COVID mortality, or both. The impacts of government restrictions on total consumer spending (Table 4) remain similar to the corresponding base case impacts (coefficient of around -0.02). Impacts on restaurant and accommodations spending (Table 5) likewise remain similar to the corresponding base case impacts (coefficient of around -0.05). For initial weekly unemployment claims (Table 6), not controlling for case rate and death rate modestly increased the estimated impact of restrictions on initial unemployment claims to 0.25 percent of the 2019 workforce from 0.21 percent in the base case.\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see left panel, last row of Table 2, AIC value of -2485).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see middle panel, last row of Table 2, AIC value of -2711).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see right panel, last row of Table 2, AIC value of -981).\n\nTables 7, 8, and 9 present regression model results for the third set of sensitivity analyses, which explore alternative definitions for the Restricted variable. Models designating weeks as Restricted only after two weeks following enactment of state-imposed distancing measures (left panels in Tables 7, 8, and 9) estimated that government restrictions had smaller estimated impacts than the corresponding impacts in our base case model. In Table 7, the left panel coefficient for Restricted is -0.01, compared to -0.02 for the corresponding base case coefficient in Table 2. In Table 8, the left panel coefficient for Restricted is -0.02, compared to -0.05 for the corresponding base case coefficient in Table 2. In Table 9, the left panel coefficient for Restricted is 0.04, compared to 0.21 for the corresponding base case coefficient in Table 2. As detailed in the last rows in Tables 7, 8, and 9, these models had higher AIC values than the base case model, indicating that they do not fit the data as well as the base case model.\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see left panel, last row of Table 2, AIC value of -2485).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see middle panel, last row of Table 2, AIC value of -2711).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see right panel, last row of Table 2, AIC value of -981).\n\nFinally, we report results for other model correlation structures (Tables 10, 11, and 12). Not all alternative correlation structures we evaluated produced models that converged. For those that did, the estimated impacts of government-imposed restrictions were similar to or modestly larger than the corresponding base case estimates. The AIC goodness of fit statistics indicate, however, that models that produced estimates for the impact of government-imposed restrictions that differed the most from the corresponding base case estimates did not fit the data as well as the base case model (less negative AIC value).\n\n\n\n- AR(#) = Autoregressive (order).\n\n- MA(#) = Moving average (order).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see left panel, last row of Table 2, AIC value of -2485).\n\n\n\n- AR(#) = Autoregressive (order).\n\n- MA(#) = Moving average (order).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see middle panel, last row of Table 2, AIC value of -2711).\n\n\n\n- AR(#) = Autoregressive (order).\n\n- MA(#) = Moving average (order).\n\n* Designates a coefficient that achieved statistical significance at P < 0.05.\n\na AIC statistic value compared to corresponding base case model (see right panel, last row of Table 2, AIC value of -981).\n\n\nDiscussion\n\nWe found that government-imposed restrictions during the fall and early winter of 2020-2021 were associated with reduced economic activity. Descriptive statistics revealed lower total consumer spending, lower consumer spending on restaurants and accommodations, and a greater number of initial unemployment claims during weeks with restrictions than during weeks without restrictions (Table 1 – compare outcome means for weeks without and with restrictions). Regression analysis revealed an association with restrictions even after controlling for the number of new COVID cases, COVID mortality, and the change in those rates over the preceding two weeks (Table 2). That influence appears to be robust to modeling assumptions, as indicated by the modest impact of our sensitivity analyses on the estimated impact of government-imposed restrictions. Where sensitivity analyses yielded the most notable departures from the base case, the AIC value suggested the alternative model did not fit the model as well.\n\nSeveral factors complicated assessment of the impact of government restrictions on economic outcomes. Importantly, the restrictions imposed by state governments differed across states and over time. Our sensitivity analyses using alternative definitions for government restrictions suggest, however, that this issue does not invalidate our findings. A second complication is the fact that government-imposed restrictions tend to coincide with the events that cause voluntary reductions in economic activity. In short, the same news headlines that cause state governments to impose restrictions also cause many consumers to voluntarily stay home and reduce their spending. We attempted to isolate the impact of government-imposed restrictions by including in our models daily COVID cases and mortality, and the changes in those statistics over the preceding two weeks.\n\nWe estimated the dollar cost of restrictions as follows. Our base case analysis results imply that restrictions reduce consumer spending by 2%, reduce restaurant and accommodations spending by 5%, and increase weekly unemployment claims by 0.21% of the 2019 work force. Nationally, total annualized consumer spending amounted to $13.3 trillion in the fourth quarter of 2019;23 restaurant and accommodations spending totals approximately $1.2 trillion annually, including $863 billion spent in restaurants24 and $300 billion spent on accommodations.25 The U.S. labor force in 2019 totaled 163 million individuals.26 The model results hence imply that restrictions, if imposed by all states for a full year, would reduce total consumer spending by 2%×$13.3trillion≈$270billion, of which 5%×$1.2trillion=$60billion could be attributed to a reduction in spending on restaurants and accommodations. The model results also imply that restrictions imposed by all states would increase initial weekly unemployment claims by 0.21%×163million≈340,000 initial claims each week.\n\nThe computations just described yield cost estimates for a hypothetical, nationwide, year-long imposition of business restrictions. We scale these estimates down to characterize the impact of the restrictions actually imposed. During the fall and winter of 2020-2021, when the U.S. experienced the pandemic’s third wave, 10 states (CA, IL, KY, MI, MN, NM, OR, PA, RI, and WA) imposed restrictions for between 21 and 86 days, with an average (and GDP-weighted average) duration of 49 days. Those states represent approximately one-third of the country’s GDP.27\n\nTaking a third of the projected nationwide, annual costs ($90 billion for total spending and $20 billion for restaurant and accommodations spending), and then scaling these values down by a further 86.5 percent to impute the costs associated with the imposition of restrictions for 7 weeks (13.5 percent the year) yields costs of $12 billion in total consumer spending, of which $2.7 billion would be attributable to decreased spending on restauraunts and accommodations. Assuming employment is approximately proportional to GDP, these states would together experience an additional 114,000 initial weekly unemployment claims each week during the imposition of these restrictions. (We note that the unemployment data do not reflect seasonal adjustment, but it is not evident that this limitation introduces any particular bias; nonetheless, it does introduce some uncertainty.)\n\nWhile a total cost of $12 billion can seem modest in the context of a global pandemic with estimated costs likely amounting to trillions of dollars in lost economic activity, the losses estimated here are indeed substantial. Keep in mind that they occur over a limited time period (during the 1 or 2 months at the peak of a surge in COVID cases) and that the population can experience multiple case surges during a pandemic; as of this writing, the United States has experienced three such surges and is in the midst of a fourth due to the Delta variant. Assuming that late 2020 is representative of tendencies for the government to restrict economic activity in response to high hospital utilization, therapies reducing hospital utilization have the potential to confer substantial societal value.\n\nWhether prices charged for therapies should reflect this component of value is another question, as decision makers must also consider a range of issues, including affordability.28 Importantly, this analysis shows that estimating the cost of government-imposed restrictions is feasible, hence making it possible to extend health technology assessments beyond the typical and often exclusive focus on the valuation of health benefits.\n\n\nConclusions\n\nGovernment restrictions reduced consumer spending by 12 billion dollars and increased unemployment claims by 114,000 each week during the Fall/early Winer surge of COVID-19. Sensitivity analysis showed these findings to be robust to alternative modeling assumptions. The criteria for implementing business restrictions in various U.S. states, such as California and New York, suggest that increases in hospital utilization during COVID pandemic surges trigger such government restrictions. As COVID-19 therapies that can lower the risk of hospitalization and severe disease are developed and become available, government business restrictions may become a less necessary measure for lowering the hospital burden. Therefore, our analysis suggests that investment in the development and use of such therapies may not only provide a substantial health benefit, but also avert some of the economic impact of government restrictions, providing a substantial societal benefit.\n\nWhile a therapy’s health benefits will no doubt remain the core element of health technology assessment, for therapies addressing threats that affect others in addition to those who become ill, recognizing societal benefits will help allocate resources to promote innovations that address the most important risks society faces.\n\n\nData availability statement\n\nhttps://github.com/sweidner1/CEVR---Consortium---COVID-19-\n\nThis project contains the following underlying data:\n\n• Generated Data for Analysis – Spending.csv – Data file containing weekly observations of business restrictions data for each state.\n\n• Generated Data for Analysis – Unemployment.csv – Data file containing weekly observations of business restrictions data for each state.\n\n• Data Cleaning. R – R code file that takes raw data files and cleans them into files suitable for analysis using our model.\n\n• Base Case. R – R code file that completes our base case regression analysis for all three outcomes and produces results files.\n\n• Table 1. R – R code file that generates summary statistics for our data and produces results files.\n\n• Table A2.R – R code file that completes our ten state subgroup regression analysis for all three outcomes and produces results files.\n\n• Table A3a. R – R code file that completes our sensitivity analyses in which we remove case rate, death rate, and both as explanatory variables for the total consumer spending outcome and produces results files.\n\n• Table A3b. R – R code file that completes our sensitivity analyses in which we remove case rate, death rate, and both as explanatory variables for the restaurant and accommodation spending outcome and produces results files.\n\n• Table A3c. R – R code file that completes our sensitivity analyses in which we remove case rate, death rate, and both as explanatory variables for the initial unemployment claims outcome and produces results files.\n\n• Table A4a. R – R code file that completes our sensitivity in which we alter the definition of our business restrictions variables Restricted for the total consumer spending outcome and produces results files.\n\n• Table A4b. R – R code file that completes our sensitivity in which we alter the definition of our business restrictions variables Restricted for the restaurant and accommodation spending outcome and produces results files.\n\n• Table A4c. R – R code file that completes our sensitivity in which we alter the definition of our business restrictions variables Restricted for the initial unemployment claims outcome and produces results files.\n\n• Table A5a. R – R code file that completes our sensitivity in which we vary out assumptions for outcome correlations over time for the total consumer spending outcome and produces results files.\n\n• Table A5b. R – R code file that completes our sensitivity in which we vary out assumptions for outcome correlations over time for the restaurant and accommodation spending outcome and produces results files.\n\n• Table A5c. R – R code file that completes our sensitivity in which we vary out assumptions for outcome correlations over time for the initial unemployment claims outcome and produces results files.\n\n• README.docx – README file that gives further details on all data files and describes how to properly run all code files to replicate our analysis\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nhttps://github.com/OpportunityInsights/EconomicTracker\n\nThis project contains the following underlying data:\n\n• Affinity – State – Daily.csv – Data file containing daily observations of spending statistics for each U.S. state, including % change in total consumer spending since January 2020, and % change in restaurant and accommodation spending since January 2020.\n\n• COVID – State – Daily.csv – Data file containing daily observations of COVID statistics for each U.S. state, including new case rate and new death rate.\n\n• UI Claims – State – Weekly.csv – Data file containing weekly observations of unemployment claims statistics for each U.S. state, including initial weekly unemployment claims rates.\n\nhttps://github.com/sweidner1/CEVR---Consortium---COVID-19-\n\nThis project contains the following underlying data:\n\n• 2021 08 03a – STROBE checklist.docx – Word document containing the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) reporting guidelines checklist with all relevant information from our manuscript to show fulfillment of the checklist.\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\nFernández-Villaverde J, Jones C: Macroeconomic outcomes and COVID-19: A progress report. Cambridge, MA; 2020 October.\n\nChatterji P, Yue L: Effects of the COVID-19 Pandemic on Outpatient Providers in the US: National Bureau of Economic Research. 2020.\n\nZiedan E, Simon K, Wing C: Effects of state COVID-19 closure policy on non-COVID-19 health care utilization: National Bureau of Economic Research; 2020. Report No.: Working Paper 27621.\n\nMehrotra A, Chernew M, Linetsky D, et al.: The Impact of COVID-19 on Outpatient Visits in 2020: Visits Remained Stable, Despite a Late Surge in Cases: The Commonwealth Fund.2021 February 22.\n\nAgostinelli F, Matthias D, Sorrenti G, et al.: When the great equalizer shuts down: Schools, peers, and parents in pandemic times: National Bureau of Economic Review;2020. Report No.: Working Paper 28264.\n\nNeumann PJ, Cohen JT, Kim DD, et al.: Consideration Of Value-Based Pricing For Treatments And Vaccines Is Important, Even In The COVID-19 Pandemic. Health affairs (Project Hope) . 2021;40:53–61. PubMed Abstract | Publisher Full Text\n\nAcharya V, Johnson T, Sundaresan S, et al.: The value of a cure: An asset pricing perspective: National Bureau of Economic Research;2021. Report No.: Working Paper 28127.\n\nShorrocks A, Davies J, Lluberas R: Credit Suisse Research Institute: Wealth of Nations; 2020.\n\nU.S. Food and Drug Administration: FDA Approves First Treatment for COVID-19.2020.\n\nU.S. Food and Drug Administration: Coronavirus (COVID-19) Update: FDA Authorizes Monoclonal Antibody for Treatment of COVID-19.2020.\n\nGavin K: Flattening the Curve for COVID-19: What Does It Mean and How Can You Help? University of Michigan; 2020.\n\nRoberts S: Flattening the Coronavirus Curve. New York Times . 2020 March;27.\n\nTampone K: If NY hospitals get overwhelmed, state could shut down again, Cuomo says. Syracusecom. 2020 November 30.\n\nCowan J: California’s Governor Warns of ‘Drastic Action’ as Hospitals Near Crisis. New York Times . 2020 November 30.\n\nPan E: Regional Stay At Home Order 12/03/2020. State of California—Health and Human Services Agency - California Department of Public Health;2020.\n\nNBC10Boston: Massachusetts Is Easing Some COVID Restrictions Next Week. Here's What to Know. 2021.\n\nCox J: Jobless claims fall again as employment picture gains strength. CNBC . 2021.\n\nKerstein S: U.S. Retail Sales Update. Legislative Analyst's Office . September 2020:2020.\n\nChetty R: Opportunity Insights Economic Tracker . Opportunity Insights: Harvard University; 2021.\n\nThe Economic Impacts of COVID-19: Evidence from a New Public Database Built Using Private Sector Data”, by Raj Chetty, John Friedman, Nathaniel Hendren, Michael Stepner, and the Opportunity Insights Team. November 2020. https://opportunityinsights.org/wp-content/uploads/2020/05/tracker_paper.pdf\n\nThe New York Times: See Coronavirus Restrictions and Mask Mandates for All 50 States. New York Times. 2021.\n\nThe New York Times: nytimes/covid-19-data.2021.\n\nUnited States Consumer Spending: 2021. Reference Source\n\nNational Restaurant Association: Restaurant Industry Factbook. 2019: 2019.\n\nUS Bureau of Commerce - International Trade Administration: Travel, tourism & hospitality spotlight . The Travel, Tourism and Hospitality Industry in the United States; 2018.\n\nMonthly Labor Review: 2020. Reference Source\n\nUS Bureau of Economic Analysis: Gross Domestic Product by State. 4th Quarter and Annual 2019. 2020.\n\nCohen JT, Neumann PJ, Ollendorf DA: Valuing And Pricing Remdesivir: Should Drug Makers Get Paid For Helping Us Get Back To Work? Health Affairs Blog. 2020."
}
|
[
{
"id": "129099",
"date": "29 Mar 2022",
"name": "Franklin Dexter",
"expertise": [
"Reviewer Expertise Operating room and anesthesia group administrative modeling"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nHow does one value vaccine or therapy to treat SARS-CoV-2 in terms of the impact on an economy? One mechanism is its prevention of hospitals filling and State or Provincial governments then choosing to shut down parts of the economy (e.g., restaurants and other service industries). In this paper, the authors estimate the economic cost of such a shut-down. From the authors’ conclusions, “therapies reducing hospital utilization have the potential to confer substantial societal benefit.” Much of the supply of patients staying longer than overnight are inpatient surgical patients, only one-third of all surgery. Overnight stays routinely are without hospital admission, rather than using the surgical recovery rooms. Therapies reducing hospital utilization then are those anesthetic treatments that convert 2- or 3-day hospital stays to overnight.\nWhile the Introduction and Methods are reasonable, I have two related statistical concerns that affect the results (e.g. Table 2) and the interpretation/application of those results in the Discussion where the authors draw their conclusions.\nMajor concerns:\nThe authors' economic analysis and conclusions on page 14 reasonably depend on the base case analysis. The table has more than 10 comparisons. I do not understand the rationale for using P<0.05 without consideration of the multiple comparisons. Whether the authors consider a reduction in consumer spending by 2% (P14, paragraph 2) based on parameter uncertainty or based on the sensitivity analyses, just using 2% in the economic analyses on page 14 seems limited.\nThe authors do not rely on page 14 on the confidence interval for the 2%. The authors also do not include standard error (or equivalent) for the 1.2 trillion on page 14, paragraph 2. Therefore, the \"by 12 billion dollars\" on page 14, last paragraph does not account for uncertainty in the estimate. Please add consideration of uncertainty quantitatively on page 14, and then the abstract.\nMinor concern:\nFinally, I do not follow the \"Taking a third\" in the fourth paragraph of page 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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "154440",
"date": "22 Nov 2022",
"name": "Zeynep Kantur",
"expertise": [
"Reviewer Expertise 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 paper investigates the impact of government restrictions during the COVID-19 pandemic (Sep. 2020-Dec. 2020) on credit and debit card (consumer spending) spendings, and initial unemployment claims in United States using state-level data. The main idea of the paper is to quantify the cost of government restrictions on economic activity and compare it with the cost of COVID-19 therapies. According to the findings of the analysis, government-imposed restrictions lead to a decline in both total consumer spending and restaurant and accommodation spendings, and an increase in the initial unemployment claims. The results of the base case analysis suggest that restrictions reduce consumer spending by 2%, restaurant and accommodation spendings by 5%, and increase weekly unemployment claims by 0.21%. These results are robust to alternative model specifications. The manuscript is well written, but a few aspects need improvement. I have some suggestions on this.\nThe data should be explained in detail. Consumer spending in this paper is credit and debit card data which raises the following questions: How is the data collected? Is it collected from the banks, which includes information at the household level, or is it gathered from the POS machines (including virtual ones) of all banks operating in the U.S.? Does it include online transactions? If this is the case, then state-level analysis could be misleading since households can carry out their transactions outside their states. In other words, does the card data take into account the location of the household or the place of purchase? The authors should mention online spending since restrictions had a very limited impact on it.\n\nAlthough government restrictions reduce consumer spending, this is not the only reason. Expenditures also provide information about income level. Households may reduce their consumption due to fear of losing, or losing, their job during the COVID-19 period. The analysis itself confirms this in the initial unemployment claims analysis. The study should definitely talk about this issue. Households spend out of existing income/wealth with the debit, a consumer spends also out of expected future income/wealth with the credit card.\n\nMobility restrictions (which are not mentioned in the paper) might have directed some of the spendings that would otherwise be paid in cash to online providers that require credit/debit card transactions. This is not necessarily a change in the consumption level for those products; in fact, it is again a change in payment methods. I suggest authors check the Google mobility index which is available at the state level.\n\nWhat is the level of credit/debit card used in each state?\n\nFollowing my point on income, did government financial support programs differentiate at the state level? If it is the case, it should be included in the analysis.\n\nI have some minor comments.\nI think the empirical findings fall short in terms of commenting on a comparison of health therapies and the economic cost of restrictions.\n\nSince the article is motivated by the cost/benefit of health therapies, I found nothing about them in the article. Some information would be beneficial for readers.\n\nIn Table 3. The Restricted is not statistically significant. But in the text, it says the base case analysis and 10-state analysis have the same findings.\n\nThere is a typo in the first sentence of the Conclusion section. ('Winter')\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-856
|
https://f1000research.com/articles/10-249/v1
|
29 Mar 21
|
{
"type": "Software Tool Article",
"title": "MIREyA: a computational approach to detect miRNA-directed gene activation",
"authors": [
"Anna Elizarova",
"Mumin Ozturk",
"Reto Guler",
"Yulia A. Medvedeva",
"Mumin Ozturk",
"Reto Guler"
],
"abstract": "Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA",
"keywords": [
"microRNA",
"miRNA",
"non-coding RNA",
"enhancer",
"regulator",
"macrophage",
"tuberculosis"
],
"content": "Introduction\n\nConventionally, microRNAs (miRNAs) are considered to suppress gene expression through RNA interference (RNAi) by binding complementarily to mRNAs, forming a RISC complex, and causing RNA degradation (reviewed in detail in).1 However, recent studies provide evidence that some miRNAs act in the opposite way – stimulating gene activation. Numerous studies have demonstrated the ability of miRNAs to up-regulate genes by targeting their promoters.2,3 Ago1 from miRNA-Ago complex associates with the Ccnb1 promoter and miR-744 induces enrichment of RNA Pol II and H3K4me3 at the Ccnb1 transcription start site.3 MiRNA let-7i interacts with the TATA-box of IL-2 gene and stimulates transcription initiation by contributing to the assembly of the pre-initiation complex.4 Relatively fewer miRNAs demonstrated the ability to unconventionally target and activate enhancers, thus inducing genes regulated by these enhancers. MiR-24-1 acts as a modulator of the chromatin state of an enhancer. Furthermore, it increases p300 and RNA Pol II binding at the enhancer locus. The miR-24-1 actually originates from the enhancer locus. However, some genes regulated by other enhancers are also expressed at higher levels when miR-24-1 is transfected, and the enhancers of induced genes contain a sequence similar to the seed of the miRNA.5 These observations suggest that other miRNAs might trigger enhancers and activate gene expression.\n\nWhen miRNAs function as activators in a nucleus, different targeting mechanisms are possible: miRNA:DNA Watson-Crick duplex formation as well as miRNA:DNA Hoogsteen triple helix formation. Nuclear miRNA target prediction tools utilize are based on the idea that miRNA:DNA interaction requires an intact seed region.6 MicroPIR2 predicts targets in mouse and human promoter regions.7 Trident predicts miRNA:DNA Hoogsteen-type base pairings.8 Some tools designed to predict conventional miRNA targets may also be utilized to find nuclear activational targets, e.g. miRanda.9\n\nIn this work, we report MIREyA (MIRnas functioning through Enhancer Activation), a pipeline for detection of miRNAs and their gene targets up-regulated through triggering their enhancer in the provided expression dataset. We applied MIREyA in order to identify and characterize activational miRNAs in Mycobacterium tuberculosis (Mtb) infected macrophage dataset. MiRNAs are important regulators in macrophage responses during Mtb infection that may act as host immunity agents as well as a tool exploited by pathogen agents to manipulate host cell pathways.10 Yet, only the classical role of miRNA has been investigated so far in the context of Mtb infection.11–19 Although multiple studies have shown the possibility of the activational role of miRNAs, this potential remains neglected in the study of miRNAs in bacterial infections. MIREyA found several miRNAs, which have not been shown to be functional in TB yet, suggesting it could be useful to find candidate activational miRNAs for further experimental validation. Mir155 has previously been shown to act as a negative regulator of essential mRNAs during TB,20,21 but not as an activator.\n\n\nMethods\n\nMIREyA aims to detect miRNAs with the potential to upregulate a gene via activation of its enhancer. It consists of three major steps:\n\n1) The algorithm detects miRNA bound to the enhancers. This step is implemented with three different approaches described below.\n\n2) The algorithm selects genes regulated by the enhancers selected in step 1). For this step the output from the first step is required as well as a table with enhancer:gene pairs where an enhancer is assumed to regulate the corresponding gene.\n\n3) The algorithm calculates the Spearman’s correlation coefficient (SCC) between the expression levels of miRNAs and genes regulated by corresponding enhancers selected in step 1), and estimates the p-value of the SCC with a Benjamini-Hochberg correction using the number of the miRNA:gene pairs for one miRNA (FDR < 0.05). The input data is gene expression data with sample size ≥ 8 and the output of the previous step.\n\nFigure 1 illustrates the workflow of our algorithm implemented in Python and R.\n\nWe speculate that in order to activate an enhancer, miRNA should bind to enhancer DNA. Since the mechanism of such binding is unclear, we decided to implement several reasonable prediction strategies. The first two strategies assume that miRNA binds to DNA forming an RNA:DNA double helix, while the third assumes RNA:DNA triple helix formation.\n\n1) The first approach is to select an enhancer containing an exact match of the user-provided seed sequence of a miRNA, then expand each seed by 14 bp of the corresponding mature miRNA and align it to the enhancer with Needle tool22 and keep only enhancers with the percent identity (PI) > 0.5 (PI defined as a percent of matches between miRNA and DNA region).\n\n2) The second approach is to scan miRNA sequences against enhancer sequences and detect potential target sites with MiRanda.9\n\n3) The third approach is to predict RNA:DNA triplexes between miRNAs and enhancers with Triplexator tool.23 We relaxed the error-rate and lower-length-bound Triplexator default parameters in order to adjust the algorithm to work with extremely short miRNA sequences (error-rate=19, lower-length-bound=11).\n\nThe approaches are interchangeable, also the user can merge the results of all approaches to reflect multiple mechanisms of potential miRNA:DNA binding.\n\nThe main script to run the pipeline is src/run_mireya.py. Input and output files depend on choice of one of previously described approaches to predict miRNA-enhancer interaction and must be specified with the following flags:\n\n-d: approach to predict miRNA-enhancer interaction, accepts one of three possible values: seed_match_needle / miranda / triplexator\n\n-e: path to a fasta file with sequences of enhancers of interest\n\n-o: full path to output directory\n\n-ge: path to .tsv file with gene expression\n\n-me: path to .tsv file with expression of miRNAs of interest\n\n-ei: path to .tsv file with enhancers and corresponding genes they are assumed to regulate\n\n-m: path to a fasta file with sequences of mature miRNAs of interest\n\nPipeline mode with the first approach to predict miRNA-enhancer interaction (-d seed_match_needle) requires additional input data which must be provided with flags:\n\n-g: path to a folder with fasta files with complete genome of the organism of interest: one chromosome per file\n\n-s: path to a .tsv file with sequences of seeds of miRNAs of interest\n\n-sr: path to .tsv file with reverse complementary sequences of seeds of miRNAs of interest\n\n-eb: path to bed file with coordinates of enhancers of interest\n\n-ms: path to a directory containing directories with mature miRNA sequences: one folder per miRNA containing fasta files with one mature sequence per file. Each directory with mature mirna fastas must be named exactly as in other input files. Names of fasta files will be used further as \"mature_mirna\" column in result tables.\n\nExamples of command to run the main script, one for each approach to predict miRNA-enhancer interaction (names of files coinside with names of example input files in repository):\n\n1. python src/run_mireya.py -d seed_match_needle -e data/enhancers.macrophages.Mtb.mm9.fasta -o out/seed_match_needle_out/ -ge data/DE_gene_expression.tsv -me data/DE_mirnas_expression.tsv -ei data/enh.gene.assoc.sign.tsv -m data/DE_mirna_mature_seqs.fa -g data/db -s data/seeds_seq_forward_short -sr data/seeds_seq_reverse_compl_short -eb data/enhancers.macrophages.Mtb.bed -ms data/mature_seqs/\n\n2. python src/run_mireya.py -d miranda -e data/enhancers.macrophages.Mtb.mm9.fasta -o out/miranda_out/ -ge data/DE_gene_expression.tsv -me data/DE_mirnas_expression.tsv -ei data/enh.gene.assoc.sign.tsv -m data/DE_mirna_mature_seqs.fa\n\n3. python src/run_mireya.py -d triplexator -e data/enhancers.macrophages.Mtb.mm9.fasta -o out/triplexator_out -ge data/DE_gene_expression.tsv -me data/DE_mirnas_expression.tsv -ei data/enh.gene.assoc.sign.tsv -m data/DE_mirna_mature_seqs.fa\n\nOutput file is called mir_enh_gene_trios.tsv. Example output file is placed in the out/ directory of repository.\n\nThe pipeline is implemented as Python, R and bash scripts, and can be run with a master script run_mireya.py.\n\nPython>=3.5 and r-base are expected to be pre-installed. Besides, two modes of the pipeline require the following tools installed: MiRanda, Triplexator. The pipeline was tested in Ubuntu and Ubuntu-based linux systems (Ubuntu>=16.04).\n\n\nUse case\n\nWe applied MIREyA to three time-series (0, 4, 12, 24, 48, 96 hours) expression datasets (CAGE) of mouse bone marrow-derived macrophages infected with hypervirulent Beijing/W lineage Mycobacterium tuberculosis (Mtb) HN878 strain, 2-3 replicates per time point.24 Each dataset corresponds to the time series after infection for macrophages of different phenotypes: not pre-stimulated (M0), interferon-γ stimulated (M1-polarized) and interleukin-4/interleukin-13 stimulated (M2-polarized). Only differentially expressed (DE) miRNAs and genes were considered. We obtained enhancer-gene interactome from25 where an enhancer is predicted to regulate a gene if their expression levels correlate significantly and they belong to the same topologically associated domain (TAD).\n\nWe searched for candidate enhancers targeted by miRNAs with all three methods described previously and merged the results for further steps. CAGE enables one to estimate expression at the promoter level, while enhancers are associated with whole genes. As a proxy of gene expression, we used either an expression value of a promoter with the highest SCC (a) or summed up the expression values of all promoters of the gene (b). To reduce the number of false positive predictions, we selected among miRNA:enhancer duplexes only such cases where (1) a duplex was predicted both by miRanda and Needle-based approach; (2) an enhancer was associated with several genes since in the original paper on miRNA-activated enhancers5 one nuclear miRNA affected expression of multiple genes regulated by the triggered enhancer; (3) the miRNA-gene pair was obtained in both ways (a and b) to estimate expression of the gene. We also added miRNA-gene pairs with highly correlated expression levels (SCC ≥ 0.8) in any of four combinations of two methods to detect miRNA:enhancer interactions (seed match + Needle and miRanda) and two approaches to treat expression of different promoters (a and b). Among predicted miRNA:enhancer triplexes we selected cases where (1) an enhancer was associated with multiple genes; (2) both approaches to estimate gene expression (a and b) yielded this triplex.\n\n\nResults\n\nWe applied MIREyA to three time-series datasets of Mtb-infected macrophages with 3 different phenotypes prior to infection. In M0 macrophages 10 miRNAs were differentially expressed (DE) in at least one time point compared to the state before infection (0h), in M1 there was no DE miRNA, while in M2 only Mir1956 was DE. Figure 2 and Table S1 (Extended data43) represent detected miRNA-enhancer-gene trios for M0 macrophages (Extended data: Table S2 for M2 macrophages43). We investigated the functions of the obtained genes and miRNAs and confirmed that many of them might be involved in the response to Mtb infection. We detected Mir155, which is vastly studied, and known to subvert autophagy in human dendritic cells20 and to be a potential diagnostic marker of active tuberculosis.21 Other miRNAs and their targets which we consider promising for further investigation are summed in Tables 1 and 2. Mir22, Mir221, Mir222 are annotated with high confidence.26 Expression of only some promoters of Klf6 and BC016423 genes correlates with Mir22 expression, but we included them, because they have predicted triplexes with three different enhancers.\n\nThe length of an edge between a miRNA and an enhancer or between an enhancer and a gene is in inverse proportion to the average correlation between the expression of the miRNA and the target gene or the enhancer and the gene respectively. Full coordinates of enhancers are available in Table S1.\n\nWe reconstructed regulatory networks for these miRNAs based on miRNA-enhancer-gene trios and investigated their potential role in the response to Mtb infection. Mir22-activated gene network is highly likely to be involved in Mtb response. Klf6, a potential target of Mir22, is a transcription factor essential for macrophage motility27 and plays an important role in the regulation of macrophage polarization promoting M1 phenotype cooperatively with NF-κB.28 Nfkb1 gene, a putative target of miRNAs Mir221, Mir222 and Mir155, encodes a subunit of NF-κB protein complex, a master transcription factor in macrophage immune responses. The human ortholog of Ube2d3, potentially regulated by the same miRNAs, facilitates polyubiquitination of NFKBIA (a member of the NF-kappa-B inhibitor family) stimulating its subsequent degradation.29 A detected target of both Mir22 and Mir221, Peli1 regulates the NF-κB activity negatively and attenuates the induction of proinflammatory cytokines in T-cells.30 Cxcl1 and Cxcl2, detected targets of both Mir22 and Mir221, are chemoattractants for neutrophils contributing to tissue inflammation.31 Malt1, potentially up-regulated by Mir155, is known to activate NF-κB in lymphocytes.32 Among targets of Mir1956 detected in M2 macrophages dataset we found the Ccrl2 gene encoding a chemokine receptor-like protein which is expressed at high levels in primary neutrophils and primary monocytes. Another Mir1956 target, Dotl1, is an H3K79 methyltransferase which facilitates the expression of IL-6 and IFN-β in macrophages.33 Cd14 leads to NF-κB activation and inflammatory response,34 Cd14 KO mice infected with Mtb are protected due to reduced inflammatory responses at the chronic stage.35 Rab20 plays a role in the maturation and acidification of phagosomes and the fusion of phagosomes with lysosomes during mycobacterial infection.36 Ticam1 is involved in native immunity against pathogens: it interacts specifically with toll-like receptor 3, activates NF-κB.37 Tnfaip3 (A20) is an important regulatory protein that down-regulates NF-κB activity.38\n\nWe further investigated protein networks associated with the selected miRNAs. Proteins regulated by miRNAs Mir22, Mir155, Mir221, Mir222 are involved in regulation of NF-κB – a vital orchestrator of the response of the innate immune cells to pathogens39 (Figure 3A). Cxcl1 and Cxcl2 regulated by Mir22 and Mir155 (Figure 3B) are chemokines which signal through CXC receptor 2 to attract neutrophils to the place of inflammation, which is essential to control tissue infection.31\n\nRelationships are depicted with arrows of a different colour: green – activation, red – repression. Dashed arrows indicate predicted relationships, solid – known from published studies and described previously. Full coordinates of enhancers are available in Table S1.\n\n\nDiscussion\n\nMIREyA aims to easily find candidate activating miRNAs which trigger an enhancer and genes up-regulated by the enhancer. New emerging methods for studying RNA–DNA interactome detect previously unknown miRNAs bound to chromatin40,41 which might be promising for further experimental investigation in terms of understanding complex gene regulation networks in detail. Although high-throughput data on RNA:DNA interactions in several cell types but not macrophages are available now, we could not confirm MiRNAs detected with MIREyA for Mtb infection using either RADICL-seq41 or GRID-seq,42 which is unsurprising since the ncRNA:DNA interactions are highly cell-type-specific.41\n\nAlthough the implemented algorithm considers multiple aspects of the suggested mechanism of gene activation, several factors remain unaccounted for. To run MIREyA a user requires a priori knowledge of enhancer-gene interactions. A common fast computational approach to determine gene-enhancer pairs is to use genes and enhancers co-localized in the genome, ignoring the long-distance spatial interactions. One of solutions is the approach suggested in:25 to calculate the correlation between expression of genes and enhancers which belong to the same TAD.\n\nAlthough the exact mechanism of RNA activation of enhancers remains unclear, we do know that miRNA as a mediator facilitates epigenetic modifications in the enhancer region. At this stage, MIREyA does not consider chromatin availability or any other epigenetic information. In order to reduce the number of false positive predictions, nuclear localisation of specific predicted miRNAs should be validated experimentally.\n\nDespite the discussed limitations, using MIREyA we detected several promising miRNA candidates. We suggest that MIREyA provides a promising approach to select miRNAs which up-regulate genes by triggering enhancers for further experimental validation.\n\n\nConclusion\n\nOur method extends the study of activational miRNAs and provides a basis for further research. The use case on Mtb-infected macrophages demonstrates the possibility of existence of novel miRNAs up-regulating gene expression.\n\n\nData availability\n\nThe CAGE time series expression datasets from the use case are available at https://fantom.gsc.riken.jp/data/ in mm9 Phase 2 release and can be selected to download with FANTOM5 Table Extraction Tool by «macrophage, TB infection» key words.\n\nZenodo: MIREyA: Extended data, http://doi.org/10.5281/zenodo.4549445.43\n\nThis project contains the following extended data:\n\n- Table S1: Detected miRNA-enhancer-gene trios for M0 macrophages\n\n- Table S2: Detected miRNA-enhancer-gene trios for M2 macrophages\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\n\nSoftware availability\n\nPipeline available from: https://github.com/veania/MIREyA.\n\nArchived pipeline as at time of publication: https://doi.org/10.5281/zenodo.4635578.44\n\nLicense: Open Software License 3.0",
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PubMed Abstract | Publisher Full Text | Free Full Text\n\nDe Filippo K, Dudeck A, Hasenberg M, et al.: Mast cell and macrophage chemokines CXCL1/CXCL2 control the early stage of neutrophil recruitment during tissue inflammation. Blood. 2013; 121: 4930–4937. PubMed Abstract | Publisher Full Text\n\nHailfinger S, Nogai H, Pelzer C, et al.: Malt1-dependent RelB cleavage promotes canonical NF-kappaB activation in lymphocytes and lymphoma cell lines. Proc Natl Acad Sci U S A. 2011; 108: 14596–14601. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen X, Liu X, Zhang Y, et al.: Methyltransferase Dot1l preferentially promotes innate IL-6 and IFN-β production by mediating H3K79me2/3 methylation in macrophages. Cell Mol Immunol. 2020; 17: 76–84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaziot A, Ferrero E, Köntgen F, et al.: Resistance to endotoxin shock and reduced dissemination of gram-negative bacteria in CD14-deficient mice. Immunity. 1996; 4: 407–414. PubMed Abstract | Publisher Full Text\n\nWieland CW, van der Windt GJW, Wiersinga WJ, et al.: CD14 contributes to pulmonary inflammation and mortality during murine tuberculosis. Immunology. 2008; 125: 272–279. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeto S, Tsujimura K, Koide Y: Rab GTPases regulating phagosome maturation are differentially recruited to mycobacterial phagosomes. Traffic. 2011; 12: 407–420. PubMed Abstract | Publisher Full Text\n\nOshiumi H, Matsumoto M, Funami K, et al.: TICAM-1, an adaptor molecule that participates in Toll-like receptor 3–mediated interferon-β induction. Nat Immunol. 2003. pp. 161–167. PubMed Abstract | Publisher Full Text\n\nWertz IE, O’Rourke KM, Zhou H, et al.: De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling. Nature. 2004. pp. 694–699. PubMed Abstract | Publisher Full Text\n\nDorrington MG, Fraser IDC: NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration. Front Immunol. 2019; 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGavrilov AA, Zharikova AA, Galitsyna AA, et al.: Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics. Nucleic Acids Res. 2020. pp. 6699–6714. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBonetti A, Agostini F, Suzuki AM, et al.: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nat Commun. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi X, Zhou B, Chen L, et al.: GRID-seq reveals the global RNA–chromatin interactome. Nat Biotechnol. 2017. pp. 940–950. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElizarova A, Ozturk M, Guler R, et al.: MIREyA: Extended data (Version 1.0.0) [Data set]. Zenodo. 2021. Publisher Full Text\n\nveania. (2021, March 25). veania/MIREyA: v1.0.1 (Version v1.0.1). Zenodo.Publisher Full Text"
}
|
[
{
"id": "82451",
"date": "19 Apr 2021",
"name": "Michiel Jan Laurens De Hoon",
"expertise": [
"Reviewer Expertise Computational genomics",
"bioinformatics",
"microRNA regulation."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: This manuscript describes a novel software tool to detect interactions between miRNAs, enhancers, and the genes they regulate. Though the analysis performed by this software pipeline seems straightforward, it is a welcome addition as a bioinformatics tool, as the activation of enhancers by miRNAs has not been studied in much detail compared to the well-known mechanism of gene regulation by miRNAs via the RNAi pathway.\nComments and suggestions for improvement:\nSome of the references to the scientific literature are appropriate but quite old (for example, references 1, 9, and 26). Can these references be updated?\n\nOn page 4, I assume that \"percent identity (PI) > 0.5\" should be \"percent identity (PI) > 50\".\n\nOn page 5, the format and contents of the output file mir_enh_gene_trios.tsv is not clearly explained.\n\nIn Table 2, should a column with the number of enhancers be added (same as in Table 1)?\n\nOptional:\nIn the results, what is the evidence that miRNA-gene interactions shown in Table 1 and 2 are true? If no such evidence is available, can the pipeline be used to rediscover the miRNA/enhancer/gene interactions described in reference 3, 4, and 5? I understand that this may be difficult as currently there are not many examples available together with suitable expression data sets, but perhaps it can be shown that at least the first step in the pipeline (detecting miRNA-enhancer interactions by Needle, MiRanda, or Triplexator) gives results consistent with what is described in these three references? That would make the paper more convincing.\n\nAs a general point: Are both Python and R needed to run the pipeline? Could the pipeline be designed such that only Python or only R are needed?\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6986",
"date": "26 Aug 2021",
"name": "Anna Elizarova",
"role": "Author Response",
"response": "Thank you for leaving the review. As for the questions: Some of the references to the scientific literature are appropriate but quite old (for example, references 1, 9, and 26). Can these references be updated? We replaced reference 1 with a reference of a more recent review. The 9th reference is a reference to the original article of miRanda tool which is rather old but still functioning and suitable for our needs. The 26th reference is the most recent (2014) article to cite for miRBase database. On page 4, I assume that \"percent identity (PI) > 0.5\" should be \"percent identity (PI) > 50\". We replaced 0.5 with 50 in the text of the article and we replaced PIs in the algorithm with values from 0 to 100 instead of 0 to 1. On page 5, the format and contents of the output file mir_enh_gene_trios.tsv is not clearly explained. We added the following explanation to the main text of the article: One line in the output file corresponds to one trio of a mature miRNA, an enhancer and a gene (“mature_mirna”, “Gene.Name”, “enhancer” columns). Columns “corr(miRNA, gene)” and “p.value adj” correspond to Spearman’s correlation coefficient of the miRNA and the gene expression and FDR respectively. “PI” column corresponds to percent identity and is present only in the output of seed_match_needle approach. In Table 2, should a column with the number of enhancers be added (same as in Table 1)? We added a column with the number of enhancers to table 2. Optional: In the results, what is the evidence that miRNA-gene interactions shown in Table 1 and 2 are true? If no such evidence is available, can the pipeline be used to rediscover the miRNA/enhancer/gene interactions described in reference 3, 4, and 5? I understand that this may be difficult as currently there are not many examples available together with suitable expression data sets, but perhaps it can be shown that at least the first step in the pipeline (detecting miRNA-enhancer interactions by Needle, MiRanda, or Triplexator) gives results consistent with what is described in these three references? That would make the paper more convincing. As for the evidence that miRNA-gene interactions shown in Table 1 and 2, we do understand that the output of our pipeline needs to be validated experimentally. The redescovering of the miRNA/enhancer/gene interactions described in reference 3, 4, and 5 is impossible since there’s no expression dataset available in these references. MiRNA expression is highly dependent on cell type and conditions, thus any other expression dataset would have a different set of expressed miRNAs which might not include miRNAs studied in the papers. Repeating the first step (miRNA/enhancer interaction prediction) in the pipeline is impossible for the references 4, 5, since they describe other mechanisms of gene activation by miRNA without enhancer activation. The miRNA MiR-24-1 is apparently present in the sequence of the enhancer in the reference 3, because the enhancer contains a gene sequence of the miRNA as described in the article. Therefore an alignment of miRNA to the enhancer automatically will be successful. As a general point: Are both Python and R needed to run the pipeline? Could the pipeline be designed such that only Python or only R are needed? We started developing our pipeline as a set of R and bash scripts and added Python later due to the need of Biopython functions to work with fasta files. We will consider using only Python for MIREyA as a further step."
}
]
},
{
"id": "87525",
"date": "29 Jun 2021",
"name": "Xiangfu Zhong",
"expertise": [
"Reviewer Expertise bioinformatics",
"microRNA annotation and target predication",
"epigenetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The manuscript describes a python pipeline to predict the interaction between miRNA, gene and enhancer, based on the expression data. Their interaction may help us have a better understanding of miRNA regulation mechanisms.\nComments and suggests for improvement:\nPage 3, the methods section, the third step, \"the input data is gene expression data with sample size >=8\". Does this sample size requirement include replicates? Why does MIREyA require this number of sample size?\n\nPage 5, in the ”Use case” section, \"2-3 replicates per time point\". However, the reference 24 says \"Three-four biological replicates were prepared per time point\".\n\nCan the authors provide some script or functions for users to process the raw data into MIREyA input format? For example, the first column in data/DE_mirnas_expression.tsv, is the miRNA names, but not in the format of mostly used.\n\nThe example expressions are normalized, it would be clear to mention when explaining -ge on page 4.\n\nImprove the logging and exit message of running the pipeline.\n\nOptional:\nThe current code looks like in the script format, wrapping them into package and release to pypi may improve the package popularity and availability. The code looks much like customer scripts for analysis for case use data, generation of them into wider usage.\n\nSome genes have multiple copies across the genome, when calculating the correlation between gene expression and enhancer/miRNA, will copy/genomic coordinate be given to the correlation test? At least 3 line expression data about Ccdc59 in the example expression data data/DE_gene_expression.tsv, which one is used in the correlation test?\n\nI could not reproduce the first example 1 on page 5:\n\ngit clone git@github.com:veania/MIREyA.git Rename the out folder within this repo code, then create another out for testing, python src/run_mireya.py -d seed_match_needle -e data/enhancers.macrophages.Mtb.mm9.fasta -o out/seed_match_needle_out/ -ge data/DE_gene_expression.tsv -me data/DE_mirnas_expression.tsv -ei data/enh.gene.assoc.sign.tsv -m data/DE_mirna_mature_seqs.fa -g data/db -s data/seeds_seq_forward_short -sr data/seeds_seq_reverse_compl_short -eb data/enhancers.macrophages.Mtb.bed -ms data/mature_seqs/\n\nFirst error in step 1:\nError: Unable to open file out/seed_match_needle_out//Mir146_seed_pos_in_genome. Exiting.\nEven with this error, the pipeline keeps running without exit. For the step 2, I got another error:\nFile 'Mir146_enh_with_seeds.bed' has size 0. Returning a NULL data.table. Execution halted Calculation is finished. Please find the results in mir_enh_gene_trios.tsv\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6987",
"date": "26 Aug 2021",
"name": "Anna Elizarova",
"role": "Author Response",
"response": "Thank you for leaving the review. As for the questions: Page 3, the methods section, the third step, \"the input data is gene expression data with sample size >=8\". Does this sample size requirement include replicates? Why does MIREyA require this number of sample size? Yes, the stated sample size includes replicates. We added this constraint because the pipeline relies on calculation of correlation coefficient. It is possible to try it on an expression dataset of smaller size but the result might be less reliable. Page 5, in the ”Use case” section, \"2-3 replicates per time point\". However, the reference 24 says \"Three-four biological replicates were prepared per time point\". Authors of the original paper prepared up to 4 replicates, but sequenced only 2-4. To check the exact number of replicates sequenced for each time point one can browse FANTOM5 data (https://fantom.gsc.riken.jp/5/) or have a look at Supplementary table 1 in the reference 2 as well. We changed the description in our article to “2-4 replicates”, since unstimulated macrophages’ time point 24h has 4 sequenced replicates. Can the authors provide some script or functions for users to process the raw data into MIREyA input format? For example, the first column in data/DE_mirnas_expression.tsv, is the miRNA names, but not in the format of mostly used. It is unclear what exactly the reviewer means by mentioning the raw data. If the reviewer has in mind any specific format we can provide a script for the conversion. For now, one may use miRNA names in any format. The only thing to keep in mind is that they should be named consistently in all input files. Sequences of mature miRNAs may be downloaded from miRBase database: http://www.mirbase.org/ftp.shtml. Seed sequences of miRNAs could be retrieved from, e.g. http://www.targetscan.org/cgi-bin/targetscan/data_download.cgi?db=mmu_72. The example expressions are normalized, it would be clear to mention when explaining -ge on page 4. We specified that gene expression is expected to be normalized. Improve the logging and exit message of running the pipeline. Thank you for the suggestions. We added more logging in the latest release. The pipeline now exits if in seed_match_needle mode there is no match of miRNA seeds in the genome and genome as fasta files per chromosome are provided in incorrect format. Optional: The current code looks like in the script format, wrapping them into package and release to pypi may improve the package popularity and availability. The code looks much like customer scripts for analysis for case use data, generation of them into wider usage. We believe that for now it is out of the scope of this work. This is an option to consider in the future. Some genes have multiple copies across the genome, when calculating the correlation between gene expression and enhancer/miRNA, will copy/genomic coordinate be given to the correlation test? At least 3 line expression data about Ccdc59 in the example expression data data/DE_gene_expression.tsv, which one is used in the correlation test? The expression dataset we use represents promoters not genes obtained by CAGE-seq technique. It has been shown previously that on average each human gene has 5 promoters. So in our dataset “copies” represent different promoters of genes. The pipeline will consider them separately. If one has a similar dataset, they may choose a maximum correlation coefficient per gene after running the pipeline. Alternatively, it is possible to sum promoter expression into gene expression from the beginning and pass it to the pipeline using a flag -ge. In the example dataset we used promoter separetely. I could not reproduce the first example 1 on page 5: git clone git@github.com:veania/MIREyA.git Rename the out folder within this repo code, then create another out for testing, python src/run_mireya.py -d seed_match_needle -e data/enhancers.macrophages.Mtb.mm9.fasta -o out/seed_match_needle_out/ -ge data/DE_gene_expression.tsv -me data/DE_mirnas_expression.tsv -ei data/enh.gene.assoc.sign.tsv -m data/DE_mirna_mature_seqs.fa -g data/db -s data/seeds_seq_forward_short -sr data/seeds_seq_reverse_compl_short -eb data/enhancers.macrophages.Mtb.bed -ms data/mature_seqs/ First error in step 1: Error: Unable to open file out/seed_match_needle_out//Mir146_seed_pos_in_genome. Exiting. Even with this error, the pipeline keeps running without exit. For the step 2, I got another error: File 'Mir146_enh_with_seeds.bed' has size 0. Returning a NULL data.table. Execution halted Calculation is finished. Please find the results in mir_enh_gene_trios.tsv We repeated your actions on two computers and could not catch this error. To try to reproduce this error we need information about versions of your Linux distribution, Python, bedtools. Nevertheless, we did add a message about exiting for the case if this error occurs."
}
]
},
{
"id": "87527",
"date": "05 Jul 2021",
"name": "Chaogang Shao",
"expertise": [
"Reviewer Expertise miRNA data mining",
"bioinformatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have developed a pipeline, MIREyA, to predict miRNA gene-enhancer trios based on an expression dataset. This manuscript covers an important aspect of miRNA-target research by presenting a useful tool that technically sound. I have some questions:\nA newly developed software needs to prove its function is correct before it is applied. However, the manuscript lacks this important part. Though the authors applied the pipeline to primary murine macrophages infected by Mycobacterium tuberculosis and detected some miRNAs could up-regulate genes related to immune responses, these predicted results need to be proved by experiments. At present, we can’t determine whether these regulatory relationships are correct, so the reliability of MIREyA can not be proved. The authors can use the published miRNAs with activation function, such as MiR-24-1, miR-744 and MiRNA let-7i, to verify the reliability of the pipeline.\n\nAre there any miRNAs coming from primary murine macrophases affected by Mycobacterium tuberculosis that can bind to enhancers but reduce gene expression?\n\n“keep only enhancers with the percent identity (PI) > 0.5 (PI defined as a percent of matches between miRNA and DNA region)”. Will 0.5 be too low to increase false positives? What is the basis for the author to choose the parameter?\n\nAre there any other sRNAs that share very similar sequence to miRNA and express even higher than miRNA in cells? These sRNAs may be involved in the regulation of enhancers too. Whether authors can improve the software to find these co-regulated sRNAs from high throughput sequence data, so as to build a more complete regulatory network.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6988",
"date": "26 Aug 2021",
"name": "Anna Elizarova",
"role": "Author Response",
"response": "Thank you for leaving the review. As for the questions: A newly developed software needs to prove its function is correct before it is applied. However, the manuscript lacks this important part. Though the authors applied the pipeline to primary murine macrophages infected by Mycobacterium tuberculosis and detected some miRNAs could up-regulate genes related to immune responses, these predicted results need to be proved by experiments. At present, we can’t determine whether these regulatory relationships are correct, so the reliability of MIREyA can not be proved. The authors can use the published miRNAs with activation function, such as MiR-24-1, miR-744 and MiRNA let-7i, to verify the reliability of the pipeline. To find already studied miRNAs with this tool, we need an expression dataset for the same cell types and conditions as in the references. MiRNA expression is highly dependent on cell type and conditions, thus any other expression dataset would have a different set of expressed miRNAs which might not include miRNAs studied in the papers. Another limitation is that the expression dataset must include at least 8 samples so that correlation analysis would make sense. For now we are not aware of such a complete dataset. In case of MiR-24-1, there was no expression dataset to run our pipeline, but the first step of the algorithm (miRNA/enhancer interaction prediction) would automatically find the enhancer from the article: the miRNA sequence is apparently present in the sequence of the enhancer in the reference 3 as the enhancer contains a gene sequence of the miRNA. We found an article (doi.org/10.1038/srep12987) reporting gene activation by miR-744 and an article (doi.org/10.1073/pnas.1803384115) reporting similar activation by miR-744 but the authors did not demonstrate that these miRNAs do that through enhancer activation. Lack of a known enhancer in a regulatory circuit makes the use of MIREyA impossible. Are there any miRNAs coming from primary murine macrophases affected by Mycobacterium tuberculosis that can bind to enhancers but reduce gene expression? Since we focused on the activatory role of miRNA, we believe that the analysis of repressor miRNAs bound to enhancers is beyond the scope of the current paper. “keep only enhancers with the percent identity (PI) > 0.5 (PI defined as a percent of matches between miRNA and DNA region)”. Will 0.5 be too low to increase false positives? What is the basis for the author to choose the parameter? We believe that 0.5 is high enough. We chose the threshold by comparison with experimentally validated examples of miRNA interaction with RNA, where the minimum 11/22 miRNA bases represented an exact match. We hypothesized that such PI would be sufficient for miRNA interaction with DNA. Are there any other sRNAs that share very similar sequence to miRNA and express even higher than miRNA in cells? These sRNAs may be involved in the regulation of enhancers too. Whether authors can improve the software to find these co-regulated sRNAs from high throughput sequence data, so as to build a more complete regulatory network. So far we have not seen any article describing sRNAs with similar to miRNA properties which are able to regulate enhancers. We believe that for now this suggestion is beyond the scope of this work."
}
]
}
] | 1
|
https://f1000research.com/articles/10-249
|
https://f1000research.com/articles/10-532/v1
|
05 Jul 21
|
{
"type": "Case Report",
"title": "Case Report: Penetrating Thoracic Trauma by A Gunshot Involving the Heart",
"authors": [
"Alok Atreya",
"Ritesh G. Menezes",
"Ashal Timalsina",
"Geeta Bashyal",
"Lokaratna Gyawali",
"Sushila Gyawali",
"Alok Atreya",
"Ritesh G. Menezes",
"Ashal Timalsina",
"Lokaratna Gyawali",
"Sushila Gyawali"
],
"abstract": "Firearm related mortality is not frequently encountered in a country like Nepal where there us a stringent law prohibiting buying, selling, carrying or storing of firearms. It is required to have a valid license to have a firearm in possession. Wounds produced by firearm have a typical characteristic the knowledge of which helps to identify the type of firearm used, range of fire, position of the victim and whether the manner of death was homicidal, suicidal or accidental. The present case is a first autopsy-based study from Nepal which discusses the wounds produced by firearm with interpretation of such findings for medicolegal purposes. The present case highlights a social problem where the victim, a psychiatric patient, had no access to prescription medication due to coronavirus disease (COVID-19) related lockdown.",
"keywords": [
"entry wound",
"exit wound",
"Forensic Pathology",
"gunshot",
"hemothorax",
"Nepal",
"smooth bore"
],
"content": "Introduction\n\nThere are stringent laws regarding firearms in Nepal. However, illegal possession of firearms is not uncommon in rural part of this mountainous country. Self-suspension by hanging and consumption of agricultural poisons are the common methods of suicides in Nepal. Use of firearms for committing suicide is rare. We report a case of firearm related fatality from Nepal, where a flint-lock type muzzle loader smooth bore firearm was used to commit suicide and discuss the interpretation of firearm related wounds during a medicolegal examination. The victim in the present case was a schizophrenic patient, who had to discontinue his prescription medication due to coronavirus (Covid-19) related lockdown.\n\n\nCase report\n\nThe dead body of 45-year-old male was brought for autopsy. The body was stiff at all the joints. The hands were clenched and the whole body smeared in blood. Post mortem lividity could not be appreciated. A rectangular contusion was noted in the front of the chest which measured 10 × 8 cm. An oval perforated lacerated wound (entry wound) having 1.8 cm diameter was present in the middle of the contusion [Figure 1]. The wound was charred, black in color with surrounding black tattooing. The perforated wound was 48 cm from the vertex in midline, 115 cm from the sole of the foot and 18 cm from the supra sternal notch. It was 17 cm from the right mid axillary line and 20 cm from the left mid axillary line. A linear slit-like laceration (exit wound) was present on the back in the left side which measured 0.5 × 0.2 cm and was located 25 cm from the vertex, 129 cm from the sole of the foot [Figure 1].\n\nA, An oval entry wound is present on the front of the chest. B, A linear, slit-like lacerated exit wound on the back.\n\nOn opening the chest, a perforating fracture was noted in the xiphoid process [Figure 2]. The heart was pulverized [Figure 3] with exsanguination of the blood into pericardial cavity. The clotted blood in the pericardial cavity weighed about 650 gm. When a probe was directed through the heart from the defect, it was noted that the entry point was located on the right side of the anterior interventricular septum and exited through the left ventricle [Figure 3]. The direction was right to left and below upwards. The left lung was completely collapsed and there was a penetrating injury noted at the upper lobe. The rest of the findings were unremarkable.\n\nA, A perforating fracture in the xiphoid process. B, Punctured laceration is seen in the posterior chest wall.\n\nA, Pulverized heart. B, A wooden probe passed through the defect showing the direction of the bullet.\n\nAs per the history provided by the victim’s brother, the deceased was an unmarried male. He was diagnosed with schizophrenia since adolescence for which he was on the prescription medicine Quetiapine. The medicine was not available at his rural pharmacy and due to the Covid-19 pandemic lockdown, he was unable to visit the tertiary hospital for his regular prescription. The medicine was therefore discontinued for 3 months prior to death. The victim consumed homemade arrack (a distilled alcoholic drink) regularly which they prepared at their home.\n\nThe crime scene photograph provided by the investigating officer showed a single barrel, smooth-bored firearm which was a flint lock type muzzle loader [Figure 4].\n\n\nDiscussion\n\nShotgun wounds vary in characteristics depending upon type, distance, position and the number of shots. On entering the body cavity, pellets follow the tissue of least resistance.1 A shotgun wound in the chest cannot point well towards the manner of death. However, contact shots are more likely to be suicidal than homicidal and are more fatal for single shot.2\n\nShots to the heart are very common, with only the head being a more common target.3 Suicidal victims are aware of the lethality of gunshots to this vital organ and some victims even locate the cardiac impulse before taking the shot. Furthermore, suicidal fire is more likely to be directed right to left with homicidal direction commonly being left to right.4\n\nThe crime scene visit in cases of firearm related mortality is equally important in interpreting the manner of death. In suicides, the offending weapon is usually found at the scene of crime in contrast to homicides where the perpetrator usually carries away the weapon after committing the crime.\n\nIn contrast to stab wounds, gunshot cause more exsanguination of blood due to jagged tearing of myocardium. 60 ml to 200 ml of clotted blood is enough to cause death. Penetrating thoracic trauma as a result of gunshot injuries are associated with traumatic hemothorax, hemopneumothorax, or pneumothorax.5 If the penetrating injury involves the heart, the chances of survival are less than 1%,5 as seen in our case. There are increased number of suicides from Nepal reported during the COVID-19 pandemic.6 The patients with underlying psychiatric disorder could not get access to their prescription medication due to the lockdown as all the public transportation was halted and people were afraid to get out of home. Discontinuation of medication in schizophrenic patients has shown to exacerbate the syndrome.7 This might have been the underlying reason for suicide in the present case. The present case further highlights the social concern the pandemic has brought where patients are restricted of access to their health care needs due to lack of transport in the lockdown.\n\n\nConclusion\n\nFirearm fatalities are medicolegal cases where the autopsy surgeon is required to determine the manner of death based upon the injuries present over the body. Meticulous examination of the wound not only gives clues about the entry and exit wounds but also the range of fire and the weapon used. The manner of death can also be interpretated from the position and characteristics of the wound. A crime scene visit is also mandated in firearm related fatalities which will further help to corroborate the findings.\n\n\nAuthors’ declaration statements\n\nThe authors’ guarantee that the work is original and does not infringe copyright or other party’s property rights. All authors have read and approved this submission and have given appropriate credit to everyone who participated in this work.\n\n\nEthics approval and consent to participate\n\nWritten informed consent was obtained from the deceased patient’s elder brother for publication of this case report.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAuthors’ contributions\n\nAA conceptualized the study and wrote the first draft. RGM and AT reviewed the literature and revised the manuscript. GB, LG and SG conducted the autopsy, provided the case information, and revised the manuscript. All authors read and approved the final version of the manuscript.",
"appendix": "References\n\nOrdog GJ, Wasserberger J, Balasubramaniam S: Shotgun wound ballistics. J Trauma. 1988; 28(5): 624–631. PubMed Abstract | Publisher Full Text\n\nCave R, DiMaio VJ, Molina DK: Homicide or suicide? Gunshot wound interpretation: a Bayesian approach. Am J Forensic Med Pathol. 2014; 35(2): 118–123. PubMed Abstract | Publisher Full Text\n\nAvis SP: Suicidal gunshot wounds. Forensic Sci Int. 1994; 67(1): 41–47. PubMed Abstract | Publisher Full Text\n\nStrajina V, Živković V, Nikolić S: Forensic issues in suicidal single gunshot injuries to the chest: an autopsy study. Am J Forensic Med Pathol. 2012; 33(4): 373–376. PubMed Abstract | Publisher Full Text\n\nZeiler J, Idell S, Norwood S, et al.: Hemothorax: A Review of the Literature. Clin Pulm Med. 2020; 27(1): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPokhrel S, Sedhai YR, Atreya A: An increase in suicides amidst the coronavirus disease 2019 pandemic in Nepal. Med Sci Law. 2021; 61(2): 161–162.\n\nLiu-Seifert H, Adams DH, Kinon BJ: Discontinuation of treatment of schizophrenic patients is driven by poor symptom response: a pooled post-hoc analysis of four atypical antipsychotic drugs. BMC Med. 2005; 3: 21."
}
|
[
{
"id": "89057",
"date": "13 Jul 2021",
"name": "Panagiotis K. Stefanopoulos",
"expertise": [
"Reviewer Expertise Maxillofacial surgery",
"ballistic 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\nThe article is very well presented with respect to the case reported, with clear photos that help the reader understand the nature of the lethal injury described therein.\nHowever, the authors use in their references an article on shotgun wound ballistics, whereas the wound from the flintlock rifle was most likely produced by a single projectile, such as those normally used by this type of weapon (otherwise the authors should clarify whether there were multiple projectiles such as pellets). On the other hand, the literature on wound ballistics as applied to flintlock rifles is virtually non-existent, which is another reason why this article is interesting.\n\nThe entrance wound, in addition to the description given, appears to show some muzzle imprint, which can be expected from a contact shot, since according to DiMaio's Gunshot Wounds (3rd ed., CRC Press 2016, p. 115) the expanding gases that enter the chest (or the abdominal) cavity cause a bulging out of the skin against the muzzle, resulting in an imprint often significantly larger than the actual diameter of the muzzle.\n\nWhile in hard contact wounds most of the soot is directed into the wound, with little soil of the surrounding skin, in this case the use of black powder in the muzzle loader may account for the extensive blackening of the skin. However, the term \"tattooing\" used by the authors may be inappropriate, since it is used to indicate the marking of the skin from powder particles, not the blackening from the smoke.\n\nAn important finding of the autopsy is the complete destruction of the heart. The authors described it simply as pulverized. In my opinion, this is the impressive result of the hydrodynamic pressure generated by the passage of the projectile through the heart, which caused blowout of its walls. I suggest that this is added to their report.\n\nThank you for giving me the opportunity to review this interesting article.\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": "6994",
"date": "26 Aug 2021",
"name": "Geeta Bashyal",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for the analysis of this manuscript and your valuable remarks. The manuscript has been corrected according to the comments. All changes you suggested are incorporated as follows: Comment: However, the authors use in their references an article on shotgun wound ballistics, whereas the wound from the flintlock rifle was most likely produced by a single projectile, such as those normally used by this type of weapon (otherwise the authors should clarify whether there were multiple projectiles such as pellets). Response: The following sentence is added to the text \"In the present case as the projectile had exited from the body it could not be ascertained on the type and number of projectiles (pellets).\" Comment: The entrance wound, in addition to the description given, appears to show some muzzle imprint, which can be expected from a contact shot, since according to DiMaio's Gunshot Wounds (3rd ed., CRC Press 2016, p. 115) the expanding gases that enter the chest (or the abdominal) cavity cause a bulging out of the skin against the muzzle, resulting in an imprint often significantly larger than the actual diameter of the muzzle. Response: As per the reviewer's suggestion we did go through the reference and have detailed the entry wound \"The entry wound showed some muzzle imprint, signifying a contact shot. The expanding gases that enter the chest cavity cause a bulging out of the skin against the muzzle, resulting in an imprint often significantly larger than the actual diameter of the muzzle. 3\" Comment: While in hard contact wounds most of the soot is directed into the wound, with little soil of the surrounding skin, in this case the use of black powder in the muzzle loader may account for the extensive blackening of the skin. However, the term \"tattooing\" used by the authors may be inappropriate, since it is used to indicate the marking of the skin from powder particles, not the blackening from the smoke. Response: We have corrected the manuscript and have deleted the term tattooing. Comment: An important finding of the autopsy is the complete destruction of the heart. The authors described it simply as pulverized. In my opinion, this is the impressive result of the hydrodynamic pressure generated by the passage of the projectile through the heart, which caused blowout of its walls. I suggest that this is added to their report. Response: As per the suggestion the following sentence is added to the manuscript \"There was complete destruction of the heart noted at autopsy which was due to the hydrodynamic pressure generated by the passage of the projectile through the heart that caused blowout of its walls.\""
}
]
},
{
"id": "89003",
"date": "02 Aug 2021",
"name": "Navneet Ateriya",
"expertise": [
"Reviewer Expertise Forensic Pathology",
"Forensic Ballistics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 presented clearly and accurately by the authors. Flow is good, easy to read and understandable to the readers. There is one one minor correction in Abstract line 1: replace word \"us\" with \"is\". Overall, it flows good.\nIntroduction is sufficient to give background image of article.\nCase report - Other findings present on skin surrounding fire arm entry wounds such as blackening, tattooing may also be mentioned if present. Author did not mention whether the deceased was subjected to radiological examination prior to autopsy. Images are very helpful in understanding and corelating the findings.\nDiscussion part is okay and the conclusions drawn adequately support the findings.\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": "6995",
"date": "26 Aug 2021",
"name": "Geeta Bashyal",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for your valuable comments. We have corrected the manuscript as instructed. Regarding your query about the radiological examination, due to limited resources at the mortuary radiological examination was not done in the present case. This statement has been added to the manuscript text."
}
]
}
] | 1
|
https://f1000research.com/articles/10-532
|
https://f1000research.com/articles/10-469/v1
|
14 Jun 21
|
{
"type": "Case Report",
"title": "Case Report: Heparin-induced thrombocytopenia during COVID-19 outbreak: the importance of scoring system in differentiating with sepsis-induced coagulopathy",
"authors": [
"Louisa Fadjri Kusuma Wardhani",
"Ivana Purnama Dewi",
"Denny Suwanto",
"Meity Ardiana",
"Louisa Fadjri Kusuma Wardhani",
"Ivana Purnama Dewi",
"Denny Suwanto"
],
"abstract": "Background: COVID-19 disease is accompanied by derangement of coagulation with a risk of fatal thromboembolic formation. COVID-19 patients are among those indicative for heparin treatment. Increased heparin administration among COVID-19 patients increased heparin induced-thrombocytopenia's risk with/without thrombocytopenia. Case presentation: We present a 71-year-old male patient who came to the emergency department (ED) with a COVID-19 clinical manifestation that PCR nasopharyngeal swab confirmed. He was assessed to have acute respiratory distress syndrome (ARDS), as shown by rapid progression of hypoxemic respiratory failure and bilateral pulmonary infiltrate. He was then treated with moxifloxacin, remdesivir, dexamethasone, heparin pump, and multivitamins. During admission, his respiratory symptoms got worse, so he transferred to the ICU for NIV support. On the ninth day of admission, he had gross hematuria followed by a rapid fall of platelet count. We used two different scoring systems (4Ts and HEP scoring system) to confirm the diagnosis of heparin-induced thrombocytopenia (HIT). Following the discontinuation of heparin injection, the thrombocyte continued to rise, and hematuria disappeared. Conclusion: Heparin-induced thrombocytopenia is associated with an increased risk of severe disease and mortality among COVID-19 patients. The differential diagnosis of HIT could be difficult among COVID-19 patients as thrombocytopenia can also be caused by infection progression. We use two scoring systems, 4Ts and HEP scoring, that can help us to manage the patient. With good management, we can avoid patient morbidity and mortality.",
"keywords": [
"Heparin Induced Thrombocytopenia",
"HIT",
"COVID-19",
"mortality"
],
"content": "Background\n\nThe outbreak of the novel-coronavirus named SARS-CoV-2 was first identified in Wuhan, China, in January 2020. This was later classified as a pandemic because it affected more than 114 countries with more than two million cases. The infection can be manifested as fever, dry cough, myalgia, diarrhea, and anosmia. The more severe cases can present as acute respiratory distress syndrome (ARDS), as shown by rapid progression of hypoxemic respiratory failure and bilateral pulmonary infiltrate. It can also be manifested as derangement of coagulation that ranges from hypercoagulability to venous thromboembolism (VTE). It has been previously described that 64 out of 150 COVID-19 patients complicated by ARDS developed various thromboembolic complications from ischemic strokes to pulmonary embolism.1 COVID-19 patients have elevated D-dimer concentration, increased fibrin degradation products (FDP), and lower antithrombin levels. These are the reasons for anticoagulation administration among COVID-19 patients. Heparin is the agent of choice for anticoagulation, especially in those with severe COVID-19 manifestation.2–5\n\nAlthough heparin is commonly used in COVID-19 patients, its side effects cannot be forgotten. The most avoided side effect, which is potentially fatal with 20% mortality rates, is heparin induced thrombocytopenia (HIT) with/without thrombocytosis. This is caused by the formation of antibodies (IgG) against the complex of platelet factor 4 (PF4) and heparin. The PF4/IgG antibodies complex can activate platelets, which can cause catastrophic thrombosis. It can occur within 5–10 days of heparin therapy in 0.5–3% of patients. It can also develop rapidly within 24 hours after re-exposure of heparin in some patients with a recent heparin administration history.2,6,7 An increasing incidence of HIT occurs among COVID-19 patients, explained by exacerbated immune reactions and probably by an increased release of PF4, linked to platelet activation. However, the underlying pathophysiology of increased HIT risk and thrombosis risk in COVID-19 patients is not yet well understood.8 We present a HIT case with severe thrombocytopenia followed by gross hematuria manifestation in a COVID-19 patient.\n\n\nCase presentation\n\nA 71-year-old male patient presented to the emergency department (ED) with a chief complaint of dry cough for one week followed by dyspnea that had increased three days before admission. He had a fever one week prior that decreased with NSAIDs, and no other complaints were claimed. He had no contact history with confirmed COVID-19 patients. His past medical illnesses consisted of diabetes mellitus, hypertension, and old myocardial infarction (OMI). He previously consumed aspirin, bisoprolol, lisinopril, diltiazem, and atorvastatin. He also had a history of routine subcutaneous insulin usage.\n\nHis blood pressure (BP) was 132/75 mmHg, heart rate (HR) 79 beats per minutes (bpm) regular, and apparent dyspnea with a respiratory rate (RR) of 28 breaths per minute. He had desaturation, with oxygen saturation of 85% (free air) that improved with a non-rebreathing oxygen mask (NRM) 15 Liters per minute to 95%. He was also pyretic (38oC). His physical examination showed no increased jugular venous pressure, bilateral lung crackles, pleural friction rub, and no leg edema.\n\nComprehensive evaluations were performed, including ECG, COVID-19 antigen swab, laboratory examination, and chest radiography. His initial ECG showed normal sinus rhythm of 79 bpm, left axis deviation, with inferior OMI. Laboratory data showed increased CRP (195.3 mg/L), hypokalemia (3.2 mEq/L), respiratory failure, and respiratory acidosis. Chest radiography showed cardiomegaly and bilateral pneumonia. COVID-19 antigen swab was positive. Thus patient and family were consent for isolation and tracing procedure. As respiratory failure presented with severe ARDS (PaO2/FiO2 82 mmHg) and hypoxemia, the patient was informed about the need for performing an intubation procedure. Since our intensive care unit was occupied, we planned a referral to another facility. The patient and family refused it, so we hospitalized the patient in our lower care unit.\n\nHe was then started on antibiotic treatment with moxifloxacin, antiviral therapy with remdesivir, dexamethasone, heparin pump, and multivitamins. He also continued his daily medication (insulin, aspirin, lisinopril, beta-blockers, nitrates, and atorvastatin). Tocilizumab 400 mg was also given on the second day before admission. His vital signs and laboratory examinations were routinely monitored.\n\nDuring the sixth day of admission, his oxygen saturation deteriorated. He was then transferred to the unoccupied intensive care unit to receive non-invasive ventilation (NIV). The vital signs showed BP 168/87 mmHg, HR 65 bpm regular, and RR 30 breaths per minute. During the following days, the patient's symptoms showed slight improvement. His laboratory examination on the tenth day showed leukocytosis, thrombocytopenia, increased neutrophil–lymphocyte ratio (NLR), increased D-Dimer, and PCR remained positive for COVID-19. No prolonged hemostatic values were found. Plasma prothrombin time (PPT) was 20 sec, and activated partial thromboplastin time (APTT) was 38.6 sec.\n\nOn the ninth day of admission, the patient seemed anxious with complaints of urinary pain. It showed that he had gross hematuria while he was on heparin therapy within targeted APTT. His vital signs showed BP 120/77 mmHg, tachycardia 110 bpm, and tachypnea 30 breaths per minute. Laboratory data showed significantly reduced thrombocytes (40,000 mg/L). Urine examination showed gross hematuria with leukocyturia (10–15 cells/field), nitrituria, and proteinuria (2+). The patient underwent ECG and chest radiography evaluation, which showed no significant changes (Figure 1).\n\nHeparin was thought to be the underlying cause of thrombocytopenia in this patient. Since heparin antibody was not routinely checked in the developed country, we choose to switch our anticoagulant with rivaroxaban 20 mg twice daily. The symptoms were then improved with the absence of hematuria and reduced dyspnea. The thrombocyte evaluation showed normalization to 177,000 on the eleventh day. The patient was transferred back to the low care unit on the twentieth day of admission. PCR was showed negative one day later, and the patient was then discharged. One month after discharge, the patient returned to the outpatient clinic without symptoms. The patient and family have then suggested the need for routine control for a better outcome after surviving COVID-19 infection.\n\n\nDiscussion\n\nWe report a patient presented to the ED with clinical manifestation of COVID-19 disease that was diagnosed by positive antigen swab for SARS-CoV-2 and confirmed by PCR nasopharyngeal swab the day after. He was also presented with desaturation and severe hypoxemia, leading to severe ARDS (PaO2/FiO2 of 82 mmHg). COVID-19 patient is among those indicative for heparin treatment. Low-molecular-weight heparin is used as prophylaxis for the thromboembolic complication of COVID-19, while unfractionated heparin is commonly used in severe manifestations.\n\nA routine evaluation of both physical and laboratory examination is needed to evaluate treatment and side effects of infection and therapy of COVID-19. A fatal side effect that can occur during heparin treatment is HIT. HIT is characterized by a fall of platelet count with/without a sign of arterial and venous thrombosis during heparin administration and disappears equally quickly once the heparin is withdrawn. The widely known diagnostic criteria for HIT includes (1) HIT antibodies to PF4-heparinoid complexes, (2) HIT antibodies-mediated platelet activation, (3) progressive platelet fall 40-50% from baseline, (4) thrombocytopenia occurs within 5–10 days after initiation or 24–48 hours after re-exposure of heparin, and (5) thrombosis occurs in patients treated with heparin. It should also be suspected of an unexplained fall in platelet count by 50%, skin lesion at the heparin injection site, and systemic reaction to heparin injection. Thrombocytopenia in HIT is usually moderate to severe, with the fall of platelet rarely <100,000 platelets/μL. It has been reported that 30–60% of patients can suffer venous events while 15–20% can suffer arterial events while bleeding manifestation is rare.2,5,9,10\n\nThe differential diagnosis of HIT could be difficult among COVID-19 patients as thrombocytopenia can also be caused by infection progression. Disseminated intravascular coagulopathy (DIC) can complicate the septic status of COVID-19, called sepsis-induced coagulopathy. Thrombocytopenia is associated with an increased risk of severe disease and mortality among COVID-19 patients. On the other hand, heparin exposure is correlated with severe thrombocytopenia, suggesting that HIT may be responsible for severe thrombocytopenia in COVID-19. PF4/H antibodies or a scoring system makes the presumptive diagnosis of HIT. The measurement of PF4/H is not commonly checked in our center, so we use the scoring system to measure the possibility of HIT.2,5,7,9,11\n\nOur patient experienced a rapid fall of thrombocytes on a ninth day following gross hematuria manifestation. The clinical suspicion laid on HIT as it is known to be a fatal side effect of heparin administration. We use two scoring systems, which showed a high probability of HIT in our patient using the 4Ts (5 points) and HEP scoring (5 points) system (Figure 2). The use of two different methods reduces the possibility of overdiagnosis since improper anticoagulation in COVID-19 patients can lead to worse prognosis. The 4Ts scoring system valued thrombocytopenia, timing of platelet fall, thrombosis (or other sequelae of HIT), and the absence of other thrombocytopenia cause (medication, DIC) in which the fourth indicator is subjective to the discretion of the observer. On the other hand, the HEP scoring system listed infection as a marker of thrombocytopenia which is found in COVID-19 patients. The clinician can confidently reduce the use of alternative anticoagulation due to false diagnosis in clinically oriented HIT assessment using the HEP scoring system.\n\nBoth measurements show high probability of HIT in this patient.\n\nWhen isolated HIT is suspected clinically, the discontinuation of heparin-based therapy is recommended. Clinicians shall consider the initiation of other anticoagulant agents using direct thrombin or factor Xa inhibitors to prevent thrombus formation.7,9 Following the discontinuation of heparin injection and switching to rivaroxaban, the thrombocyte continued to rise, and hematuria disappeared. It was consistent with HIT in which is rapidly disappeared once heparin administration stopped (Figure 3).\n\n\nConclusion\n\nThere is an increased use of heparin therapy during the outbreak of SARS-CoV-2 infection as it is a known risk of fatal thromboembolic formation. HIT is a rare but fatal complication following heparin administration. As the progression of COVID-19 also shows thrombocytopenia, it is somehow ambiguous to perform discontinuation of heparin. Moreover, the measurement of PF4/H antibodies is not available in most of the centers. It makes the clinical assessment of HIT critical to risk-stratify the need to stop heparin as it also led to poor prognosis. The use of 4Ts scoring system is subjective to the observer's discretion to determine the involvement of other thrombocytopenia. However, the HEP scoring system has multiple values that help physicians determine the HIT risk probability. We used two different scoring systems (4Ts and HEP scoring systems) that show a high HIT probability, so switching therapy to rivaroxaban is initiated.\n\n\nDeclaration\n\nThis case report does not require ethical approval as it is not human or animal research.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.",
"appendix": "Data availability\n\nAll data underlying the results are presented within the manuscript, and no additional source data are required.\n\n\nReferences\n\nHelms J, Jin H, Wang M: High risk of thrombosis in patients with severe SARS-CoV-2 infection: a multicenter prospective cohort study. Intensive Care Med. 2020; 46: 1089–96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFabiana T, Angela S, Jacopo M, et al.: COVID-19 and Thrombocytopenia: Heparin or Sepsis-Induced? J Geriatr Med Gerontol. 2020; 6: 6–8. Publisher Full Text\n\nLiltjos J-F, Leclerc M, Chochols C, et al.: High incidence of venous thromboembolic eventd in anticoagulated severe COVID-19 patients. J Thromb Haemost. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRiker RR, May TL, Fraser GL, et al.: Heparin-induced thrombocytopenia with thrombosis in COVID-19 adult respiratory distress syndrome. Res Pract Thromb Haemost. 2020; 4: 936–41. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu X, Zhang X, Xiao Y, et al.: Heparin-induced thrombocytopenia is associated with a high risk of mortality in critical COVID-19 patients receiving heparin-involved treatment. medRxiv. 2020. Publisher Full Text\n\nAly R, Gupta S, Gupta S, et al.: Case Report: Heparin-induced thrombocytopenia in a patient with COVID-19. F1000Res. 2020; 9: 704. Publisher Full Text\n\nCuker A, Arepally G, Crowther MA, et al.: The HIT Expert Probability (HEP) Score: A novel pre-test probability model for heparin-induced Thrombocytopenia based on broad expert opinion. J Thromb Haemost. 2010; 8: 2642–50. PubMed Abstract | Publisher Full Text\n\nDaviet F, Guervilly C, Baldesi O, et al.: Heparin-induced thrombocytopenia in severe COVID-19. Circulation. 2020; 142: 1875–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan M, Malynn E, Shaz B, et al.: Utility of consecutive repeat HIT ELISA testing for heparin-induced Thrombocytopenia. Am J Hematol. 2008; 83: 212–7. PubMed Abstract | Publisher Full Text\n\nFranchini M: Heparin-induced thrombocytopenia: An update. Thromb J. 2005; 3: 1–5. PubMed Abstract | Publisher Full Text\n\nLingamaneni P, Gonakoti S, Moturi K, et al.: Heparin-Induced Thrombocytopenia in COVID-19. J Investig Med High Impact Case Reports. 2020; 8: 4–7. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "87581",
"date": "30 Jun 2021",
"name": "Alan Yean Yip Fong",
"expertise": [
"Reviewer Expertise Cardiovascular diagnostics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis case report illustrates a clinical scenario that has to be identified early. Early risk stratification of the unwell patient and institution of an aggressive management plan will improved outcomes. This has been discussed in this draft, which is commendable. Therefore, this case report is relevant during this COVID pandemic.\nHowever, language editing is recommended, for better presentation of this manuscript in your journal.\nTherefore, minor revision, and then suitable for indexing.\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": "7018",
"date": "26 Aug 2021",
"name": "Louisa Fadjri Kusuma Wardhani",
"role": "Author Response",
"response": "This case report illustrates a clinical scenario that has to be identified early. Early risk stratification of the unwell patient and institution of an aggressive management plan will improved outcomes. This has been discussed in this draft, which is commendable. Therefore, this case report is relevant during this COVID pandemic. However, language editing is recommended, for better presentation of this manuscript in your journal. Therefore, minor revision, and then suitable for indexing. Thank you for your kind suggestion and comment. We have reviewed our manuscript and restructured with a better language editing"
}
]
},
{
"id": "90612",
"date": "09 Aug 2021",
"name": "Anggoro Budi Hartopo",
"expertise": [
"Reviewer Expertise Cardiovascular 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 authors report a case of COVID-19 pneumonia with HIT complication and finally can survive the disease. The emphasis of recognition of HIT, by two scoring system assessment, and proper discontinuation of heparin (UFH?) benefit the patient survival.\n\nHowever several concerns were addressed regarding the case presentation, as follows:\n\"Tocilizumab 400 mg was also given on the second day before admission\", is it true that before hospital admission the tocilizumab already be given?\n\nWhat kind heparin is used in this case? Continuous infusion of unfractionated heparin or subcutaneous LMWH? Please describe clearly the heparin type.\n\n\"Since heparin antibody was not routinely checked in the developed country,\" what developed country this refers to?\n\nThe use of 4Ts and HEP scoring must be reported in the Case presentation which recite the patient situation and management given, not in the Discussion session. In the Case presentation, there is no statement/narration about the use of these scores during patient management.\n\nAuthor switch to rivaroxaban as alternative anticoagulant in HIT replacing heparin, please give comment and reference/guideline which support this management.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "7019",
"date": "26 Aug 2021",
"name": "Louisa Fadjri Kusuma Wardhani",
"role": "Author Response",
"response": "The authors report a case of COVID-19 pneumonia with HIT complication and finally can survive the disease. The emphasis of recognition of HIT, by two scoring system assessment, and proper discontinuation of heparin (UFH?) benefit the patient survival. However several concerns were addressed regarding the case presentation, as follows: \"Tocilizumab 400 mg was also given on the second day before admission\", is it true that before hospital admission the tocilizumab already be given? Thank you for your correction. Tocilizumab was given in the second day admission. The following correction has been submitted in the case presentation section. What kind heparin is used in this case? Continuous infusion of unfractionated heparin or subcutaneous LMWH? Please describe clearly the heparin type. Thank you for your correction. We used unfractionated heparin (UFH) pump at first. We have been decribed it in the revision format. \"Since heparin antibody was not routinely checked in the developed country,\" what developed country this refers to? The correct statement is “Since heparin antibody was not routinely checked in the developing country” since its not applicable in our country (Indonesia). The use of 4Ts and HEP scoring must be reported in the Case presentation which recite the patient situation and management given, not in the Discussion session. In the Case presentation, there is no statement/narration about the use of these scores during patient management. Thank you for your kind suggestion. We have added the use of both scoring system in our case presentation section. Author switch to rivaroxaban as alternative anticoagulant in HIT replacing heparin, please give comment and reference/guideline which support this management. The drug of choices for whom suspected for HIT is argatroban and danaparoid. There is several recommendations regarding secondary prevention of HIT using rivaroxaban and fondaparinux (A Cuker, 2010; Lori Ann Linkins, BMJ 2015). Since the availability of some drug is limited and patient with ongoing hematuria, We prefer rivaroxaban as an exchange. Moreover, the use of rivaroxaban twice daily has non-inferior efficacy than those with fondaparinux (ESC Guidelines for Pulmonary Embolism)."
}
]
}
] | 1
|
https://f1000research.com/articles/10-469
|
https://f1000research.com/articles/10-315/v1
|
23 Apr 21
|
{
"type": "Research Article",
"title": "Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics",
"authors": [
"Nash Rochman",
"Yuri I Wolf",
"Eugene V Koonin",
"Yuri I Wolf"
],
"abstract": "Background: The start of 2021 was marked by the initiation of a global vaccination campaign against the novel coronavirus SARS-CoV-2. Formulating an optimal distribution strategy under social and economic constraints is challenging. Optimal distribution is additionally constrained by the potential emergence of vaccine resistance. Analogous to chronic low-dose antibiotic exposure, recently inoculated individuals who are not yet immune play an outsized role in the emergence of resistance. Classical epidemiological modelling is well suited to explore how the behavior of the inoculated population impacts the total number of infections over the entirety of an epidemic. Methods: A deterministic model of epidemic evolution is analyzed, with seven compartments defined by their relationship to the emergence of vaccine-resistant mutants and representing three susceptible populations, three infected populations, and one recovered population. This minimally computationally intensive design enables simulation of epidemics across a broad parameter space. The results are used to identify conditions minimizing the cumulative number of infections. Results: When an escape variant is only modestly less infectious than the originating strain within a naïve population, there exists an optimal rate of vaccine distribution. Exceeding this rate increases the cumulative number of infections due to vaccine escape. Analysis of the model also demonstrates that inoculated individuals play a major role in the mitigation or exacerbation of vaccine-resistant outbreaks. Modulating the rate of host–host contact for the inoculated population by less than an order of magnitude can alter the cumulative number of infections by more than 20%. Conclusions: Mathematical modeling shows that optimization of the vaccination rate and limiting post-vaccination contacts can perceptibly affect the course of an epidemic. The consideration of limitations on post-vaccination contacts remains relevant for the entire duration of any vaccination campaign including the current status of SARS-CoV-2 vaccination.",
"keywords": [
"Virus infection",
"epidemics",
"vaccination",
"escape mutants",
"contact limitation"
],
"content": "Introduction\n\nThe emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the Covid-19 pandemic motivated dramatic public health intervention including recommendations for isolation and quarantine throughout most of 2020 and early 2021.1 The beginning of 2021 was marked by widespread vaccine distribution which continues at an accelerating pace at the time of this writing. Optimizing distribution is challenging and subject to a myriad of social and economic constraints.2–4 The potential emergence of vaccine-resistant variants of the virus5,6 introduces additional complications. Vaccination applies new selective pressures which can lead to diverse intermediate outcomes even under conditions admitting eventual pathogen eradication.7–13 The larger the size of the vaccinated population, the greater the pressure towards escape of vaccine-resistant variants.\n\nEscape variants emerge within individual hosts after infection with the originating strain. Naïve, unvaccinated, hosts are more easily infected than vaccinated hosts but mutations conferring resistance are unlikely to provide a selective advantage in the naïve background. Thus, naïve hosts are likely to shed escape variants at low, likely, negligible rates. The reverse is true for vaccinated hosts. Recently vaccinated, inoculated, hosts that are not yet immune remain highly susceptible to infection with the originating strain, and in these hosts, mutations conferring resistance are more likely to provide a selective advantage. As a result, a substantial fraction or even most of the virus shed by such hosts will be resistant mutants. This situation is analogous to the administration of a low-dose antibiotic regime.14,15 In both cases, the pathogen is introduced to a susceptible host and is subject to elevated selective pressure towards the emergence of resistant (escape) variants.\n\nWe sought to establish the constraints on optimal vaccine distribution that might be imposed by virus escape and the role played by the small, but critical, population of inoculated hosts. To this end, we constructed an epidemiological compartment model to simulate vaccination campaigns over a broad parameter regime. This minimally computationally intensive approach enabled us to simulate many possible scenarios for epidemic evolution, in order to determine the optimal vaccination strategy for each condition.\n\n\nMethods\n\nWe divided the population into seven compartments (Figure 1A). Three compartments are susceptible to infection by either the originating strain or escape mutants: naïve (N; unvaccinated and fully susceptible to the originating strain and escape mutants), inoculated (I; recently vaccinated and still partially susceptible to the originating strain, and fully susceptible to escape mutants), and vaccinated (V; minimally susceptible to the originating strain, but fully susceptible to escape mutants). Two compartments represent ongoing infection with the originating strain and are distinguished by the host’s previous compartment: infected–naïve (F) and infected–inoculated (M). The third infected compartment represents infection by an escape variant, infected–escape (E). The remaining compartment, recovered (R), contains all hosts who were previously infected. Vaccination is represented by a reduction in susceptibility to infection with the originating strain. Naïve hosts are inoculated at rate kV. Inoculated hosts do not immediately acquire immunity and mature into the vaccinated compartment at rate kM. All infected hosts recover at rate kR.\n\nA. Schematic of the seven-compartment model with three susceptible, three infected, and one recovered compartments. B. Simulated epidemics for kI = [0.15,0.175,0.2(solid line),0.225,0.25], α = 0.001, β = 0.01. C. The ratio of cumulative escape infections to all cumulative infections for an epidemic over a range of α. β = [0.5,0.67,0.83,1], darker color indicates higher value, kI = 0.2. The dotted line specifies the benchmark value of α = 0.001.\n\nWithin the timescale of the model, recovery is assumed to grant stable immunity, and any variation in population size due to birth/death is assumed to be negligible. It should be noted that, if recovery from the Infected-Naïve or Infected-Inoculated compartments does not confer immunity against escape infection, the key results in this work will have an even greater impact on the vaccination outcome. Hosts come into contact at rate kC. For simplicity, we assume that contact with an escape-infected host can only produce an escape infection. Also, vaccine efficacy is assumed to be perfect such that vaccinated hosts cannot be infected with the originating strain. The inoculated–infected compartment is assumed to represent a symmetric composition of escape and originating infections such that the total probability of a naïve or inoculated host being infected after contact with a naïve–infected or inoculated–infected host is the same. Finally, we assume that the probability of escape infection is the same for naïve and vaccinated hosts across all three types of infected-susceptible host interactions. This construction yields the following transition probability matrices for naïve, inoculated, and vaccinated hosts:\n\nAn escape mutant can emerge in an infected–naïve or infected–inoculated host. The parameter α represents the infectivity of the escape variant relative to the originating strain when a naïve host interacts with an infected–naïve host. The parameter β represents the infectivity of an escape variant when a naïve host interacts with an infected–escape host relative to the infectivity of the originating strain when a naïve host interacts with an infected–naïve host. Informally, α reflects the ratio of escape variant to originating strain shed by infected–naïve hosts, whereas β reflects the fitness of an escape variant relative to the originating strain. Finally, we introduce the parameter q to represent the impact of varying the rate of host-host contact for Inoculated hosts relative to that for the other compartments. q>1 represents increased contact, and q<1 corresponds to decreased contact. This completes the model description and structures the differential equations:\n\nkI is the principal determinant of epidemic magnitude and duration, with larger kI leading to a greater cumulative number of infections over a shorter period of time (Figure 1B). However, feedback between the size of the infected population and the rate of host–host contact as well as spatial structure can decouple these variables. Throughout this work, kI is set to a benchmark value of 0.2 resulting in 50% of the population being infected over a period of approximately 4 months.\n\nThe values of α and β impact the size of the infected–escape compartment. Even in the absence of vaccination, large α/β results in the emergence of would-be resistant variants (Figure 1C). In all analyses in this work, α is fixed at the benchmark value of 0.001 resulting in a modest number of would-be resistant infections for β close to 1 in the absence of vaccination. Although a larger α would result in a greater total number of escape infections, the fraction of those infections attributable to contact with inoculated hosts would be smaller.\n\nThe solutions of the ordinary differential equations (ODEs) were obtained using the MATLAB ode45 method.16 ode45 is based on the Dormand-Prince pair,17 an explicit Runge-Kutta formula which could be implemented in a variety of open-access alternatives. Epidemics are simulated until the size of the Recovery compartment at arbitrarily long times is approached. The principal quantity of interest is the cumulative number of infections. When kV is selected to minimize this value, minima are found through explicit simulation over a range of rates. In the subsequent analysis, some values are expressed relative to the cumulative number of infections in the absence of vaccination, RNull~50%.\n\n\nResults\n\nIn addition to the rate of vaccination, the outcome of a vaccination campaign depends on how far the epidemic has progressed before vaccination begins, which can be measured by the relative size of the recovered compartment. The results also depend on β, informally, the fitness of an escape variant relative to the originating strain. We considered two values for β (low: 0.01; high: 0.875) and varied both the start and the rate of vaccination. When β is low, that is, the escape mutant is much less fit than the originating strain (Figure 2A), vaccinating earlier and distributing the vaccine faster decreases the cumulative number of infections. If distribution is sufficiently prompt, the cumulative number of infections becomes negligible.\n\nA. The cumulative number of infections relative to no vaccination, RNull, for a range of vaccine initiations and distribution rates. Here β is low, 0.01. B. The cumulative number of infections relative to no vaccination, RNull, for a range of vaccine initiations and distribution rates and a large β (0.875). A/B. 3840 values were computed for each panel and 4x by 4x bilinearly interpolated points are displayed. C. The cumulative number of infections relative to no vaccination, RNull, for β = [0.75(dotted),0.875(dashed),1(solid)] and three relative contact rates, q = [0.2(brown),1(black),5(gray)]. D. Simulated epidemics comparing a high fixed rate of vaccination, kV = 0.03 (solid) representing the inoculation of 3% of naïve hosts per day, and the optimal vaccination rate for each condition (dashed). β = 0.875 is fixed and q = [0.2(brown),1(black),5(gray)]. E. Same as D. with a low fixed rate of vaccination, kV = 0.01. C/D/E. The minima for the dashed lines in C correspond to the dashed lines in D/E.\n\nHowever, the outcome substantially differs for high β (Figure 2B). Due to the vaccine escape, at high rates of distribution, the cumulative number of infections remains large. Furthermore, there is an optimal rate of distribution such that exceeding this rate increases the cumulative number of infections. In this regime, the benefit of reducing the size of the population susceptible to infection by the originating strain is outweighed by the cost of increasing the selective pressure for the emergence of escape variants. In all subsequent analyses, the vaccination rate is varied but vaccination is fixed to begin when 1% of the population has recovered from infection.\n\nInfections can be mitigated by reducing contacts among the hosts. We sought to determine how perturbing the contact rates for hosts in the inoculated compartment relative to that of all other compartments, q, affects the outcome. For β ranging between 0.75 and 1, we considered three relative contact rates, q = [0.2,1,5] (Figure 2C). Increasing the rate of host–host contact only within this compartment has a significant impact on the cumulative number of infections. The optimal vaccination rate is also perturbed. Furthermore, if the optimal vaccination rate it exceeded, reducing q below 1 slows the accumulation of infections (Figure 2D). The converse is true for increasing q, and the landscape is similar when vaccination falls below the optimal rate (Figure 2E).\n\nHaving demonstrated how q perturbs the optimal vaccination rate and how reducing q below 1 can mitigate or delay the cumulative number of infections even if this rate is not met or, conversely, is exceeded, we sought to establish the impact of q on the cumulative number of infections across a wide range of β at the optimal vaccination rate for each condition (Figure 3A). The cumulative number of infections is sensitive to q across the entire range of β. Varying q within an order of magnitude can substantially aid or hinder the vaccination campaign, and when q>>1, the optimal rate of vaccination is 0. Note that the maximum vaccination rate considered is kV=0.03 representing the inoculation of 3% of naïve hosts per day. This rate is sufficiently high that the cumulative number of infections at this rate (Figure 3B) is similar or higher compared with the hypothetical case where the entire naïve population is immediately inoculated (Figure 3C). Some of these effects are not specific to the inoculated compartment. Increasing the rate of contact for any arbitrary subpopulation can increase the cumulative number of infections. We define the effective kI, kIeff, such that the cumulative number of infections for kI = kIeff and q = 1 is equal to the cumulative number of infections for kI = 0.2 (the benchmark) and arbitrary q. Increasing q within an order of magnitude is equivalent to substantially increasing kI for the entire population for the entirety of the epidemic (Figure 3D).\n\nA. The cumulative number of infections relative to no vaccination, RNull, for a range of β and q, optimizing kV for each condition. B. Same as in A. for fixed kV=0.03 representing the inoculation of 3% of naïve hosts per day. C. Same as in A. for the case where all naïve hosts are immediately inoculated. D. Log of the effective kI, kIeff, relative to kI=0.2, the benchmark, versus log of q for b=[0.5 (dotted line), 0.7 (dashed line), 1 (solid line)]. E. The cumulative number of infections relative to RNull and q=1 scaled by the fraction of infections due to vaccine escape, ∑Escape(q)/∑Infections(q)(∑Infections(q)-∑Infections(q=1))/RNull, for a range of β and q, optimizing kV for each condition. F. Same as in E for fixed kV=0.03. A-C/E/F. 961 values were computed for each panel and 4x by 4x bilinearly interpolated points are displayed.\n\nWe additionally consider the cumulative infections added or subtracted relative to the outcome corresponding to q = 1 and scaled by the fraction of infections due to vaccine escape (Figure 3E). Varying q within an order of magnitude alters the cumulative number of infections added or subtracted by more than 20% of the cumulative number of infections in the absence of vaccination, RNull, again demonstrating the critical role played by inoculated hosts with respect to vaccine escape. The landscape is similar when then rate of vaccination is fixed (Figure 3F).\n\n\nDiscussion\n\nEpidemics can be mitigated through the reduction of contact among the hosts via quarantines and other similar measures, and vaccination. A reduction in contact carries non-negligible social and economic burdens so that, when vaccination becomes possible, the continuation of such interventions might appear unnecessarily costly. Formulating an optimal vaccination strategy to balance these pressures is challenging and is further complicated by the possibility of vaccine escape. Escape variants emerging as a result of vaccination are likely to be less infectious than the originating strain. More infectious variants, which are also capable of vaccine escape, would likely already be in circulation. Indeed, multiple variants of SARS-CoV-2 capable of antibody evasion emerged prior to the onset of mass vaccination,18–23 indicating that this virus has a large mutational repertoire for evading antibodies while maintaining host receptor binding.\n\nHowever, newly emergent variants after the onset of mass vaccination can still be substantially infectious and result in non-negligible disease incidence.24,25 Here, we demonstrate that, even when escape variants are modestly less infectious than the originating strain, there exists an optimal vaccination distribution rate such that exceeding this rate increases the cumulative number of infections. This optimal rate depends on the infectivity of the escape variants. Such a prediction is impractical at the time of writing, that is, in the middle of a vaccination campaign, and the cost of overestimation of the optimal vaccination rate is far less than that of underestimation. However, to our knowledge, this phenomenon, analogous to the evolution of antibiotic resistance, is not widely appreciated and, as such, seems to warrant consideration.\n\nOf more practical concern is the role of inoculated hosts in the emergence of escape variants. Within low-dose antibiotic regimes,14,15 hosts are susceptible to infection with the originating variant, and in such hosts, the pathogen is subjected to elevated selective pressures towards the emergence of resistance. Similarly, within inoculated hosts, the virus is subjected to gradually increasing selective pressures towards the emergence of resistance while the intra-host population remains sufficiently large to explore a substantial fraction of the mutation space. We demonstrate that moderately increasing or decreasing the host-host contact rates for inoculated hosts only can substantially aid or hinder the vaccination campaign. The time between vaccination and the acquisition of immunity can be readily approximated from clinical endpoints26,27 and is likely to be short enough that the societal costs of limiting post-vaccination contact would be outweighed by these benefits.\n\n\nLimitations\n\nIn this study, we leveraged classical modelling techniques to elucidate the factors that could substantially impact the outcome of any vaccination campaign. Although these results are broadly applicable, they are not necessarily instrumental for predicting quantitative outcomes of the current SARS-CoV-2 pandemic or any other particular epidemic. Furthermore, the model presented here is not designed to forecast long-term outcome, a topic that has been thoroughly addressed for the case of SARS-Cov-2 and more generally.7–13,28–30\n\n\nConclusions\n\nDepending on the infectivity of variants, which emerge as a result of mass vaccination, the optimal vaccination rate with respect to the cumulative number of infections can be lower than the maximum rate. Contact rates for inoculated hosts can have a substantial impact on the outcomes of vaccination campaigns. Even a brief and moderate limitation of contacts in this well-defined population can potentially mitigate epidemics.\n\nThe results presented here appear to be of immediate interest in relation to the vaccination campaign against SARS-CoV-2, which is ongoing at the time of this writing. Diversification of the virus is apparent31–33 and, as discussed above, antibody evasion had been investigated early on and demonstrated prior to mass vaccination.5,6,18–23,34,35 The existence of these variants indicates that evolution of the SARS-CoV-2 antigen is not subject to constraints that would prohibit reduction in antibody affinity to achieve immune evasion, while maintaining host receptor affinity sufficient for infection. In other words, the emergence of novel, infectious, vaccine-resistant variants remains possible if not probable for the duration of the ongoing vaccination campaign and beyond.\n\nObviously, virus evolution during a pandemic is a fast-moving target, so that some aspects of this analysis unavoidably will be outdated by the time of publication. In particular, vaccine efficiency is assumed to be perfect within this model, reflecting the expectation as of December 2020. As of March 2021, this is no longer the case. In this work, we emphasize the role played by individuals who recently received their vaccination. The selective environment within such a partially susceptible host in the days immediately following the administration of a perfect vaccine is not completely equivalent to that within a host that remains partially susceptible in the months following the administration of an imperfect vaccine. Nonetheless, we believe that this and related work36,37 unequivocally demonstrates the continued importance of reducing host-host contact well after the onset of mass vaccination.\n\n\nAuthor contributions\n\nConceptualization and Formal Analysis: NDR, YIW, and EVK\n\nWriting – Original Draft Preparation: NDR and EVK\n\nWriting – Review & Editing: NDR, YIW, and EVK\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nThe authors thank Koonin group members for helpful discussions.\n\n\nReferences\n\nCDC: Public Health Guidance for Potential COVID-19 Exposure Associated with Travel.2020.\n\nNeumann-Böhme S, Varghese NE, Sabat I, et al.: Once we have it, will we use it? A European survey on willingness to be vaccinated against COVID-19. The European Journal of Health Economics Springer; 2020.\n\nQuinn SC, Kumar S, Freimuth VS, et al.: Public willingness to take a vaccine or drug under Emergency Use Authorization during the 2009 H1N1 pandemic. Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science. 2009; 7(3): 275–290. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMills MC, Salisbury D: The challenges of distributing COVID-19 vaccinations. EClinicalMedicine. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi Q, Wu J, Nie J, et al.: The impact of mutations in SARS-CoV-2 spike on viral infectivity and antigenicity. Cell 2020; 182(5): 1284–94. e9. Publisher Full Text\n\nKennedy DA, Read AF: Monitor for COVID-19 vaccine resistance evolution during clinical trials. PLoS Biol. 2020; 18(11): e3001000. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMagpantay F, King A, Rohani P: Age-structure and transient dynamics in epidemiological systems. Journal of the Royal Society Interface. 2019; 16(156): 20190151. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRestif O, Grenfell BT: Integrating life history and cross-immunity into the evolutionary dynamics of pathogens. Proceedings of the Royal Society B: Biological Sciences. 2006; 273(1585): 409–416. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodrigues HS, Monteiro MTT, Torres DF: Vaccination models and optimal control strategies to dengue. Math Biosci. 2014; 247: 1–12. PubMed Abstract | Publisher Full Text\n\nSafan M, Kretzschmar M, Hadeler KP: Vaccination based control of infections in SIRS models with reinfection: special reference to pertussis. J Math Biol. 2013; 67(5): 1083–1110. PubMed Abstract | Publisher Full Text\n\nScherer A, McLean A: Mathematical models of vaccination. British Medical Bulletin. 2002; 62(1): 187–199. PubMed Abstract | Publisher Full Text\n\nvan Boven M, Mooi FR, Schellekens JF, de Melker HE , Kretzschmar M: Pathogen adaptation under imperfect vaccination: implications for pertussis. Proceedings of the Royal Society B: Biological Sciences 2005; 272(1572): 1617–1624. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGandon S, Day T: The evolutionary epidemiology of vaccination. Journal of the Royal Society Interface. 2007; 4(16): 803–817. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLivermore DM: Minimising antibiotic resistance. The Lancet Infectious Diseases. 2005; 5(7): 450–459. PubMed Abstract | Publisher Full Text\n\nRoberts JA, Kruger P, Paterson DL, et al.: Antibiotic resistance—what’s dosing got to do with it? Crit Care Med. 2008; 36(8): 2433–2440. PubMed Abstract | Publisher Full Text\n\nShampine LF, Reichelt MW: The matlab ode suite. SIAM Journal on Scientific Computing. 1997; 18(1): 1–22. Publisher Full Text\n\nDormand JR, Prince PJ: A family of embedded Runge-Kutta formulae. Journal of Computational and Applied Mathematics. 1980; 6(1): 19–26. Publisher Full Text\n\nFaria NR, Claro IM, Candido D, et al.: Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. Virological. Publisher Full Text\n\nTegally H, Wilkinson E, Giovanetti M, et al.: Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv. 2020. Publisher Full Text\n\nVoloch CM, Ronaldo da Silva F, de Almeida LG , et al.: Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil. medRxiv 2020. PubMed Abstract | Publisher Full Text\n\nZhang W, Davis BD, Chen SS, et al.: Emergence of a Novel SARS-CoV-2 Variant in Southern California. JAMA. 2021. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEngland PH: Variants: distribution of cases data.\n\nBrejová B, Hodorová V, Boršová K, et al.: B. 1.258_Delta, a SARS-CoV-2 variant with Delta_H69, Delta_V70 in the Spike protein circulating in the Czech Republic and Slovakia. arXiv preprint arXiv:210204689 2021.\n\nCarman WF, Karayiannis P, Waters J, et al.: Vaccine-induced escape mutant of hepatitis B virus. The Lancet. 1990; 336(8711): 325–329. PubMed Abstract | Publisher Full Text\n\nBrueggemann AB, Pai R, Crook DW, et al.: Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog. 2007; 3(11): e168. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPolack FP, Thomas SJ, Kitchin N, et al.: Safety and efficacy of the BNT162b2 mRNA covid-19 vaccine. N Engl J Med. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Zeng G, Pan H, et al.: Safety, tolerability, and immunogenicity of an inactivated SARS-CoV-2 vaccine in healthy adults aged 18–59 years: a randomised, double-blind, placebo-controlled, phase 1/2 clinical trial. The Lancet Infectious Diseases. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaad-Roy CM, Wagner CE, Baker RE, et al.: Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science. 2020; 370(6518): 811–818. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDay T, Gandon S, Lion S, et al.: On the evolutionary epidemiology of SARS-CoV-2. Curr Biol. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRochman ND, Wolf YI, Koonin EV: Evolution of Human Respiratory Virus Epidemics. medRxiv 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKumar S, Tao Q, Weaver S, et al.: An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic. bioRxiv 2020.\n\nRochman ND, Wolf YI, Faure G, Zhang F, Koonin EV: Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. bioRxiv 2020.\n\nvan Dorp L , Acman M, Richard D, et al.: Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. Infection, Genetics, Evolution 2020; 104351. Publisher Full Text\n\nGarrett ME, Galloway J, Chu HY, et al.: High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies. bioRxiv 2020.\n\nStarr TN, Greaney AJ, Hilton SK, et al.: Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 2020; 182(5): 1295–310. e20. Publisher Full Text\n\nMakhoul M, Ayoub HH, Chemaitelly H, et al.: Epidemiological impact of SARS-CoV-2 vaccination: mathematical modeling analyses. Vaccines. 2020; 8(4): 668. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRella S, Kulikova Y, Dermitzakis E, Kondrashov F: SARS-CoV-2 transmission, vaccination rate and the fate of resistant strains. medRxiv 2021."
}
|
[
{
"id": "89322",
"date": "16 Jul 2021",
"name": "Sebastian Maximilian Schloer",
"expertise": [
"Reviewer Expertise virology",
"pharmacology",
"zoonotic diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the manuscript entitled “Substantial impact of post-vaccination contacts on cumulative infections during viral epidemics”, the authors refer to the interaction between vaccination rate and limiting post-vaccination contacts for the course of an epidemic/pandemic.\nNaturally, this is a very relevant issue that deserves the careful attention of researchers working in this field. By modeling the epidemic/pandemic spreading of zoonotic diseases considering the vaccination rate may provide new insights for the future management of COVID-19.\nWhile study design and work are technically sound correct, the presentation of the results could be improved by adding figure legends (figure 2 C/D/E). To increase the readability of the data, it might be helpful to use a similar scale in figure 2 AB for easier comparison between the two different scenarios. The authors also assumed a very high vaccination rate for the calculation of epidemic/pandemic spreading, a lower vaccination rate (kV=0.005 like observed in the USA) would be better at covering a realistic influence of vaccination and post-vaccination contacts for the course of the epidemic. Thus, the author should include data obtained with a lower daily vaccination rate to verify the relevance of the model and results for the management of future epidemics/pandemics.\nThe authors should also consider the pulsatile spreading and vaccination (that is normally, and currently observed in the SARS-CoV-2 pandemic) for zoonotic diseases and their management.\nIn sum, this is a relevant and timely topic. The manuscript is well-written and the comprehensive overview of vaccination rate and limiting post-vaccination contacts for the management of the ongoing COVID-19 pandemic is clearly presented. I hope that the authors can expand the section by adding the required changes and considerations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7034",
"date": "26 Aug 2021",
"name": "Eugene Koonin",
"role": "Author Response F1000Research Advisory Board Member",
"response": "We thank the reviewer for their kind and constructive remarks. While study design and work are technically sound correct, the presentation of the results could be improved by adding figure legends (figure 2 C/D/E). Legends have been added. To increase the readability of the data, it might be helpful to use a similar scale in figure 2 AB for easier comparison between the two different scenarios. We appreciate the reviewer’s suggestion; however, we found if we set the color scale to run from 0 to 1 for both panels, the variation in Figure 2B is hard to see with the same colormap. We have elected to keep separate scales but have modified the Figure description to emphasize that the color scales are different. The authors also assumed a very high vaccination rate for the calculation of epidemic/pandemic spreading, a lower vaccination rate (kV=0.005 like observed in the USA) would be better at covering a realistic influence of vaccination and post-vaccination contacts for the course of the epidemic. Thus, the author should include data obtained with a lower daily vaccination rate to verify the relevance of the model and results for the management of future epidemics/pandemics. We apologize for any confusion. Figures 2A/B/C display results for a range of vaccination rates from 1e-5 to 3e-2. Figure 2D displays two fixed rates 0.01 and 0.03 in addition to the vaccination rate which yields the fewest cumulative number of infections which in some parameter regimes is approximately the rate suggested by the reviewer. Figure 3 displays both a fixed rate of 0.03 and the vaccination rate which yields the smallest cumulative number of infections. Regarding realism for the choice of fixed rates, we acknowledge and state in the text that 0.03 represents a high rate of vaccination; however, we also do not attempt (and have modified the language in the revised version to this effect) to make empirical projections which could be explicitly interpreted in the context of any specific epidemic. We do not model age structure, for example, which significantly affects both the natural history of SARS-CoV-2 as well as the vaccine rollout (administered to older individuals first). Our goal in selecting the range of rates displayed was to demonstrate that the dependence on the cumulative number of infections on vaccine distribution rate is nonmonotonic within a nontrivial parameter regime (the majority of the population is vaccinated over a period of months to a year). The authors should also consider the pulsatile spreading and vaccination (that is normally, and currently observed in the SARS-CoV-2 pandemic) for zoonotic diseases and their management. We appreciate the reviewer’s input. Incorporating pulsatile or periodic forcing into the model would require significant changes to be made which we feel are outside the scope of the current work. We do, however, cite Rella et al. (2021) and have modified the text to indicate that cyclical models are addressed in this reference. In sum, this is a relevant and timely topic. The manuscript is well-written and the comprehensive overview of vaccination rate and limiting post-vaccination contacts for the management of the ongoing COVID-19 pandemic is clearly presented. I hope that the authors can expand the section by adding the required changes and considerations. We thank the reviewer for their interest and hope they find the revised version satisfactory."
}
]
},
{
"id": "83821",
"date": "12 Aug 2021",
"name": "Fyodor A. Kondrashov",
"expertise": [
"Reviewer Expertise Evolution"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe ongoing SARS-CoV-2 pandemic is driving the need to explore a new set of SIR models. One new feature that has not been considered previously is the impact of the state of individuals in the model that have just been vaccinated (inoculated) but have not yet achieved full immunity.\nThe authors took a classical SIR model and expanded it to include three new states: Infected with an Escape variant (E), Inoculated with the vaccine (I) and Inoculated but subsequently infected (M). The authors then explored the dynamics influenced by different parameters in this model. First, the higher contribution of Inoculated individuals to produce an Escaped variant. Second, a parameter that models limited interaction of inoculated hosts with others in the population. Third, the rate of vaccination.\nIn light of the ongoing debates on infection rate of those individuals that have been vaccinated with currently available vaccines against SARS-CoV-2, this study appears particularly timely and with potential to provide critical insight to contribution of the Inoculated but not fully vaccinated to the ongoing dynamics. However, some aspects of this model potentially reduce its applicability. Nevertheless, as a theoretical, rather than an empirical, model it does present an interesting view of the dynamics based on the model’s structure and assumptions, and even suggests a specific chokepoint of Escape variant evolution that may be controlled with simple policy solutions (the contact behavior of the Inoculated).\nI have but two general criticisms, mostly related to presentation rather than design.\nFirst, the presentation of the model made it challenging to understand the setup. Figure 1A could be more useful (for example, it could introduce the states I, F, M, etc), and it could even represent the transition parameters. The naming of the states departs from the SIR model, (so I is not Infected anymore, but Inoculated), which is fine, but added to the confusion. Finally, I was not a big fan of the equation representations. The authors have chosen to represent the equations in the shortest possible form. I prefer representation where each part of the equation reflects some transition state. To checkout the current equations I had to expand all of them and make my own determination of each transition state and how it fits to Figure 1A. Perhaps a more mathematically savvy reader would not have had to do it.\nSecond, as a theoretical model, it aims to describe some new understanding of interaction of parameters within the limitations of the model. A very successful example of this in the model is the analysis of the higher contribution of the Inoculated and Inoculated Infected states to dynamics and the introduction of another parameter, q, which limits the interaction of the Inoculated with other individuals. So, it explores the impact of the news states in the model and then introduces a specific way to mitigate their dangerous impact, which has important policy implications (granted that the underlying assumptions hold up). However, some aspects of the model cannot be applied directly to policy. Specifically, in several places of the manuscript the authors talk about the need for the determination of “optimal vaccination strategy”. While the model does explore vaccination rate as a parameter, I do not believe that their model is applicable to determination of a vaccine strategy at all. The reason for that is because a vaccine strategy considers some other parameters that are absent in the model. Specifically, an optimal vaccination strategy would consider, and probably prioritize, the short/medium term mortality rate and the hospital burden, something that is absent here.\nThe design of the model in the confines of the classical SIR structure (where the pandemic geos through the population without any negative feedback loops leading to waves) also makes it unrealistic in providing an optimization of policy. In sum, the conceptual description of the model, and the subsequent discussion, should avoid references to quantitative optimization of potential policy decisions that are likely to be influenced by parameters and outcomes that are not inherent in the model.\nMinor issues: Equation of V’ has a missing parenthesis.\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": "7035",
"date": "26 Aug 2021",
"name": "Eugene Koonin",
"role": "Author Response F1000Research Advisory Board Member",
"response": "We thank the reviewer for their interest and constructive comments. The model presented has 7 compartments. There are two compartments which represent uninfected, vaccinated hosts: those recently inoculated (I) and those who have “matured” into the fully vaccinated compartment. In light of the ongoing debates on infection rate of those individuals that have been vaccinated with currently available vaccines against SARS-CoV-2, this study appears particularly timely and with potential to provide critical insight to contribution of the Inoculated but not fully vaccinated to the ongoing dynamics. However, some aspects of this model potentially reduce its applicability. Nevertheless, as a theoretical, rather than an empirical, model it does present an interesting view of the dynamics based on the model’s structure and assumptions, and even suggests a specific chokepoint of Escape variant evolution that may be controlled with simple policy solutions (the contact behavior of the Inoculated). We thank the reviewer again for their interest. This is precisely our motivation and we completely acknowledge the limitations of our model which is theoretical not empirical. As discussed below, we have modified the language in the text to emphasize this point. I have but two general criticisms, mostly related to presentation rather than design. First, the presentation of the model made it challenging to understand the setup. Figure 1A could be more useful (for example, it could introduce the states I, F, M, etc), and it could even represent the transition parameters. The naming of the states departs from the SIR model, (so I is not Infected anymore, but Inoculated), which is fine, but added to the confusion. Finally, I was not a big fan of the equation representations. The authors have chosen to represent the equations in the shortest possible form. I prefer representation where each part of the equation reflects some transition state. To checkout the current equations I had to expand all of them and make my own determination of each transition state and how it fits to Figure 1A. Perhaps a more mathematically savvy reader would not have had to do it. We apologize for the confusion associated with the lack of detail in Figure 1A, which has been modified to include the state abbreviations (I,F,M, etc.) and the transition rates. Second, as a theoretical model, it aims to describe some new understanding of interaction of parameters within the limitations of the model. A very successful example of this in the model is the analysis of the higher contribution of the Inoculated and Inoculated Infected states to dynamics and the introduction of another parameter, q, which limits the interaction of the Inoculated with other individuals. So, it explores the impact of the news states in the model and then introduces a specific way to mitigate their dangerous impact, which has important policy implications (granted that the underlying assumptions hold up). However, some aspects of the model cannot be applied directly to policy. Specifically, in several places of the manuscript the authors talk about the need for the determination of “optimal vaccination strategy”. While the model does explore vaccination rate as a parameter, I do not believe that their model is applicable to determination of a vaccine strategy at all. The reason for that is because a vaccine strategy considers some other parameters that are absent in the model. Specifically, an optimal vaccination strategy would consider, and probably prioritize, the short/medium term mortality rate and the hospital burden, something that is absent here. We agree, and have modified the text accordingly, explicitly indicating that the model presented does not contain enough detail to define an optimal vaccination strategy. In many places in the revised version, we still refer to the “MCI”, which is the vaccination rate yielding the minimum cumulative number of infections for the given parameter set. We emphasize in the revised version that the MCI does not necessarily correspond to an “optimal” strategy given the many additional factors to consider. The design of the model in the confines of the classical SIR structure (where the pandemic geos through the population without any negative feedback loops leading to waves) also makes it unrealistic in providing an optimization of policy. We acknowledge this limitation and have briefly, but explicitly stated in the text that the reviewer’s work treats the impact of modeling cyclical transmission. In sum, the conceptual description of the model, and the subsequent discussion, should avoid references to quantitative optimization of potential policy decisions that are likely to be influenced by parameters and outcomes that are not inherent in the model. We have generally avoided language referring to optimization in the revised version. Minor issues: Equation of V’ has a missing parenthesis. We apologize for the oversight and thank the reviewer for bringing this to our attention."
}
]
}
] | 1
|
https://f1000research.com/articles/10-315
|
https://f1000research.com/articles/10-850/v1
|
25 Aug 21
|
{
"type": "Review",
"title": "Nanoparticles in traumatic spinal cord injury: therapy and diagnosis",
"authors": [
"Ahmed Hafez Mousa",
"Salwa Agha Mohammad",
"Hassan Mohammed Rezk",
"Khadijah Hassan Muzaffar",
"Asim Muhammed Alshanberi",
"Shakeel Ahmed Ansari",
"Salwa Agha Mohammad",
"Hassan Mohammed Rezk",
"Khadijah Hassan Muzaffar",
"Asim Muhammed Alshanberi",
"Shakeel Ahmed Ansari"
],
"abstract": "Nanotechnology has been previously employed for constructing drug delivery vehicles, biosensors, solar cells, lubricants and as antimicrobial agents. The advancement in synthesis procedure makes it possible to formulate nanoparticles (NPs) with precise control over physico-chemical and optical properties that are desired for specific clinical or biological applications. The surface modification technology has further added impetus to the specific applications of NPs by providing them with desirable characteristics. Hence, nanotechnology is of paramount importance in numerous biomedical and industrial applications due to their biocompatibility and stability even in harsh environments. Traumatic spinal cord injuries (TSCIs) are one of the major traumatic injuries that are commonly associated with severe consequences to the patient that may reach to the point of paralysis. Several processes occurring at a biochemical level which exacerbate the injury may be targeted using nanotechnology. This review discusses possible nanotechnology-based approaches for the diagnosis and therapy of TSCI, which have a bright future in clinical practice.",
"keywords": [
"Nanoparticles",
"Neurosurgery",
"Spinal cord injuries",
"Trauma",
"Therapy"
],
"content": "Introduction\n\nTraumatic spinal cord injuries (TSCIs) occur due to damage to the spinal cord from trauma, resulting in transient or permanent loss of motor, sensory, and autonomic functions in the parts of the body served by the spinal cord below the level of the injury.1 Knowledge of the causes of TSCI is an essential aspect that aids in the development of modalities for prevention and treatment of the condition.2 A previous study conducted in the United States to examine the specific etiologies of TSCI was carried out using data from the NSCID & NSSCID, and assessed various parameters to determine the etiology including age, sex, race, ethnicity, day and month of injury, and neurological outcomes.3,4 The study concluded that the most common cause of TSCI was automobile crashes. Other significant causes included falls and gunshot wounds. Another in-depth analysis of the causes showed that automobile crashes were the leading cause of TSCI until age 45 years, whereas falls were the leading cause after age 45 years. Gunshot wounds, motorcycle crashes, and diving caused more TSCIs in men than in women.5\n\nSpinal cord injuries (SCIs) consist of two main stages, primary and secondary. The primary stage occurs due to the direct effect of the initial mechanical injury or infarction affecting the spinal cord,6 and its severity can serve as a prognostic indicator for recovery.1 The main mechanisms of primary injury include impact with persistent compression, followed by impact with transient compression, distraction and laceration or transection.7 The majority of SCIs in humans were found to be contusion injuries6, and as a result, the most commonly used experimental animal models for studying SCIs are contusion models, followed by transection and compression models.8\n\nThe initial traumatic impact to the spinal cord, in the form of fracture or dislocation, causes microhemorrhages in the white and grey matter, axonal damage, and cellular membrane destruction.9 Following the primary injury, the more complex secondary stage, composed of a cascade of pathophysiological events, takes place within minutes to weeks following the initial injury.6 It has been observed that measures taken for preventing and managing this phase are critical for enabling early ambulation in patients with incomplete SCI.1\n\nThe American Spinal Injury Association Impairment Scale (AIS) classifies SCIs into two main types: complete and incomplete. A complete SCI is the absence of all motor and sensory functions, including sacral roots, distal to the site of injury, and is designated as being Grade A. An incomplete SCI is one with some degree of retained motor or sensory function below the site of injury and is graded B through E depending on severity.10\n\nThis review aims to discuss the recent therapeutic and diagnostic options provided via the use of nanoparticles (NPs). NPs are solid colloidal particles with diameters ranging from 1–1000 nm. They are comprised of macromolecular materials that can act as therapeutic drug carriers in a variety of applications, such as drug delivery, imaging, and detection of apoptosis.11 Nanotechnology could provide future potential minimally invasive management options for TSCI, which would decrease the burden that comes with managing TSCI.\n\n\nDiagnosis of SCI\n\nPhysical examination aids in determining the affected motor and sensory levels and eventually classifying the injury according to the AIS grades.12,13 In patients who cannot participate in a reliable physical examination, the integrity and function of axons in the spinal cord can be measured with the use of electrophysiological recordings, such as somatosensory evoked potentials and motor evoked potentials.14 This non-invasive method can provide real-time display of nerve function, and can detect the latency and amplitude of nerves, so that the neurological function of the spinal cord can be timed for quantified evaluation, making the assessment of neurological function after SCI and intraoperative monitoring of spinal cord function possible.15\n\nComputer tomography (CT) is used in the diagnosis of SCIs resulting from spinal fractures as well as lesions that result from ischemia and other vascular injuries.16 Traditionally, a thorough neurological examination was considered sufficient for the acute diagnosis of SCIs and assessing the severity and level of the injury.14 However, magnetic resonance imaging (MRI) has recently become the diagnostic modality of choice, especially in lesions that result from ischemia and other vascular injuries.16 A typical lesion appears spindle shaped, containing an epicenter of hemorrhage surrounded by a halo of edema on an MRI.14\n\nDue to the challenges accompanying the use of MRI in patients with medical implants and devices, many efforts have been made to innovate new rapid diagnostic biomarkers for SCIs. Several prognostic biomarkers in cerebral spinal fluid and blood have been identified. They include neurofilament proteins, glial fibrillary acidic protein, Tau and S100 calcium-binding protein β, as well as other cell damage-associated proteins and even microRNAs.17 A review article published in 2015 suggests that structural proteins, such as α-II spectrin breakdown products (SBDPs) and ubiquitin C-terminal hydrolase-L1 (UCH-L1), have potential as promising biomarkers in animal TSCI models and in human patients with SCIs.18\n\nA study reported the use of ferumoxytol-labeled human neural progenitor cells transplanted into the porcine spinal cord for diagnostic MRI-based cellular tracking.19 Superparamagnetic iron oxide NPs are bioactive molecules that can localize inflammation and can therefore be used as contrast agents in imaging.20,21 Campbell et al. developed injectable composite of hydrogel poly(N-isopropylacrylamide) reinforced by superparamagnetic iron oxide NPs as a good contrast material for MRI.22 In addition, quantum dots have been used, which are are metal-cored particles with improved photostabilizing properties that can aid in tracking specific proteins or surface antigens for molecular imaging.20\n\n\nTSCI therapy with NPs\n\nThe challenges in TSCI therapy are diverse. They range from psychological effects on often traumatized patients to socioeconomic effects on healthcare systems and individuals. Additional challenges are present in many countries where there is an absence of medical equipment, comprehensive rehabilitation, and lack of adequate support to allow community reintegration.23 From a medical perspective, the main challenge for treating TSCIs is the requirement of severe intensive approaches, either to surgically remove foreign bodies in the spine or performing permanent surgical fixation, which if not applied might lead to damage and could even be fatal. Current management options for TSCI are limited. Among the most common management approaches is the use of high-dose IV methylprednisolone, which in the long run leads to a wide variety of corticosteroid-induced side effects. Given the diversity in the mechanism of action of glucocorticoids, they can cause a wide array of adverse effects ranging from mild to severe, some of which are unavoidable.24 Other current treatment modalities being applied at a preclinical stage include the use of vasopressor medications for mean arterial blood pressure augmentation to improve spinal cord perfusion, and early surgical decompression and fixation for acute cases.25\n\nBelow, we introduce therapies with highest potential for TSCI that involve NPs.\n\n\nNatural polymeric NPs\n\nBackground to chitosan\n\nChitosan is a linear polysaccharide composed of N-acetyl-d-glucosamine and d-glucosamine linked by 1-4-β-glycosidic bonds. It is a deacetylated derivative of the naturally occurring polysaccharide chitin found in the shells of crustaceans.26 Depending on the parameters during the synthesis procedure, chitosan NPs can range in size between 30 nm27 to 2500 nm.28 Due to its deacetylated structure, a net positive charge is imparted on its surface which enables its interaction with the negatively charged mucous membranes. As a result, chitosan is classified as a mucoadhesive compound, with the ability to pass through the otherwise impermeable blood-brain barrier.29 It is water insoluble at physiologic conditions, as a result, chitosan derivatives, such as quaternized chitosan may be used to produce injectable formulas, as was experimented using quaternized chitosan, gelatin and dopamine to produce hydrogels for localized drug delivery.30 Chitosan NPs are nontoxic, biocompatible, biodegradable and have antimicrobial activity,29 with potential antioxidant properties.31 Other important properties are their high drug entrapment efficiency31 and sustained drug release.32\n\nChitosan NPs in TSCI models\n\nIn a new published study, valproic acid labeled chitosan NPs (VA-CN) were evaluated for use in targeted delivery of the drug to injured spinal cord. Spinal cord contusion was induced to the exposed spinal cord of Sprague-Dawley rats after performing a laminectomy at the level of 10th thoracic vertebra. To compare the concentration of VA-CN NPs against that of plain valproic acid, both structures were labelled by Cy5.5 to detect fluorescence intensities.33 Following intravenous injection, the results indicated a significant increase in the effectiveness and maintenance of drug delivery to injured spinal cord when using the NP compared to the drug alone. In addition, to evaluate the tissue and function repair, Basso, Beattie and Bresnahan (BBB) scale scores, void frequency, void volume, and residual urine volume in rats were compared using VA, CN and VA-CN. Again VA-CN revealed early and higher BBB scores and void frequency, and lower void volume and residual urine volume compared to the others. VA-CN also reduced astrocytic reactivity (based on percentage of GFAP+ nestin+ cells produced). In addition, the treatment promoted neuroprotection by decreasing the numbers of microglia and enhanced NF160 immunoreaction, reducing inflammation by lowering IL-1β, IL-6 and TNF-α expression compared to VA alone. Lesion cavity volume was significantly decreased, and the integrity of the blood-spinal cord barrier was enhanced after treatment with VA-CN based on higher Claudin-5, and lower albumin and IgG marker levels. Finally, no histological changes were seen between the organs of control rats and treated injured rats, suggesting the lack of systemic adverse effects of VA-CN.33\n\nIn a compression mouse model of SCI, following a bilateral hemilaminectomy at the lower thoracic region, the spinal cord was crushed to 10% of its original width using compression forceps. Then the spinal cord was injected using antibody conjugated siRNA-chitosan NP solutions and layers were sutured. After 24 hours, the mice were euthanized, and the injured cord segments removed for examination. Results demonstrated both a reduction in iNOS expression and nitric oxide levels, reduced pro-apoptotic Bax expression, and a two-fold increase in the anti-apoptotic Bcl-2 protein expression, leading to an overall inhibition of cellular apoptosis.34\n\nAnother study employed the use of tubular chitosan scaffolds filled with neurotropin-3-releasing chitosan carriers (C-NT3 implant) to investigate tissue formation, neurogenesis, electrophysiology, and hind limb function in a complete spinal cord transection model using female Wistar rats. Results suggest that the C-NT3 implants elicits endogenous neurogenesis and supports its potential for tissue modeling in the injured adult spinal cord.35\n\nAnother study loaded chitosan scaffolds with strontium-doped hydroxyapatite NPs, creating nanocomposites to be used for drug delivery in SCIs. Results revealed that the use of these materials lead to the formation of functional neurons decreasing the gap in the injured area, with more synaptic connections formed among them via myelination, in addition to hindered growth of scar-like tissue, which can be beneficial for the effective treatment of SCIs.36\n\nMoreover, a study developed chitosan/polyvinyl alcohol (PVA) nanofiber scaffolds loaded with genistein. Following laminectomy at the level of T9-10 in female Sprague Dawley rats, a right lateral hemi-section SCI was induced using micro iris scissors to create the spinal injury model. This was followed by the application of the nanofibers with or without genistein on the injured area. Results revealed increased activity of super oxide dismutase and higher levels of IL-10, while nitric oxide levels, lipid peroxidation, and TNFα were lower in both nanofiber treated groups compared to the control groups, although nanofiber+genistein revealed slightly better results.37\n\nA study investigating the in vitro profiles of dexamethasone sodium phosphate (DEXP)-loaded chitosan NPs embedded in a poly-ε-caprolacton (PCL)/gelatin nanofiber scaffold demonstrated them to have good mechanical properties, hydrophilicity, as well as controlled release of dexamethasone. This may be used as a bridging biomaterial construct that allows the axons to grow while avoiding glial scar formation by inhibiting astrocyte proliferation and reducing the oligodendrocyte apoptosis for the repair of SCIs.38\n\nOne study utilized chitosan and gelatin NPs to produce a composite hydrogel, which was then loaded with endometrial stem cells. This biomimetic hydrogel composite was then transplanted in the spinal cord of T9 dorsally hemisected male Wistar rat followed by Atorvastatin injection. Locomotor function assessed using the BBB scale revealed over three-fold higher advancement in motor function in this group compared to the control. In addition, histopathological study using hematoxylin & eosin (H&E) stain revealed axonal remyelination and neuronal regeneration.39\n\nOn the other hand, a study evaluated and compared the use of cerium oxide (CeO2) NPs and CeO2/chitosan nanocomposites for SCI. The in vitro drug release tests revealed the chitosan loaded NPs to provide more sustained release (drug release rate 28%) compared to the bare CeO2 NP (45%). When cell viability tests were conducted using spinal cord cells from euthanized rats, CeO2/chitosan nanocomposite led to lower cell death. As a result, it was concluded that loading CeO2 NPs with chitosan enables them to behave as an effective biocompatible material causing enhanced antioxidant properties, and auto regenerative and neuroprotective activity in spinal cord regeneration.40\n\nAnother paper investigated the in vitro protective effects of quercetin encapsulated in chitosan-alginate NPs against oxidative stress injury in neuronal SH-SY5Y cells. The results revealed that the highest protective effects were registered with quercetin loaded in the positively charged NPs that were formulated with a higher concentration of chitosan.41\n\nAnother study employed chitosan NPs to encapsulate nerve growth factor (NGF). Canine bone marrow derived mesenchymal stem cells were used to evaluate the effect of these NPs on the delivery of NGF to these cells and its influence on their differentiation into neuronal cells. Results obtained were promising and can enable opportunities for the use of these NPs for targeted differentiation of stem cells for in vitro and in vivo nerve tissue regeneration in the future.42\n\nIn another study, chitosan-dextran sulfate NPs were used to study its neuroprotective effect on BV-2 mouse microglia treated with H2O2 (to mimic acute post-SCI H2O2 release). Cell viability measured by Trypan blue showed lower cell death in chitosan NP preserved cells than those without.43\n\nA paper published in 2019 proposed an experimental protocol for inducting transgene expression in neural stem cells obtained from the brain of the mouse embryo through chitosan NPs loaded with pDNA. Hyaluronic acid is used as a ligand for neuronal cell receptor attachment. This protocol can be utilized for investigating its efficiency in treating SCI.44\n\n\nSynthetic polymeric NPs\n\nBackground to PLGA\n\nPLGA is a member of polyesters, being the copolymer of lactide and glycolide45 whose degradation produces lactic acid and glycolic acid as a result of spontaneous ester chain hydrolysis.46 As a copolymer, PLGA inherits the intrinsic properties of poly (glycolic acid) which is a crystalline, hydrophilic polymer with low water solubility and fast degradation rate under physiological conditions, and poly (lactic acid) which is a stiff, hydrophobic polymer with low mechanical strength.47 This also explains why the rate at which PLGA degrades is influenced by its lactic acid to glycolic acid ratio.46\n\nDepending on the parameters used during the synthesis procedure, PLGA NPs can range in size between 100 to 5000 nm.48 However, the average size varies between 107.7 nm and 245.7 nm for effective intracellular delivery.49 Due to PLGA’s hydrophobic nature, surface modification using polymers such as polyethylene glycol (PEG), PVA, and d-α-tocopheryl PEG 1000 succinate plays an important role with respect to targeting strategy, biocompatibility, and blood half-life.50 PLGA NPs are nontoxic, biocompatible, biodegradable,47 and produce minimal inflammatory response in the body.46\n\nPLGA NPs in TSCI models\n\nThe intravenous administration of PLGA NPs has been investigated in spinal cord contusion models. In one study, Sprague-Dawley rats and female Yucatan miniature pigs were used, where following a laminectomy, spinal cord contusion was performed at the level of 10th thoracic vertebra using an impactor. Then, to see the effects of therapeutic delay after the SCI, the BSA-containing PLGA nanoparticle formulation was injected at 6 hours, 1, 2 and 4 weeks to four different SCI rat groups beside the control group without an SCI injected at 6 hours.51\n\nAdditionally, the porcine SCI model groups were injected at 30 minutes and 3 hours post-SCI. Following euthanasia, the animals’ spinal cords were harvested. Results for nanoparticle dose localization revealed more NPs at the lesion site in both rat and porcine SCI models, while the control group animals showed a bimodal distribution in the thoracic and lumbar enlargement regions. Regarding delay in administration after SCI, localization of NPs at the site of injury decreased with delayed administration, but despite this, there was an increase in the uptake of NPs in the entire spinal cord, probably due to the sustained release properties of PLGA NPs and the blood-spinal cord barrier at the lesion site being accessible to NPs for longer.51\n\nIn a similar study, PLGA NPs loaded with the two antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT), named nano-SOD/CAT, were evaluated for their neuroprotective quality in SCIs via intravenous route, specifically on their ability to protect mitochondria from oxidative stress, neuronal cell apoptosis, and hence secondary SCI. Results demonstrated that treatment with nano-SOD/CAT protects the mitochondria, reduces reactive oxygen species activity, prevents the release of cytochrome c, and inhibits activation of caspase-3.52\n\nOne paper describes the production of immune-modifying NPs (IMPs) using PLGA NPs. A laminectomy was performed on C57BL/6 mice, followed by induction of a contusion SCI using an impactor. The IMPs were then injected intravenously at 2, 24 and, 48 hours post-SCI. It was observed that IMPs decrease inflammatory cells infiltration into the injured spinal cord without altering the number of microglia, as well as lower the chances of chronic fibrotic scarring after SCI substantially. Behavioral scoring based on Basso Mouse Scale (BMS) open field scoring was also done at 24 hours, with the IMP-treated group demonstrating significant and sustained behavioral improvement and recovery in comparison to the control group. So, it was concluded that IMPs may provide a practical and easily translatable means of improving outcome after SCI.53\n\nAnother study developed PLGA-g-PEI (PgP) polymeric micelle NPs and assessed their use in the treatment of SCIs by loading them with the drug Rolipram. The effect of PgP on cultured rat primary cerebellar granular neurons in hypoxia condition did not show any cytotoxicity, but there was a slight increase in cAMP levels and neurite length compared to the untreated group. Furthermore, the rat clip compression SCI model (dorsal T9 spinal cord) was employed using Sprague Dawley rats in hypoxia condition. Rolipram-loaded PgP NPs were then injected into the spinal cord in the area of injury. The data demonstrated a prolonged therapeutic effect of the drug with sustained release, a feature that may improve patient compliance. It was also found that this formulation can affect important aspects of secondary SCI such as restoring cAMP levels and decreasing apoptosis and inflammatory response.54\n\nThe use of PLGA nanospheres modified using 3β-[N-(N’ ,N’ - dimethylaminoethane) carbamoyl] cholesterol (DC-Chol) for gene delivery (in this case being the luciferase pDNA (pSV-Luc)) in comparison to polyethyleneimine (PEI) complex has also been demonstrated. In vitro investigations revealed these NPs underwent sustained drug release with a minimum release period of 20 days and there was no difference in the structural integrity of the released pDNA compared to unencapsulated pDNA. Also, tests for cellular uptake of the NPs using mouse neural stem cells shows that these NPs localize more in the nuclei and cytoplasm and are less toxic than the PEI complex. Additionally, in vivo investigations were performed on SCI model using Sprague-Dawley rats, with PLGA/DC-Chol nanosphere being injected into their injured spinal cords. Apoptosis based on TUNEL staining was shown to be reduced with NP usage, while luciferase gene expression was detected in both neurons and astrocytes in the spinal cord. In addition, rats injected with PLGA/DC-Chol/VEGF or PLGA/VEGF showed better recovery of locomotor function compared with rats not treated with NPs.55\n\nNeuregulin-1 (Nrg-1) and Nrg-1-encapsulated PLGA NPs were evaluated for intrathecal vs intraspinal delivery, respectively, in a model of severe clip-compression SCI at T6-8 using adult female Sprague Dawley. In this study, the group that received intraspinal PLGA-Nrg-1 microparticles showed a significantly higher level of Nrg-1 compared to the group receiving intraspinal bolus of Nrg-1, which indicates the importance of PLGA encapsulation. On the other hand, the group undergoing intrathecal infusion of Nrg-1 using an osmotic pump showed less improvement compared to the PLGA-Nrg-1 microparticles group, but better results in comparison to the bolus group.56\n\nIn another study, resveratrol and puerarin-loaded PLGA NPs were prepared to enhance the oral bioavailability of the drugs resveratrol and puerarin, then examined both in vitro and in vivo using male Wistar rats. Results indicated high entrapment efficiency of 74.85% drug loading capacity of 15.50% for this 1:3 drug-polymer formulation, in addition to slower drug release rates compared to the plain resveratrol and puerarin solutions. Moreover, for the in vivo studies, surgery where a small aneurysm clip used to cause ischemia was performed, followed 48 hours later by ischemia-reperfusion treatment. Then blood samples and L3-5 spinal cord segments were collected. It was then observed that the plasma nitrite/nitrate level were lower in the SCI rats when using NPs. Also, there was lowering of increased levels of iNOS protein expression to normal levels, decreased levels of Malondialdehyde and AOPP, and increased antioxidant activity of GSH, SOD and CAT. These findings suggest the protective property of using PLGA NPs in human spinal cord reperfusion injuries.57\n\nFurthermore, resveratrol loaded PLGA NPs coated with chitosan were synthetized to test for its effectiveness when employed in treating SCI in female adult Sprague-Dawley rat. The drug release profiles were measured to be 44.4% for coated and 79.9% for the uncoated NPs, indicating prolonged availability of the drug when using chitosan coating. In addition, following laminectomy at the 9th thoracic vertebra, a 2 mm piece of spinal cord was dissected to mimic spinal contusion injury. This was followed by intraperitoneal injection of the resveratrol solution or resveratrol NPs in rats of different groups. Regarding the behavioral changes observed via grid and beam walking, there was significant improvement in the groups treated with both coated and uncoated NPs, however coated drug revealed slightly better results. ELISA was used to test for the anti-inflammatory potential of the NPs, and results revealed significant reduction in the level of IL-1β and TNF-α and significant increase in the level of IL-10 in animals treated with both NPs, however, chitosan-coated particles were found to be more efficacious in the reduction of the level of these cytokines.58 On histopathological examination, efficient re-establishment of the spinal cord integrity was observed with significant reduction in the area of pseudocyst, intensity of the cell infiltration and hemorrhage.58\n\nAnother identical study was performed using chitosan to stabilize PLGA NPs loaded with methylprednisolone and minocycline and coupled with albumin acting as a ligand of gp60 receptors. Injury was induced at the 11th thoracic vertebra to investigate the utility of the ligand-based polymeric NPs in the simultaneous delivery of methylprednisolone and minocycline when injected intravenously for the treatment of SCI.59\n\nAnother study compared the use of PLGA NPs loaded with the natural antioxidant α-Tocopherol with that of pure antioxidant drug solution for treatment against oxidative stress in SCIs. Human astrocyte–spinal cord cells were used to test for in vitro toxicity and antioxidant activity. Results demonstrated that the NPs were less toxic and had a two-fold antioxidant activity compared to the pure drug.60\n\nFour similar studies investigated the benefit of PLGA NPs for alleviating pain in rat models of spinal nerve ligation (performed at L5) using Sprague-Dawley rats, by loading PLGA NPs with Foxp3 plasmid,61 p66shc siRNA,62 p38 siRNA63 and encapsulating PLGA with CX3CR1 siRNA,64 respectively. All four studies indicated that the use of the aforementioned PLGA NPs effectively reduced neuropathic pain in SNL-induced rats by reducing microglial activity and expression of proinflammatory mediators.\n\nPLGA NPs have been used in the form of nanocomposite hydrogels made in combination with sodium hyaluronate and methylcellulose. Female Sprague Dawley rats were used as compression models of SCI using the clip compression method following a laminectomy at the level of T2. Then the PLGA hydrogel, HAMC hydrogel and artificial cerebrospinal fluid were then injected intrathecally in three different groups, after which the overlying muscles and fascia were sutured closed. Open field locomotor function was assessed using the BBB scoring, which revealed slight improvement of motor function in all three groups with no significant difference between them. Similarly, the parasagittal sections of the spinal cord stained with Luxol fast blue (LFB)/H&E to assess cavity shape, another stained using ED-1 for assessing inflammation and a third series stained with GFAP for astrogliosis assessment showed no significant difference between the three groups, hence supporting the safety and biocompatibility of PLGA hydrogels as a platform for sustained combination therapy in SCIs.65\n\nSimilarly, another study utilized PLGA NPs dispersed in a HAMC hydrogel as a local drug delivery system for NT-3 and anti-NogoA into the injured spinal cord. Moderate impact/compression injury was induced in female Sprague-Dawley rats following a laminectomy at T1-2 level using a modified aneurysm clip. Immediately after inducing the SCI, the hydrogel solution was injected intrathecally at the site of injury, and the overlying muscles and fascia were sutured closed. Locomotor function was then assessed using the ladderwalk task, BBB score, and the BBB motor subscore, all showing significant improvement. This nanocomposite enabled the sustained co-delivery of the two factors to the injured area, which led to increased axonal density, however tissue sparing and cavitation after injury were not affected.66\n\nPrevious studies focus on drug release profiles of PLGA NPs based on degradation or erosion of PLGA encapsulating the drug, or on the diffusion of the drug through it. However, a recently published study demonstrated the possibility of eliminating the need for encapsulating drugs in PLGA NPs, instead, simply mixing in the drug with the NPs in a hydrogel solution. This study was based on the adsorption of drug on the PLGA nanoparticle via electrostatic interactions in the hydrogel. Results obtained for drug release profiles in both PLGA-encapsulated and PLGA-mixed protein formulations were remarkably similar for the three proteins (stromal cell–derived factor 1a (SDF), neurotrophin-3 (NT-3), and brain-derived neurotrophic factor (BDNF)) tested.67\n\nIn another study, crosslinked methylcellulose hydrogel loaded with chondroitinase ABC and stromal cell-derived factor 1α in addition to PLGA NPs were evaluated against its counterpart hydrogel containing no NPs.68 Similar to Elliott et al.,66 after a laminectomy at the level of T1-2, a moderate impact/compression injury was induced in female Sprague-Dawley rat, after which the hydrogel was injected intrathecally. Despite improvement with both formulation, better results were obtained when using PLGA NPs in the hydrogel, since the transient electrostatic interaction between PLGA and SDF allow the controlled release of bioactive SDF without encapsulation, as explained by Pakulska et al.67\n\nAlginate hydrogel embedded with minocycline and paclitaxel-loaded PLGA microspheres embedded in a minocycline-loaded alginate hydrogel were utilized for dual drug delivery in a left lateral hemisection model of SCI using male Wistar rats in which the hydrogels were injected into the spinal cord at the site of injury. The ED1 level of Gel/MH and the Gel/MH.PTX groups used for monitoring inflammatory responses was lower than the untreated group, in addition to a reduction in the immune response, and reduced expression of caspase-3. Cell density used to assess tissue scar formation was shown to be lower in the rats receiving Gel/MH.PTX or Gel/MH, and neural regeneration in the microenvironment of the damaged tissue based on NF200-positive cells density was high in Gel/MH.PTX and Gel/PTX. BBB locomotor score, BBB sub-score and footprint analysis also indicated better results with Gel/MH.PTX.69\n\nAnother study fabricated electrospun graphene oxide-PLGA hybrid nanofiber immobilized with IGF-1 and BDNF for use as scaffolds in the local delivery of said factors in a rat spinal cord hemisection model. After inducing the injury at the level of T9-10 in female Sprague Dawley rats, a piece of the nanofiber mat was placed, covering the hemisected area. Motor function evaluated via BBB scale and motor function regeneration assessed according to MEP amplitude revealed significantly increased BBB scores and MEP amplitude, respectively. H&E staining of the longitudinal spinal cord sections also showed decreased cavity size in the injured area. In vitro investigations on neural stem cells isolated from the cerebral cortex of embryonic mice were also performed to study their possible effect on endogenous stem cells, with results revealing good neural stem cell proliferation, survival and neuronal differentiation on the PLGA/GO nanofibers.70\n\nIn another study, electrospun PLGA scaffolds were modified to carry FTY720 and neural stem cells. Results suggest that the local application of PLGA/FTY720 scaffolds can be used in treating SCIs due to their positive effects on neural stem cell proliferation and differentiation. In the T9 spinal cord transection model using female Sprague Dawley rats, the implanted scaffold effectively promoted nerve function recovery. Moreover, the immobilization of neural stem cells on electrospun PLGA/FTY720 scaffolds may have potential applications as a nerve implant for treating SCIs.71\n\nFurthermore, hyaluronic acid-based hydrogel scaffolds modified with anti-Nogo receptor antibody were implanted with PLGA microspheres loaded with BDNF and VEGF to treat T9-10 dorsal hemisection rat model. Injury repair was observed to be markedly enhanced by displaying excellent biocompatibility, inhibiting inflammation, and promoting angiogenesis.72\n\nMoreover, another study produced novel PLGA scaffolds inoculated with olfactory ensheathing cells, which were then implanted in a complete spinal cord transection rat model. Results of this study showed improved locomotor function recovery, as well as neuroprotection and enhanced remyelination, which suggests their potential success in human SCIs.73\n\nA study prepared PDA-PLGA scaffolds with NGF immobilized on them. These scaffolds were then implanted into a rat spinal cord transection model which revealed their ability to promote nerve function recovery by sustained release of the growth factor.74\n\nSince published reports demonstrated that without proper scaffolding, human mesenchymal stem cells (hMSCs) or neural stem cells would quickly die in the lesion gap of an SCI model, PLGA-polylysine nanofiber scaffolds seeded with human mesenchymal stem cells were produced for implanting in male Sprague Dawley rats with T9-10 level hemisection model. In this study both hard and soft scaffolds were used for evaluating the effect of scaffold stiffness on SCI recovery. Motor function test using the BBB scale and downward-facing inclined plane performance indicated better results when using soft scaffolds in comparison to hard scaffolds. Spinal cord reflexes and nociceptive withdrawal reflex were also better in groups implanted with soft PLGA-scaffolded hMSCs, in addition to less neuropathic pain. There was also smaller cavity area indicating less tissue loss and more interneuron sparing in the soft scaffold groups, while hard scaffold groups showed the worst tissue loss at the epicenter region. It was also observed that hard PLGA scaffolds diminished the anti-inflammatory and anti-oxidative properties of hMSCs, further supporting the use of soft PLGA scaffolds with stem cells.75\n\nIn addition, several papers published over the years investigated PLGA-based scaffolds used in association with stem cells for promoting their neuronal differentiation.76 Kim et al. seeded NSCs into a PLGA scaffold, which was then implanted into canine hemisection models, which promoted the recovery of neural function.77 Pritchard et al. reported a similar result in a primate model.78 Subsequently, Liu et al. observed restoration of the continuity of the spinal cord and reduced cavity formation following the implantation of a PLGA/PEG scaffold loaded with NSCs.79\n\nBackground to PCL\n\nPCL is a synthetic polyester that is partially crystalline, having a low melting point of 60°C and a glass transition temperature of −60°C. It is made by ring-opening polymerization of ε-caprolactone.80 PCL is degraded by hydrolysis of its ester linkages in physiological conditions and has therefore received a great deal of attention for use as an implantable biomaterial. Also, a variety of drugs have been encapsulated within PCL beads for controlled release and targeted drug delivery.81\n\nPCL NPs in TSCI models\n\nA study investigated the use of minocycline-loaded PCL NPs injected into the site of injury in a compression model of SCI using C57BL/6J mice or B6.129PCx3cr1tm1Litt/J mice. Results were compared to those obtained from intraperitoneal injection of the drug alone. It was revealed that only early treatment with the NPs was able to improve behavioral outcome assessed using the BMS score while intraperitoneal injection did not cause any improvement. Furthermore, it was demonstrated that microglia inhibitory treatment delivered immediately after injury induces a significant long-lasting recovery up to 63 days post-injury.82\n\nAnother study fabricated biodegradable monomethyl poly (ethylene glycol)poly(e-caprolactone) (MPEG-PCL) nanomicelles as a drug delivery vehicle for dexamethasone acetate (DA). Following a laminectomy at the level of T9-10, a spinal cord hemisection was induced, succeeded by intravenous injection of the DA-loaded nanomicelles (DA-M). Motor function was evaluated by means of serial BBB score analysis which showed significantly higher values than the blank micelle group, free DA group and normal saline group. In addition, histopathological examination using H&E staining revealed that administration of DA-M possessed the ability to significantly reduce the volume of the spinal cord lesion and cavity formation in injury site as compared to the other treated groups.83\n\nTo overcome the high incidence of adverse effects upon systemic administration of methylprednisolone, a study embedded methylprednisolone sodium succinate-loaded PCL-based NPs in an implantable fibrin gel, which was then tested in male Wistar rats with a spinal cord contusive injury for localized drug delivery. Results showed that IL-1β, IL-6 and caspase-3 levels were significantly lowered in the group treated with these NPs, showing a similar decrease with 25-fold lower dose of drug compared to intraperitoneally administered drug.84\n\nOnce study also embedded minocycline-loaded PCL NPs in an agarose hydrogel and implanted this into the site of the contusion. Results demonstrated that a selective microglia treatment with minocycline-loaded PCL NPs, only when administered immediately after injury before macrophage infiltration, reduced the proinflammatory response, maintained a pro-regenerative milieu and ameliorated the behavioral outcome up to 63 days post injury.85\n\nA study fabricated polycaprolactone/polysialic acid (PCL/PSA) hybrid nanofiber scaffold loaded with the drug methylprednisolone. This was then transplanted in a T10 complete spinal cord transection model using female Sprague Dawley rats to evaluate its efficacy in comparison to PCL scaffold loaded with methylprednisolone (MP). Motor function was assessed using BBB scores, which revealed blank PCL nanofiber scaffold to have limited therapeutic effects, with the addition of PSA leading to slightly better results, while the PCL/PSA/MP nanofiber scaffold group had the best BBB scores out of all groups. An array of stains was also used for histopathological investigations of tissue sections for the rat groups including H&E, which showed the lesion cavity and glial scarring in PCL/PSA/MP nanofiber scaffold group to be absent similar to the control group, LFB stains (together with transmission electron microscopy), which revealed more myelin sheaths number and more intact myelin structure, and immunofluorescence staining, which showed enhanced therapeutic effects towards axonal survival and reactive astrocytes inhibition in the PCL/PSA/MP group compared to the others groups.86\n\nAnother study, incorporated NT-3 and miR-222 into PCLEEP nanofibers distributed within a collagen hydrogel for use in a C5 hemi-section model using female Sprague Dawley. This hybrid scaffold was implanted into the site of injury such that the nanofibers were aligned to the longitudinal axis of the spinal cord. The scaffold was shown to provide localized and sustained release of drugs and nucleic acid molecules for non-viral transfection to enhance axon regeneration and remyelination in vivo, besides demonstrating good host-implant integration.87\n\nOne study employed the use of PCL/gelatin nanofibrous scaffolds seeded with human endometrial stem cells cocultured with human Schwann cells to evaluate its regenerative potential in a T9 dorsal hemisection model of male Sprague Dawley rats. This method was based on the finding that coculturing of these stem cells with Schwann cells led to their differentiation into nerve-like cells. Following induction of injury, the scaffolds were implanted into the spinal cord. Hindlimb function recovery based on the BBB score demonstrated that implanting of these scaffolds showed the most promising recovery compared to the other animals in the study, in addition to regeneration assessed using immunohistochemical staining against neuronal marker NF-H, which revealed increased density of NF-H positive neural fibers.88\n\nBackground to CNTs\n\nCNTs are hollow cylinders made of graphene sheets rolled in on themselves to form a tube.89,90 They have a great role in the advancement of nanotechnology due to their unique architecture with high aspect ratio, high surface area, rich surface chemistry, small size, cell membrane penetrability and size alterability. They are also non-immunogenic, nontoxic, photostable, ultra-lightweight and biocompatible.91 CNTs possess excellent electrical and mechanical properties, such as neutral electrostatic potential, extremely high drug cargo ability, ultimate electrical and thermal conductivities making them an attractive tool for biomedical applications which is useful in the detection and treatment of neurological diseases.89,91 Due to their various thermal, optical, electrical, mechanical and chemical characteristics, CNTs have potential applications in different fields of nanomedicine, drug delivery, biosensors, energy storage and neural prosthetics.91\n\nCNTs in TSCI models\n\nIn a study, nano-scaffolds of nonwoven PCL generated by electrospinning and carbon nanomaterials were created. The carbon nanomaterials in nanofibers was confirmed by Fourier transform infrared spectroscopy. This design of nanofibers ensures therapeutic cell delivery to a neural lesion with excellent electrical conductivity suitable for cell adhesion and neural tissue regeneration in traumatic brain and SCI. The study indicated the nano-scaffolds were biocompatible to the cells. To generate nanomaterials scaffold that resemble the extracellular matrix, the artificial PCL scaffolds encapsulating CNTs were successfully fabricated. The diameters of the nanofibers (80 to 200 nm) were close to the actual architecture within the central nervous system (CNS). Under this fabrication the diameters of PCL-CNT were higher than those of PCL nanofibers. The alamarBlue assay’ bioanalysis showed the PCL nanofibers were not toxic to the astrocytes grown on the scaffolds. The nano-scaffolds showed growth of multiple processes of the glial fibrillary acidic protein (GFAP) positive astrocytes.92\n\nIn another study, vertically super-aligned MWCNTs (VA-MWCNTs) were manufactured using chemical vapor deposition to create nanoelectrodes for diagnosis of diseases and for the development of the nanocarrier to deliver drugs to the diseased site in various neurological disorders. VA-MWCNTs were purified with HCl, carboxylated with H2SO4:HNO3 and acylated with SOCl2. After purification and functionalization, they became highly hydrophilic, electrically conductive, highly stable and reduced in size for use in biomedical application. Specific VA-MWCNTs grown on silicon wafer were incorporated in epoxy resin to develop an application in diagnosing neurological disorders such as ischemic stroke.91\n\nIn SCI excessive glutamate concentration abnormally increases around the synaptic cleft leading to the apoptosis of neuron.93 Chemically functionalized water-soluble single walled-CNT (SW-CNT)-PEG (carboxyl group) 5 μg/ml increases GFAP immunoreactivity and glutamate transporter expressions in astrocytes and upregulates the uptake of glutamate by astrocytes. Astrocyte plated into well-plates with SW-CNT-PEG 5 μg/ml for four days also enhanced the uptake of glutamate. Therefore, the reduction of extracellular glutamate leads to decreased excitotoxicity. The increase in GFAP immunoreactivity decreases tissue damage and neuronal loss and demyelination. These results suggest that functionalized CNTs play a role in various brain disease therapies.89 Another study shows that SW-CNT-PEG solute causes a reduction in the ATP-induced glutamate release but does not affect the intracellular Ca2+ elevations in astrocytes.94\n\nIn a study, self-standing 3D meshes of interconnected MWCNTs were manufactured. Such three-dimensional (3D) mesh of pure carbon nanotubes can open new horizons in treating injured CNS tissues, such as the spinal cord. MWCNTs – based 3D structure was interfaced in vitro with long-term, cocultured pairs of mouse organotypic spinal cord explants that led to the development of spinal networks over extended periods. For the first time the study also reported in vivo implantation of 3D carbon nanotube frame materials in four adults male Wistar rats led to tissue reaction and glial scar formation.95\n\nIn a study neurite outgrowth from primary dorsal root ganglia (DRG) was evaluated in the presence or absence of electrical stimulation and SWCNT were selected as model nanofiller to manipulate the electrical properties of a collagen type I-10% Matrigel™ composite hydrogel. DRG were encapsulated within SWCNT-collagen I-10% Matrigel™ composite hydrogel (20-100-μg/ml) and nanomaterial-free collagen I-10% Matrigel™. The nanofillers influence on neurite outgrowth, with or without electrical stimulation. Neurite outgrowth were measured in response to both nanomaterials loading and electrical stimulation. Increased SWCNT loading (10-100-μg/ml) resulted in great bulk conductivity up to 1.7-fold whereas neurite outgrowth increases 3.3-fold in 20-μg/ml SWCNT loaded biomaterials. Electrical stimulation of SWCNT-free control resulted in a 2.9-fold increase in outgrowth. In concurrent electrical stimulation of SWCNT-loaded with biomaterials resulted in a 7.0-fold increase in outgrowth relative to unstimulated nanofiller- free controls. Therefore, SWCNT-composite hydrogels do enhance neuronal outgrowth, and with combination of electrical stimulation a further increase to neurite extension is expected.96\n\nCNTs can accumulate due to consequent reduction in size leading to multifunctional defects in organ systems, particularly hearts and lungs. Metal traces available in nanotubes can also cause toxicity. SWCNTs affect the spinal cord or DSR due to high degree of accumulation, reduces the DNA content in the cells and causes ultrastructural and morphological changes in cultured skin cells.89\n\nMWCNTs are more toxic as compared to SWCNTs. MWCNT toxicity causes loss of cell viability through programmed cell death thus having genotoxicity effects leading to mutations. Recently, researchers have warranted of nonoxidative stress-mediated pathway of cellular damage.89 A study has reported that environmental and occupational exposure to respirable particulates such as MWCNT can induce acute neuroinflammation.\n\nPulmonary interactions of MWCNTs can generate secondary bioactive factors that enter the systemic circulation and causes Cerebrovascular inflammation leading to loss of blood brain barrier and neuroinflammation. The mechanism and potential intermediate drivers of such neuroinflammatory outcomes remains unclear.97\n\nThe current data of CNT toxicity is inadequate and contradictory, therefore extensive research is required on toxicity, safety, and efficacy studies on animal models, including humans.89\n\nBackground to IONPs\n\nGenerally, there are three IONPs available: magnetite (Fe3O4), hematite (α-Fe2O3) and maghemite (γ-Fe2O3). However, due to their superparamagnetic property, where no magnetism remains after removal of the magnetic field, Fe3O4 nanoparticles are used in clinical applications.98 Hence the name, superparamagnetic iron oxide nanoparticles (SIONPs).\n\nIONPs in TSCI models\n\nThe use of IONPs and magnetic fields for alleviating pain in SCI was studied on male CD1 mice in which an inflammatory pain condition was induced using Complete Freund’s Adjuvant. Then, the nonsteroidal anti-inflammatory drug Ketorolac was conjugated with IONPs, dissolved in PBS, injected intrathecally into the mice’s spinal cord, and a neodymium magnet was placed at the lumbar spine level for 30 minutes. Then, the analgesic effect of the drug was evaluated. The results obtained from this experiment deduced that different polarity alignments can significantly affect the analgesic effect of Ketorolac-SIONPs.99\n\nA study conducted on female Wistar rats employed the use of IONPs and exposure to magnetic field to evaluate their efficacy in treating SCI. This experiment was performed on six groups of rats, with every two groups undergoing 50%, 80% and complete spinal cord transection via a laminectomy at T9/T10 vertebrae. Then each three corresponding groups were divided into study and control groups, with study groups being administered a suspension of IONPs intrathecally via a polyethylene catheter and exposed to electromagnetic field. Behavioral assessment based on the BBB score and electrophysiological assessment evaluated using compound motor evoked potential (MEP) testing revealed marked improvement in the IONP-treated groups with 50% and 80% transection over the course of four weeks, but no significant improvement in the remaining four groups. Regarding histopathological examination, there were greater viable motor neuron counts and thicker myelinated fibers in the IONP-treated groups. In addition, measurement of the cavity area was revealed to be smaller in the 50% transection group, with lower collagen content despite pronounced glial reactions in the areas next to the lesions in the same group.100\n\nAnother similar study was performed on male Wistar rats, where following a bilateral laminectomy, their spinal cord was completely transected at the level of the 11th thoracic vertebra (13th spinal segment). Then, immediately, IONPs embedded in agarose hydrogel was implanted at the site of SCI via intrathecal injection. Eventually, motor responses to stimulation of nociceptive afferents, beside somatosensory evoked potential and MEP were assessed, with the group treated with both IONPs and magnetic field (MF) having the most favorable results such as recovery of the extensive movements of all three joints of hindlimb, plantar placement of paw with no weight support, in addition to complete recovery of autonomic and partial recovery of locomotor function. On histological analysis, IONPs concentration near the site of TSCI was greater in the IONP and IONP+MF groups, suggesting their diffusion from the agarose hydrogel into the spinal cord as well as their intracellular localization in the motor neurons and their axons. Myelination was also higher in the IONP+MF group, besides more intense expression of GAP-43 at week 5, indicating spinal cord regeneration. It was also observed that the use of magnetic field with IONPs enhanced the latter’s antioxidant effect, thereby decreasing secondary injury cascades after SCIs.101\n\nIONPs were utilized by a study for labelling porcine mesenchymal stem cells and canine glial restricted progenitors. These labelled cell type groups were then individually embedded in a hyaluronic acid-based hydrogel which was then intrathecally injected under the guidance of MRI into the porcine and canine animal models. Dynamic imaging following hydrogel injection showed signal stability indicating cells remained at the injection site within the intrathecal space, unlike stem cells embedded in PBS in which the injected cells rapidly disperse, quickly becoming undetectable by MRI. This approach can potentially show success when used for treating SCIs.102\n\nOne paper investigated the magnetic targeting ability of SIONPs in vitro using D1 mouse bone marrow-derived mesenchymal stem cells. The NPs used in this case were oleic acid-coated SIONPs, which were further surface modified with dopamine, rendering them hydrophilic and amine-functionalized. Transmission electron microscopy analysis showed that the cellular uptake of SIONPs was mediated by endocytosis, placing them in the cytoplasm of the MSCs as SIONP-containing vesicles, mostly seen close to the cell membrane, nuclear membrane, and some even in the nucleus. Then, these SIONP-labeled D1 MSCs were further labeled with a fluorescent marker. After exposure to magnetic field, fluorescence signals were detected, showing a migration value of over 95% at 30 min. Furthermore, the D1 MSCs were induced to undergo nerve cell differentiation, and it was confirmed that SIONPs were not lost after differentiation. Results obtained from this study indicate that we can target damaged neural tissue for promoting tissue regeneration potentially by influencing endogenous stem cells to undergo neuronal differentiation using this strategy.103 Another study made use of a similar principle to study the effect of magnetic field on the migration of Schwann cells containing chondroitinase ABC-loaded SIONPs across the astrocytes in vitro.104 Also, in a third study, poly-L-lysine (PLL) coated SIONPs were loaded into Schwann cells (also by endocytosis) and under the influence of magnetic field, their migration across the astrocyte boundary and intermingling with astrocytes was investigated.105 These results can potentially open doors for the use of magnetically-driven migration of cells in vivo, and further work is necessary to validate these findings using animal models of SCI.\n\nOne study treated human mesenchymal stem cells with IONPs to produce IONP–incorporated exosome-mimetic nanovesicles (NV-IONP). Then upon in vitro investigations, it was deduced that NV-IONPs had the ability to induce angiogenesis, were antiapoptotic, neuroprotective, and had anti-inflammatory properties, all which are involved in TSCI repair. Moreover, in spinal cord injured mice, the use of magnetic field was found to markedly enhance the targeting efficacy of intravenously injected NV-IONP towards the injured spinal cord, as well as alleviate spinal cord damage and improve spinal cord function.106\n\nIt was found that the cytotoxicity of PLL-SIONPs was both time and dose dependent following the co-incubation of PLL-SIONPs with Schwann cells.105\n\nIn another study performed on male Wistar rats, injury was inflicted via a longitudinal incision into the right dorsal horn of the T10–11 segment of the spinal cord. Then, to investigate the influence of IONPs on the pathophysiology of SCI, a suspension of IONPs in Tween 80 solution was administered intravenously. It was observed that IONPs can induce mild damage in the blood-spinal cord barrier permeability after 24 hours of injury, as well as a mild increase in neuronal damage and astrocyte release. However, these changes were not seen with the non-SCI control group and the use of cerebrolysin as adjunct therapy appeared to markedly attenuate the aggravation of SCI-induced cord pathology on IONP administration and induce significant neuroprotection. This study also directs attention towards the importance of surface modifications of IONPs.107\n\nTable 1 demonstrates the challenges faced PLGA and iron oxide nanoparticles.\n\nBackground to exosomes\n\nExosomes are single-membrane vesicles released from various cell types including mesenchymal stem cells, with diameters ranging from approximately 30 to 200 nm and containing a wide variety of membrane-associated proteins, soluble proteins, nucleic acids, lipids, and glycoconjugates, giving them an otherwise unremarkable morphology compared to a cell. Once released, exosomes can perform activities such as remodeling the extracellular matrix and transporting different molecules such as coding or noncoding RNA, antigen presentation molecules, DNA, and proteins109 between cells, which can play important roles in many aspects of human health.110\n\nDue to their ability to cross the blood-spinal cord barrier and migrate to the spinal cord, exosomes can offer the potential for noninvasive, rapid, cell-free, lesion-specific, and effective treatment strategies for SCI. Exosomes can be promising nanocarriers for drug delivery and targeted therapy, as well as alternatives to stem cell therapy.111\n\nExosomes in TSCI models\n\nThe most common experimental use of exosomes in SCIs models involve gene delivery (mainly RNAs) and different growth factors since their levels and target-regulated pathways have been found to be directly associated with the pathophysiology of SCI. One study showed that serum exosomal miR-130a-3p, miR-152-3p, and miR-125b-5p are specific and easily detectable diagnostic markers in acute SCI,112 while a second study demonstrated that some serum miRNAs (such as miR-30b-5p, miR-152-3p, miR-200c-3p, miR-125b and miR-124-3p)113 in cerebrospinal fluid and serum could reflect injury severity in TSCI, indicating their use as targets for treatment and markers for diagnosis and prognosis.114 Another study demonstrated that reactive astrocytes increased proNGF expression after SCI, suggesting the involvement of exosome-like proNGF transport or release in triggering neuronal apoptosis and aggravating progression of SCI.115 Furthermore, the mRNA and protein expression levels of Nogo-A in spinal cord after injury are upregulated moderately, and the proteolyzed exosomal Nogo-A fragment called reticulon-4A can potently inhibit axon regeneration.116\n\nOne study investigated the potential therapeutic effect of human umbilical cord mesenchymal stem cells-derived exosomes in a contusion model of SCI using C57BL/6 mice. The prepared exosomes were injected intravenously, and functional recovery was evaluated through behavioral testing using BMS scoring and CatWalk-assisted gait analysis which showed significant improvement in locomotor function, electrophysiological assessment which also showed an increase in peak-to-peak amplitude, histolopathological study, which revealed decreased cavity volume. In addition, the use of hucMSC-derived exosomes led to the polarization of macrophages in vitro and reduced the pro-inflammatory cytokines levels while increasing anti-inflammatory cytokines levels.109\n\nSurprisingly, phosphatase and tensin homolog siRNA-loaded mesenchymal stem cell-derived exosomes administered intranasally in a complete spinal cord transection rat model demonstrated neuroinflammation-attracted migration of the exosomes to neurons in the lesioned area. Results showed significant motor function and sensory recovery, and faster urinary reflex restoration, in addition to decreased inflammation and gliosis, increased axonal regeneration and angiogenesis, and structural and electrophysiological improvements.111\n\nBone mesenchymal stem cell-derived exosomes injected intravenously in a contusion rat model was also shown to remarkably decrease inflammation, tissue loss, glial scar formation, and effectively protected cells from apoptosis after spinal cord trauma, while angiogenesis and axonal regeneration were promoted, in addition to significant improvement in the BBB locomotor score. The underlying mechanism in this case was thought to be the suppression of the activation of A1 neurotoxic reactive astrocytes by these exosomes.117 Another identical study supports the aforementioned data, proposing a slightly more in depth mechanism which suggests that the decrease in A1 astrocytes occurs due to bone mesenchymal stem cell-derived exosomes inhibiting nuclear translocation of NF-κB p65 to exert their anti-inflammatory and neuroprotective effects.118 Moreover, another similar study reported that intravenously administered exosomes trafficked to the lesion sites, but not uninjured spinal cord, and were specifically taken up by macrophages expressing the M2 marker CD206, but not by macrophages expressing the M1 marker iNOS, suggesting that MSC-derived exosomes may exert their therapeutic effects by regulating the actions of macrophages within the lesion.119 Furthermore, bone marrow mesenchymal stem cell-derived exosomes were found to also to inhibit complement activation by suppressing complement mRNA synthesis and release and by inhibiting SCI-activated NF-κB by binding to microglia.120 In addition, GIT1-overexpressing bone marrow mesenchymal stem cell-derived exosomes were also shown to promote recovery in a contusive injury rat model.121 Also, one study provided the first evidence that bone marrow mesenchymal stem cell-derived exosomes can effectively inhibit the migration of pericytes, thereby maintaining the integrity of the blood-spinal cord barrier following injury.122 Another study demonstrated that these exosomes attenuate neuronal apoptosis by promoting autophagy.123\n\nOn the other hand, exosomes derived from pericytes were also shown to promote blood flow, improve endothelial function, protect the blood-spinal cord barrier, alleviate the apoptotic response, thus promoting functional and behavioral recovery after injury.124\n\nThe use of neural stem cell-derived exosomes have also shown favorable results including microvascular regeneration, reduced the spinal cord cavity, and improved the BMS scores in SCI mice, suggesting an underlying mechanism of neural stem cell-derived exosome-mediated angiogenesis.125 Another study using neural stem cell-derived exosomes demonstrated that upon their exposure to insulin-like growth factor-1, inflammation and apoptosis were suppressed, while nerve regeneration was enhanced via an miR-219a-2-3p-dependent mechanism after the SCI.126\n\nExosomes derived from lncGm37494-overexpressing adipose tissue-derived mesenchymal stem/stromal cells have also been studied as a potential therapeutic for SCIs due to its ability to shift microglial M1/M2 polarization.127\n\nHuman placenta amniotic membrane mesenchymal stem cell-derived exosomes adhered on a peptide-modified hyaluronic acid-based hydrogel (Exo-pGel) were presented in one study. These materials were then implanted in a long-span spinal cord transection model. Results revealed that implanted Exo-pGel exhibited high efficiency in nerve tissue repair and functional restoration. The findings were also compared to results obtained from the intravenous injection of the exosome alone, which indicated implantation to produce better results than systemically administered exosomes.128\n\nFurthermore, several studies have investigated the use of exosomes containing miRNAs such as miR-133b,129 miR-126,130,131 miR-216a-5p,132 miR-544,133 microRNA-124-3p,134 miR-25,135 miR-21136,137 and siRNA.138-140 Results all favor the use of these miRNAs and siRNA for SCI recovery.\n\nTable 2 demonstrates the summary of the routes of administration studied for each NP for treating TSCIs.\n\n\nConclusion\n\nIn conclusion, traumatic SCIs can have devastating outcomes on patients due to the challenges in the healing process resulting from the complex secondary stage of injury. However, the field of nanotechnology has shined light on potential treatment options utilizing natural and synthetic NPs and exosomes. These are excellent candidates for drug delivery due to their ability to bypass the blood-brain barrier, and can even be used as diagnostic modalities for other central nervous system disorders\n\n\nData availability\n\nNo data is associated with this article.",
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PubMed Abstract | Publisher Full Text | Free Full Text\n\nSahin A, Esendagli G, Yerlikaya F, et al.: A small variation in average particle size of PLGA nanoparticles prepared by nanoprecipitation leads to considerable change in nanoparticles’ characteristics and efficacy of intracellular delivery. Artif Cells Nanomed Biotechnol. 2017; 45(8): 1657–1664. PubMed Abstract | Publisher Full Text\n\nRezvantalab S, Drude NI, Moraveji MK, et al.: PLGA-Based Nanoparticles in Cancer Treatment. Front Pharmacol. 2018; 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGao Y, Vijayaraghavalu S, Stees M, et al.: Evaluating accessibility of intravenously administered nanoparticles at the lesion site in rat and pig contusion models of spinal cord injury. J Control Release: official journal of the Controlled Release Society. 2019; 302: 160–168. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndrabi SS, Yang J, Gao Y, et al.: Nanoparticles with antioxidant enzymes protect injured spinal cord from neuronal cell apoptosis by attenuating mitochondrial dysfunction. J Control Release: official journal of the Controlled Release Society. 2020; 317: 300–311. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJeong SJ, Cooper JG, Ifergan I, et al.: Intravenous immune-modifying nanoparticles as a therapy for spinal cord injury in mice. Neurobiol Dis. 2017; 108: 73–82. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMacks C, Gwak SJ, Lynn M, et al.: Rolipram-Loaded Polymeric Micelle Nanoparticle Reduces Secondary Injury after Rat Compression Spinal Cord Injury. J Neurotrauma. 2018; 35(3): 582–592. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGwak SJ, Yun Y, Yoon DH, et al.: Therapeutic Use of 3β-[N-(N',N'-Dimethylaminoethane) Carbamoyl] Cholesterol-Modified PLGA Nanospheres as Gene Delivery Vehicles for Spinal Cord Injury. PloS one. 2016; 11(1): e0147389. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSanthosh KT, Alizadeh A, Karimi-Abdolrezaee S: Design and optimization of PLGA microparticles for controlled and local delivery of Neuregulin-1 in traumatic spinal cord injury. J Control Release: official journal of the Controlled Release Society. 2017; 261: 147–162. PubMed Abstract | Publisher Full Text\n\nSong Q, Chen W, Zhao Z, et al.: Resveratrol and Puerarin loaded polymeric nanoparticles to enhance the chemotherapeutic efficacy in spinal cord injury. Res Square. 2020; Publisher Full Text\n\nWang X, Li G, Zhang P, et al.: Surface engineering of resveratrol to improve neuro-protection and functional recovery after spinal cord injury in rat. J Drug Delivery Sci Technol. 2019; 49: 89–96. Publisher Full Text\n\nBin S, Zhou N, Pan J, et al.: Nano-carrier mediated co-delivery of methyl prednisolone and minocycline for improved post-traumatic spinal cord injury conditions in rats. Drug Dev Ind Pharm. 2017; 43(6): 1033–1041. PubMed Abstract | Publisher Full Text\n\nLaliwala A: Development of polymeric nanoparticles containing a natural antioxidant (α- tocopherol) for the treatment of spinal cord injury.2019. Reference Source\n\nShin J, Yin Y, Kim DK, et al.: Foxp3 plasmid-encapsulated PLGA nanoparticles attenuate pain behavior in rats with spinal nerve ligation. Nanomedicine: Nanotechnology, Biology, and Medicine. 2019; 18: 90–100. PubMed Abstract | Publisher Full Text\n\nShin N, Shin HJ, Yi Y, et al.: p66shc siRNA-Encapsulated PLGA Nanoparticles Ameliorate Neuropathic Pain Following Spinal Nerve Ligation. Polymers. 2020; 12(5): 1014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShin J, Yin Y, Park H, et al.: p38 siRNA-encapsulated PLGA nanoparticles alleviate neuropathic pain behavior in rats by inhibiting microglia activation. Nanomedicine (London, England). 2018; 13(13), 1607–1621. PubMed Abstract | Publisher Full Text\n\nNoh C, Shin HJ, Lee S, et al.: CX3CR1-Targeted PLGA Nanoparticles Reduce Microglia Activation and Pain Behavior in Rats with Spinal Nerve Ligation. Int J Mol Sci. 2020; 21(10): 3469. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaumann MD, Kang CE, Tator CH, et al.: Intrathecal delivery of a polymeric nanocomposite hydrogel after spinal cord injury. Biomaterials. 2010; 31(30): 7631–7639. PubMed Abstract | Publisher Full Text\n\nElliott Donaghue I, Tator CH, Shoichet MS: Local Delivery of Neurotrophin-3 and Anti-NogoA Promotes Repair After Spinal Cord Injury. Tissue Eng Part A. 2016; 22(9-10): 733–741. PubMed Abstract | Publisher Full Text\n\nPakulska MM, Elliott Donaghue I, Obermeyer JM, et al.: Encapsulation-free controlled release: Electrostatic adsorption eliminates the need for protein encapsulation in PLGA nanoparticles. Sci Adv. 2016; 2(5): e1600519. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPakulska MM, Tator CH, Shoichet MS: Local delivery of chondroitinase ABC with or without stromal cell-derived factor 1α promotes functional repair in the injured rat spinal cord. Biomaterials. 2017; 134: 13–21. PubMed Abstract | Publisher Full Text\n\nNazemi Z, Nourbakhsh MS, Kiani S, et al.: Co-delivery of minocycline and paclitaxel from injectable hydrogel for treatment of spinal cord injury. J Control Release: official journal of the Controlled Release Society. 2020; 321: 145–158. PubMed Abstract | Publisher Full Text\n\nPan S, Qi Z, Li Q, et al.: Graphene oxide-PLGA hybrid nanofibres for the local delivery of IGF-1 and BDNF in spinal cord repair. Artif Cells Nanomed Biotechnol. 2019; 47(1): 650–663. PubMed Abstract | Publisher Full Text\n\nKong W, Qi Z, Xia P, et al.: Local delivery of FTY720 and NSCs on electrospun PLGA scaffolds improves functional recovery after spinal cord injury. RSC Advances. 2019; 9(31): 17801–17811. Publisher Full Text\n\nWen Y, Yu S, Wu Y, et al.: Spinal cord injury repair by implantation of structured hyaluronic acid scaffold with PLGA microspheres in the rat. Cell Tissue Res. 2016; 364(1): 17–28. PubMed Abstract | Publisher Full Text\n\nWang C, Sun C, Hu Z, et al.: Improved Neural Regeneration with Olfactory Ensheathing Cell Inoculated PLGA Scaffolds in Spinal Cord Injury Adult Rats. Neuro-Signals. 2017; 25(1): 1–14. PubMed Abstract | Publisher Full Text\n\nPan S, Zhao Y, Qiao X, et al.: PLGA porous scaffolds by polydopamine-assisted immobilization of NGF for spinal cord injury repair. Materials Res Express. 2019; 6(4): 045024. Publisher Full Text\n\nHan I-B, Thakor DK, Ropper AE, et al.: Physical impacts of PLGA scaffolding on hMSCs: Recovery neurobiology insight for implant design to treat spinal cord injury. Exp Neurol. 2019; 320: 112980. PubMed Abstract | Publisher Full Text\n\nZhang Q, Shi B, Ding J, et al.: Polymer scaffolds facilitate spinal cord injury repair. Acta Biomater. 2019; 88: 57–77. PubMed Abstract | Publisher Full Text\n\nKim BG, Kang YM, Phi JH, et al.: Implantation of polymer scaffolds seeded with neural stem cells in a canine spinal cord injury model. Cytotherapy. 2010; 12(6): 841–845. PubMed Abstract | Publisher Full Text\n\nPritchard CD, Slotkin JR, Yu D, et al.: Establishing a model spinal cord injury in the African green monkey for the preclinical evaluation of biodegradable polymer scaffolds seeded with human neural stem cells. J Neurosci Methods. 2010; 188(2): 258–269. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu C, Huang Y, Pang M, et al.: Tissue-engineered regeneration of completely transected spinal cord using induced neural stem cells and gelatin-electrospun poly (lactide-co-glycolide)/polyethylene glycol scaffolds. PloS one. 2015; 10(3): e0117709. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNair NR, Sekhar VC, Nampoothiri KM, et al.: Biodegradation of Biopolymers. In: Current Developments in Biotechnology and Bioengineering. Elsevier; 2017; (pp. 739–755). Publisher Full Text\n\nMcKeen LW: Environmentally Friendly Polymers. In: Permeability Properties of Plastics and Elastomers. Elsevier; 2012; (pp. 287–304). Publisher Full Text\n\nPapa S, Caron I, Erba E, et al.: Early modulation of pro-inflammatory microglia by minocycline loaded nanoparticles confers long lasting protection after spinal cord injury. Biomaterials. 2016; 75: 13–24. PubMed Abstract | Publisher Full Text\n\nWang Y, Wu M, Gu L, et al.: Effective improvement of the neuroprotective activity after spinal cord injury by synergistic effect of glucocorticoid with biodegradable amphipathic nanomicelles. Drug Deliv. 2017; 24(1): 391–401. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarabey-Akyurek Y, Gurcay AG, Gurcan O, et al.: Localized delivery of methylprednisolone sodium succinate with polymeric nanoparticles in experimental injured spinal cord model. Pharm Dev Technol. 2017; 22(8): 972–981. PubMed Abstract | Publisher Full Text\n\nPapa SG: Characterization of a Nanoparticle Drug Delivery System for the Treatment of Inflammation in Spinal Cord Injury. PhD thesis. IRCCS - Istituto di Ricerche Farmacologiche Mario Negri. 2017. Reference Source\n\nZhang S, Wang X-J, Li W-S, et al.: Polycaprolactone/polysialic acid hybrid, multifunctional nanofiber scaffolds for treatment of spinal cord injury. Acta Biomater. 2018; 77: 15–27. PubMed Abstract | Publisher Full Text\n\nNguyen LH, Gao M, Lin J, et al.: Three-dimensional aligned nanofibers-hydrogel scaffold for controlled non-viral drug/gene delivery to direct axon regeneration in spinal cord injury treatment. Sci Rep. 2017; 7(1). Publisher Full Text\n\nBabaloo H, Ebrahimi-Barough S, Derakhshan MA, et al.: PCL/gelatin nanofibrous scaffolds with human endometrial stem cells/Schwann cells facilitate axon regeneration in spinal cord injury. J Cell Physiol. 2019; 234(7): 11060–11069. PubMed Abstract | Publisher Full Text\n\nSingh B, Lohan S, Sandhu PS, et al.: Functionalized carbon nanotubes and their promising applications in therapeutics and diagnostics. In: Nanobiomaterials in Medical Imaging. Elsevier; 2016; (pp. 455–478). Publisher Full Text\n\nMin J-O, Yoon B-E: Glia and gliotransmitters on carbon nanotubes. Nano Rev Exp. 2017; 8(1): 1323853. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu W, Wang Y, Gong F, et al.: Exosomes Derived from Bone Mesenchymal Stem Cells Repair Traumatic Spinal Cord Injury by Suppressing the Activation of A1 Neurotoxic Reactive Astrocytes. J Neurotrauma. 2019; 36(3): 469–484. PubMed Abstract | Publisher Full Text\n\nWang L, Pei S, Han L, et al.: Mesenchymal Stem Cell-Derived Exosomes Reduce A1 Astrocytes via Downregulation of Phosphorylated NFκB P65 Subunit in Spinal Cord Injury. Cell Physiol Biochem. 2018; 50(4): 1535–1559. PubMed Abstract | Publisher Full Text\n\nLankford KL, Arroyo EJ, Nazimek K, et al.: Intravenously delivered mesenchymal stem cell-derived exosomes target M2-type macrophages in the injured spinal cord. Plos One. 2018; 13(1): e0190358. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao C, Zhou X, Qiu J, et al.: Exosomes Derived From Bone Marrow Mesenchymal Stem Cells Inhibit Complement Activation In Rats With Spinal Cord Injury. 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}
|
[
{
"id": "99547",
"date": "01 Feb 2022",
"name": "Ilya Klabukov",
"expertise": [
"Reviewer Expertise Regenerative medicine and Tissue engineering"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presented review paper \"Nanoparticles in Traumatic Spinal Cord Injury: Therapy and Diagnosis\" contains many up-to-date ideas for diagnosing and treating Traumatic Spinal Cord Injury. The primary approach is believed that nanoparticles suggest a promising methodology for the target delivery of materials and biomolecules.\n2. At the same time, it seems that the paper's theme is speculative. To avoid any awkwardness, authors have used mainly PubMed sources. This is a very fruitful approach, but this is not enough, and I recommend using ONLY PubMed-indexed sources. Therefore, only 118 existing PubMed sources plus Statistics resources are recommended to be left in the Reference list.\n3. The authors use statistics based on 2010 and 2011 sources. Statistic sources should be updated, if possible.\n4. The References list needs to be updated by papers published in 2021, some are presented in the following citations:\nJavdani et al. (20211) Rong et al. (20212) Zhang et al. (20213) Lin et al. (20214) Wang et al. (20215)\n5. The paper should be shortened, especially the details of research on laboratory animals. Abstracts of original articles should be critically discussed, not retold.\n6. I recommend adding a subsection on Complications for the use of nanoparticles. Injection of nanoparticles can lead to multiple complications, such as aggregation in tissues, nonspecific binding, and a systemic immunological response. The real and potential risks of using nanoparticles should be disclosed in the manuscript.\n7. The paper has no references both to Preclinical and Clinical trials. It should be taken into account that clinical trials will be a challenge for nanoparticle-based drugs, and these trials need to be noted in the manuscript in Table form.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
},
{
"id": "142846",
"date": "18 Jul 2022",
"name": "Jonghyuck Park",
"expertise": [
"Reviewer Expertise Immunoengineering",
"nanoparticles",
"gene delivery",
"spinal cord injury",
"inflammation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 does a great job summarizing many relevant experiments and investigations done regarding various nanoparticle applications to SCI. Where it falls short for the reviewer is the lack of an overarching theme or main point.\nAfter summarizing the relevant data from various experiments, the paper fails to bring it together to talk about the relevance (why this is important) or specific pros and cons of each nanoparticle type discussed. The authors just simply summarized the many previous studies using NPs. What are the underlying mechanisms of NPs for SCI? How are they taken up by cells? Are they employed as a drug delivery vehicle? Or Immunomodulatory factors? What are the effects of physicochemical properties for each of the polymeric NPs on SCI (i.e., size, surface charge, and molecular weight - If the author could provide the table for this it would be helpful)?. The authors mentioned only chitosan and chitosan-related NPs in the natural polymeric NPs section. Is this the only natural polymeric NPs for SCI (one or two additional natural polymeric NP would be helpful)? What are the pros and cons of utilizing natural polymeric NPs and polymeric NPs for SCI treatments?\nIf the paper could bring all the information together after each section and in the conclusion to talk more about why these developments are innovative or how they could lead to a new SCI treatment, the reviewer would have no reservations.\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": []
}
] | 1
|
https://f1000research.com/articles/10-850
|
https://f1000research.com/articles/10-61/v1
|
02 Feb 21
|
{
"type": "Research Article",
"title": "Whole-exome sequencing of de novo genetic variants in a Chinese family with a sporadic case of congenital nonsyndromic hearing loss",
"authors": [
"Sijing Hu",
"Hao Zhang",
"Yunqiang Liu",
"Mohan Liu",
"Jingjing Li",
"Shunyao Liao",
"Sijing Hu",
"Hao Zhang",
"Yunqiang Liu",
"Mohan Liu",
"Jingjing Li"
],
"abstract": "Background: We examined the genetic variants of a Chinese family with a 22-month-old infant with sporadic non-syndromic sensorineural hearing loss (NSHL). Methods: The whole-exome sequence data in the family, especially the de novo variants presented in the patient, were analyzed and the effect of the disease-causing genetic variants on the protein expression level and cellular localization were examined by cell-based functional assay. Results: The infant had no known NSHL-causing variants, except two compound heterozygous variants in connexin26 gene GJB2; one was the c.79G>A, c.341A>G haplotype from the asymptomatic mother which was benign, and the other was a de novo pathogenic c.262G>C (p.A88P). In vitro, GJB2 with c.262G>C was weakly expressed and displayed a punctate distribution in the cytoplasm and cytomembrane, while wild type GJB2 was robustly expressed in the cytomembrane. We deduced that the de novo pathogenic GJB2 c.262G>C exacerbated loss-of-function in the context of leaky variants c.79G>A, c.341A>G in the patient. Interestingly, further analysis of exome sequences revealed that the occurrence of de novo pathogenic variants in the infant was frequent. Among the total~47,000 variants, 143 were de novo in the patient, whereas among all 74 variants predicted to be pathogenic/likely pathogenic, 21 were heterozygous and two were homozygous de novo. The occurrence rate of de novo deleterious variants was much higher (31.1%, 23/74) than that in total (0.34%, 143/47,000). It is notable that most genes with de novo deleterious variants were environment-sensitive, such as GJB2, MNK1, MNK2, MUC4, RAD21 and DNA copy number variations. Conclusions: The full picture of genetic variants in the exome might help us to interpret the NSHL-causing variants. More research is needed into the causes of de novo deleterious variants and gene-environment interactions in congenital NSHL.",
"keywords": [
"Whole-exome sequencing",
"de novo pathogenic variant",
"nonsyndromic hearing loss",
"compound heterozygosity",
"genetic and environmental interaction"
],
"content": "Introduction\n\nHearing loss is one of the most common birth defects. Variants in the Gap Junction Protein Beta 2 gene (GJB2, HGNC: 4284), which encodes a beta-2 gap junction protein (connexin 26; Cx26), have been shown to be the leading genetic cause of non-syndromic sensorineural hearing loss (NSHL) (OMIM: 121011). GJB2-related autosomal recessive deafness explains approximately 50% of congenital autosomal recessive deafness, and GJB2-related autosomal dominant deafness is extremely rare.\n\nGJB2 constitutes cell-to-cell channels and facilitates the intercellular exchange of ions and molecules1. The amino acid alanine at position 88 (p.A88) of GJB2, which is located in the second transmembrane domain of Cx26, is highly conserved in vertebrates. To date, five studies have reported five nucleotide changes in the p.A88 coding region that resulted in distinct clinical abnormalities and different inheritance patterns. Frei et al. first reported the heterozygous c.262G>T (p.A88S) variant in a male Austrian patient with NSHL. As the proband’s mother was an asymptomatic carrier, the authors inferred that the missense variant could be connected to deafness but not in a simple, monogenetic disease model2. Gravian et al. found that the c.262G>C (p.A88P) variant in compound heterozygosity with the nonpathogenic variant p.V27I in an Argentina child with profound deafness, implicating the destructive potential of the c.262G>T variant3. Other researchers have reported p.A88 coding variants at the 263rd nucleotide: one was the c.263C>G (p.A88G) variant in a Tunisian girl with autosomal recessive NSHL, where her consanguineous parents were healthy carriers4; another was the c.263C>A (p.A88E) variant in a Chinese patient with sporadic NSHL where the variant was in compound heterozygosity with the disease-causing c.235delC5; and another was the c.263C>T (p.A88V) variant in a Japanese girl with severe keratitis-ichthyosis-deafness syndrome and septic complications, with unaffected parents6. To date, by directly sequencing the GJB2 genetic region, studies have demonstrated that variants in GJB2 p.A88 have been associated with hearing loss in children. However, descriptions of the penetrance of the variants have been inconsistent.\n\nOn the other hand, the GJB2 c.79G>A (p.V27I, rs2274084) in cis with c.341A>G (p.E114G, rs2274083) forming a haplotype of p.[V27I; E114G] occurs frequently in East Asian populations7,8. P.V27I is located in the first transmembrane domain and p.E114G is located in the intracellular loop of Cx26.Both are classified as benign polymorphisms. However, several clinical studies have found the p.[V27I; E114G] haplotype to be a risk factor for hearing impairment7-10, and functional assays in vitro have demonstrated that the channel activities of VG (p.E114G variant only) and IG (both p.V27I; p.E114G variants) were reduced11. However, as both genotypes were detected in both patients and controls7-10, the exact pathogenic role of these variants in NSHL remains controversial.\n\nWhole-exome sequencing enables a comprehensive and precise genetic investigation of congenital disorders and allows us to search highly heterogeneous genetic causes. This study aimed to explore possible molecular abnormalities in a Chinese non-consanguineous family with a 22-month old daughter suffering from NSHL. We carried out whole-exome sequencing, assessed the cytological/clinical characteristics of the genetic variants, and evaluated the possible cause of de novo pathogenic variants in the patient’s exome.\n\n\nMethods\n\nThe family included in this study is of Han Chinese heritage and resides in Chengdu City of Southwest China. The proband was a 22-month-old girl with NSHL who had previously been born in our hospital by spontaneous delivery at full term. Both of her parents were healthy during pregnancy. The baby failed the newborn hearing examination but no prenatal or postnatal risk factors for hearing loss were identified. Similarly, no family history of hearing abnormalities was reported. When the parents brought the 22-month-old child back to the hospital in October 2018, physical, biochemical, and otoscopic examinations were carried out. A CT scan of the temporal bones and MR analysis of the child’s head were also done to search for any organic brain lesions, and pure tone audiometry was performed in the girl and her parents.\n\nWritten informed consent was obtained from both parents for them and their daughter to participate in the study. The work was approved by the Research Ethics Committee of Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China.\n\nBlood genomic DNA and mitochondrial DNA were extracted from all family members according to standard procedures (Abcam, Cambridge, UK) and stored in -20°C. The DNA concentration and quality were examined using a NanoDrop 2000 (Thermo, USA).\n\nThe whole-exome sequencing, the entire mitochondrial DNA and genetic variations analysis are described in our previous work12. The fragmented genomic DNA was enriched using a NimbleGen probe capture array SeqCap EZ Exome Kit v3.0 (Roche NimbleGen, Inc. Madison, WI). The kit using the SeqCap advanced design algorithm coupled with 2.1 million long oligonucleotide probes to achieve superior target enrichment performance, and detect genetic variants with ~98% sensitivity and 99% specificity. The enriched DNA fragments passed the qPCR test, and the size distribution and concentration were examined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). The samples were sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA), and two parallel reactions were performed. Raw image files were processed by the BclToFastq (Illumina) for base calling to generate the raw data. The low-quality variations were filtered out using the quality score =20 (Q20). The sequencing reads were aligned to the NCBI human reference genome (hg19) using Burrows-Wheeler Aligner (version 0.6.2). SAMtools and Pindel were used to analyze single nucleotide polymorphisms (SNPs) and insertion/deletion of the sequence. The coding variants and CNVs were filtered out in the dbSNP135, Exome Variant Server, 1000 Genomes, and in-house database with more than 100,000 Chinese exomes (Joy Oriental Co. Beijing, China). The variants and CNVs were also searched in the Human Gene Mutation Database (HGMD), ClinVar, and the Online Mendelian Inheritance in Man database (OMIM).\n\nThe entire mitochondrial DNA was enriched by long-range PCR followed by massively parallel sequencing.\n\nThe related primers are listed in Table 1.\n\nSanger sequencing was used to verify the variations of the candidate genes in the family members12. The primers for amplifying the targeted region of candidate genes are also shown in Table 1.\n\nThe wild-type GJB2 cDNA and GJB2 cDNA with the c.262G>C variant were amplified with the primers shown in Table 1. The HA-tagged wild-type and mutant coding sequences were inserted into the pcDNA3.1(+) vector (Invitrogen, Carlsbad, CA) using the Mut Express® II Fast Mutagenesis kit V2 (Vazyme, Nanjing, China). Human H1299 cells (ATCC, Manassas, VA) were transfected to express the vectors using the jetPRIME Transfection Kit (Polyplus, Illkirch, France) according to the manufacturer’s instructions. After 48 hours of transfection, the cells were collected for immunoblotting and immunohistochemical analysis.\n\nThe online Clustal Omega and Conseq software programs were used to align the amino acid sequences in a variety of species. The Polyphen-2, SIFT and MutationTaster programs were used to predict the variants as “damaging” or “possibly damaging”. The clinical interpretation of genetic variants by the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines was followed to classify the variants into “benign”, “likely benign”, “uncertain significance”, “likely pathogenic”, and “pathogenic”13.\n\nFor immunoblotting analysis, the cells were lysed with RIPA buffer containing protease inhibitor cocktail (Roche Diagnostics GmgH, Mannheim, Germany). The lysate was centrifuged, collected, and boiled in SDS loading buffer. Then, the proteins were separated on 10% SDS-polyacrylamide gels. After the proteins were transferred onto polyvinylidene difluoride membranes (Millipore, USA), the membranes were blocked and incubated with rabbit polyconal anti-HA antibody (Dilution: 1:1000, Cat No.: 51064-2-AP, Proteintech, Chicago, USA) and the secondary antibodies (Dilution: 1:10000, Cat No.: BA1055, Boster Wuhan, China), and the protein bands were visualized using an HRP chemiluminescent substrate kit (Millipore) and a ChemiDoc XRS+ System (Bio-Rad Company, Berkeley, CA).\n\nFor immunohistochemical analysis, the cells were fixed with 4% paraformaldehyde in 0.1 M PBS for 20 min and then rinsed three times in PBS. Then, the coverslips were immersed in cold methanol for 15 min at -20°C. The primary antisera and dilutions were as follows: rabbit anti-HA antibody at 1:100 (Proteintech) for WT/MUT GJB2. After incubation with primary antiserum at 4°C overnight, the cells were rinsed in PBS three times before adding Alexa Fluor 488- and/or Alexa Fluor 594-conjugated secondary antibodies (Dilution: 1:500, Cat. No.: A-11008, Invitrogen). ER was stained with ER-Tracker Red at 1:2000 dilutions (Beyotime, Shanghai, China) for 10 min at room temperature. Preimmune rabbit serum was used as the primary antibody for the negative controls. The images were visualized using a Zeiss Axio Imager Z2 microscope (Carl Zeiss, Jena, Germany).\n\n\nResults\n\nThe pedigree of the family is shown in Figure 1A. The kinship connection between the proband and parents is confirmed by the exome sequence data21. The proband had normal physical, biochemical and otoscopic evaluations. No abnormality was found in her cranium by MR examination or in her cochlear, vestibular, and semicircular canals by CT scan. Pure tone audiometry indicated that her left and right hearing thresholds were 78 dB and 87 dB, respectively, with severe hearing loss in both ears (Figure 1B). Since there was no family history of HL and the child’s parents had normal hearing, the affected infant is considered to be a sporadic case of NSHL.\n\nThe horizontal axis of the audiogram shows the tone frequency (Hz) and the vertical axis displays hearing level (dBHL). Severe hearing loss was classified as a pure-tone average between 70-95 dBHL. х, left ear, о, right ear.\n\nThe mitochondrial sequencing showed no NSHL-causing variants or large deletions. The exome sequences revealed no known NSHL-causing variants in the family except that the proband had a de novo heterogeneous variant c.262G>C in the GJB2 gene (MAF unknown, Table 2 and Figure 2), whereas her parents were wild type. The c.262G>C variant led to a missense variant of p.A88P, which was graded to be “damaging” with a SIFT score of 0.00 and a Polyphen-2 score of 1.00. To examine the effect of the c.262G>C variant on the protein expression level and cellular localization, we transiently transfected the GJB2 c.262G>C mutant into H1299 cells and found that the mutant was expressed weakly and displayed a punctate distribution in the cytoplasm and cytomembrane. In contrast, wild-type GJB2 was expressed robustly and was distributed mainly in the cytomembrane (Figures 3A & B). This result confirmed that the GJB2 p.A88P mutant may fail to locate into the cell membrane and subsequently reduce the formation of gap junctions in quantity.\n\n(A) The DNA sequence electropherograms (I1 father, I2 mother, II1 daughter) revealing wild-type sequence of the parents and de novo 262G to C transversion from their daughter (black arrow). (B) The schematic diagram of Cx26, where M1-M4 are transmembrane domains, E1-E2 are two extracellular loops, CL is intracellular loop, and NH2 and COOH is N- and C-cytoplasmatic termini respectively. The non-pathogenic c.79G>A (p.V27I), c.341A>G (p.E114G) is in both the M1 and intracellular loop. The c.262G>C (p. A88E) is in the M2 of Cx26. (C) The alignment of the Cx26 amino acid sequences among the different species. The alanine at codon 88 is highly conserved.\n\nThe immunofluorescence staining showed the wild-type GJB2 was expressed robustly and distributed mainly in the cytomembrane, while the p.A88P mutant was expressed weakly and displayed a punctate distribution in the cytoplasm and cytomembrane (A, arrow); the ER tracker red demonstrated the cytoplasm (A). The immunoblotting confirmed the wild-type GJB2 largely localized in the cytomembrane, while the p.A88P mutants co-localized in the cytoplasm and cytomembrane (B).\n\nBecause heterozygous c.262G>C missense variants were previously found in both patients and healthy carriers in the clinic2,4, we rechecked the exome sequences of the family to search for any other possible genetic causes of NSHL. We failed to find any other NSHL-causing variants, but noticed that the mother was a heterozygote of GJB2 c.79G>A (p.V27I), c.341A>G (p.E114G), the father was wild type, and the affected infant was a heterozygote of c.79G>A (p.V27I) and c.341A>G (p.E114G). As mentioned before, although no significant loss of function has been detected when VG and IG gap junctions coexist with the VE and IE types, the VG and IG types have displayed a moderate deficit in biochemical coupling and reduced channel activity in vitro11. Hence, we deduced that the de novo p.A88P mutants in the infant dislocated from the cell membrane, exacerbating GJB2 loss-of-function in the context of the p.[V27I; E114G], whereas the wild-type p.A88 in her mother could compensate for the loss, thus the infant’s compound heterozygosity at p.A88P and p.[V27I; E114G] was affected while her mother is an asymptomatic carrier of p.[V27I; E114G]. This result indicates that the multiple genetic variants in GJB2 could influence protein function additively.\n\nAs we noticed that the c.262G pathogenic variant was de novo, we examined the de novo variants in the patient’s exome. It showed that there were approximately 47,000 variants, of which 143 variants were de novo (0.34%, 143/47,000). Among these 47,000 variants, 74 (0.016%, 74/47,000) were predicted to be pathogenic or likely pathogenic. Remarkably,23 de novo variants were predicted to be pathogenic or likely pathogenic, including 21 heterozygous and two homozygous variants. The de novo adverse variants accounted for approximately one-third (23/74) of all pathogenic or likely pathogenic variants (Table 2). Compared with the frequency of de novo variants in total being only 0.34%, the frequency of de novo adverse variants in all de novo variants reached above 16% (23/143) which is surprisingly high. The 23 de novo adverse variants were distributed in 19 different genetic areas, including 12 known genetic regions, two unclassified gene zones (LOC100509263 and LOC81691) and five other chromosome domains without defined roles (Table 2). Except for the de novo GJB2 c.262G>C variant, the other adverse variants have not yet been reported to be NSHL-causing.\n\nNotably, eight copy number variations (CNVs) - nearly half of the infant’s 17 total adverse CNVs - were de novo. The de novo pathogenic CNVs accounted for 42% (8/19) of the total de novo adverse mutated genes (Table 2); however, the minor allele frequencies of these CNVs were below 0.05 in the Human Gene Mutation Database and our in-house database (Joy Oriental Co., Table 2). Of these CNVs, six lacked the relevant information about their function, except the exon deletion in Rho Guanine Nucleotide Exchange Factor 5 (ARHGEF5, exon 2-12, 13,006 bp) and Opsin 1, Medium Wave Sensitive 2 (OPN1MW2, exon 1-6, 13,365 bp). The ARHGEF5 and OPN1MW2 gene products are crucial proteins that transduce external environmental cues into cellular signals across the cell membrane. Indeed, most CNVs do not encode important genes related to development and are thought to be subjected to adaptation to different environments14. Here, these recurrent de novo pathogenic CNVs in the patient remind us about the environmental influence on genetic components.\n\nIn total, four missense, four frameshift, three noncoding, two splice-site, one in-frame deletion and one stop gain variant which were predicted to be pathogenic/likely pathogenic, were de novo (Table 2). Interestingly two heterozygous pathogenic variants in mitogen-activated protein kinase 8 interacting kinases 1 and 2 (MNK1 and MNK2) were de novo: one MNK1 noncoding variant c.679 C>T in chromosome 11 (exon 12, MAF=0.000046) and the other MNK2 missense variant c.1816 G>A in chromosome 22 (exon 6, MAF unknown). Both MNK1 and MNK2 are serine/threonine kinases from the Ca2+/calmodulin-dependent kinase family and take part in initiating mRNA translation in response to MAPK signaling, accordingly playing important roles concerning environmental stress and cytokines15. Also, four de novo pathogenic variants, including one homozygous missense variant c.11801C>T (MAF=0.016), accumulated in the cell surface-associated Mucin 4 gene (MUC4). Mucins are integral membrane glycoproteins on the cell surface. As the major constituents of mucus, mucins protect epithelial cells from outward stimuli. Additionally, two de novo heterozygous pathogenic variants c.1162-4(IVS9) insG (MAF unknown) and c.1162-5(IVS9) A>T (MAF=0.000008) were detected in the Rad1-like checkpoint DNA exonuclease gene (RAD21). The RAD21 gene encodes the major cohesion subunit, known as the component of a heterotrimeric cell cycle checkpoint complex, regulating the segregation of sister chromatids in cell cycle progression and connecting inducible gene expression in response to diverse stimuli16. It is assumed that the proband’s genes with de novo pathogenic variants, including the disease-causing GJB2 c.262G>C (p.A88P), were the key participants immediately linking the external stimuli and cellular signals. Therefore, we think that the causes of all these de novo adverse variants in the affected infant might.be directly linked to the fetal/maternal environmental factors.\n\n\nDiscussion\n\nThis study examined the clinical/cytological characteristics and the compound heterozygous GJB2 variants at c.79G>A, c.341A>G and c.262G>C in a Chinese family with a rare sporadic case of NSHL. In a previous cell-based functional assay, Zhang et al. demonstrated that the c.262G>T variant affected the intercellular exchange of larger molecules but left the ionic permeability intact, thus altering the kinetics of gap junction-mediated intercellular signaling and disrupting normal cochlear function17. Our study showed that the c.262G>T variant was expressed weakly and failed to regularly locate in the cell membrane, consequently reducing the formation of cell gap junctions. The GJB2 p.[V27I; E114G] variant may also additively impair GJB2 function, as the channel activities of homozygous p.[V27I; E114G] CX26 gap junctions has been previously shown to be reduced11. Thus, it seems reasonable that carriers of the simple heterozygous c.262G>C could be asymptomatic3, while carriers of c.262G>C in compound heterozygosity along with any other deafness-related variants such as c.235delC, p.V27I, etc. could experience HL, like in our study and a previous NSHL case3. Hence, the pathogenic effects of these GJB2 variants could be additive.\n\nIt should be noted that the penetrance of the GJB2 c.262G>T seemed to be undetermined in the two previous NSHL cases: the heterozygous p.A88S in the Austrian patient with NSHL and his asymptomatic mother carrier2; and the heterozygous p.A88V in the Japanese girl with severe keratitis-ichthyosis-deafness syndrome and her healthy parents6. Both studies reported no other GJB2 variants except the heterozygous c.262G. In fact, only the candidate GJB2 genetic region was sequenced in their studies, so any other genetic disease-causing variants in the patients’ genome are still unknown. Therefore, for an accurate variant interpretation and improved clinical care, we propose that more comprehensive details about the related variants, such as variant domain, effect, and reciprocal interaction, should be investigated.\n\nIn the current study, it is intriguing that there was a very high frequency of de novo adverse variants in the proband’s exome and that most de novo variants are in the genetic regions characterized as environment-sensitive. Several notable results were found. First, the gene in which the de novo NSHL-causing GJB2 c.262G>C is located is immediately responsive to the surrounding changes. The gene product GJB2 is essential for gap channels, which allows the exchange of small substances including nutrients, metabolites, ions and second messengers, and regulates signaling pathways in intracellular communication1,17. Second, variants in MNK1 and MNK2 - two downstream MAPK signaling effectors located in different chromosomes - were also de novo. Both MNKs are involved in guiding cellular responses to a diverse array of stimuli, such as mitogens, osmotic stress, heat shock and proinflammation15,18. Third, the de novo pathogenic variants were aggregated in the MUC4 gene region. Mucins are integral membrane glycoproteins on the cell surface, covering epithelial surfaces such as those in the trachea, colon and cervix, and exert anti-adhesive effects on cell-cell and cell-extracellular matrix interactions19. Fourth, there were two de novo pathogenic variants in the RAD21 gene. RAD21 participates in repairing DNA double-strand breaks and chromatid cohesion and can be affected by various agents, including ionizing radiation, topoisomerase inhibitors, cycloheximide, proteasome inhibitors, cytokines agents and inflammatory stimuli16,20. Finally, there was a very high incidence of de novo pathogenic CNVs which have quite low MAFs. CNVs are often enriched in genes related to sensory perception of the external environment (e.g., smell, sight, and taste), neurodevelopmental processes, and response to chemical stimuli, immunity and other processes14. Therefore, we wonder whether there might have been any direct external stimuli to trigger the fetal adaptive responses for the occurrence of such a considerable amount of de novo pathogenic variants, which thus led to the disease.\n\nIt should be noted that the sporadic congenital NSHL in the family that we studied here was rare and limited; more research in similar birth defect cases is needed to confirm the role of environmental factors in transformation of genetic variants in the fetus/offspring.\n\nIn summary, by whole-exome sequencing, we examined overall genetic variants, especially the compound heterozygous GJB2 variants and the high frequency of de novo pathogenic variants in a Chinese family with a rare sporadic case of NSHL. Though the reported case here is limited, we think the detailed full picture of genetic variants could improve our interpretation of the HL-associated genetic variants. In order to further advance our understanding of disease biology in birth defects, further research on environmental causes for de novo pathogenic variants may be needed.\n\n\nData availability\n\nOpen Science Framework: Whole-exome sequencing of de novo genetic variants in a Chinese family with a sporadic case of congenital nonsyndromic hearing loss. https://doi.org/10.17605/OSF.IO/DS7TW21\n\nThis project contains the following underlying data:\n\n\n\nThe immunoblotting of the p.A88P Cx26 mutants in cells. (mut*.tif)\n\nThe immunoblotting of the wild type Cx26 in cells. (WT*.tif)\n\nThe data comparison of the exome DNA sequences of the family members. (*.xlsx)\n\nNCBI Gene: Exome sequencing of a Chinese family with a sporadic congenital NSHL. Accession number PRJNA688744.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nEthical approval\n\nThe data were de-identified as sufficiently as possible and data sharing was approved by the Research Ethics Committee of Sichuan Provincial People’s Hospital, School of Medicine, UESTC (approval number 2019-065).",
"appendix": "Acknowledgments\n\nWe sincerely thank the study participants, without their permission, this work would not be possible.\n\n\nReferences\n\nKikuchi T, Kimura RS, Paul DL, et al.: Gap junctions in the rat cochlea: immunohistochemical and ultrastructural analysis. AnatEmbryol (Berl) 1995; 191(2): 101–118. PubMed Abstract | Publisher Full Text\n\nFrei K, Szuhai K, Lucas T, et al.: Connexin 26 mutations in cases of sensorineural deafness in eastern Austria. Eur J Hum Genet 2002; 10(7): 427–432. PubMed Abstract | Publisher Full Text\n\nGravina LP, Foncuberta ME, Prieto ME, et al.: Prevalence of DFNB1 mutations in Argentinean children with non-syndromic deafness. Report of a novel mutation in GJB2. Int J Pediatr Otorhinolaryngol 2010; 74(3): 250–254. 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Cytogenet Genome Res 2008; 123: 17–26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWaskiewicz AJ, Flynn A, Proud CG, et al.: Mitogen-activated protein kinases activate the serine/threonine kinases Mnk1 and Mnk2. EMBO J 1997; 16(8): 1909–1920. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPati D, Zhang N, Plon SE: Linking sister chromatid cohesion and apoptosis: role of Rad21. Mol Cell Biol 2002; 22(23): 8267–8277. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Tang W, Ahmad S, et al.: Gap junction-mediated intercellular biochemical coupling in cochlear supporting cells is required for normal cochlear functions. Proc Natl Acad Sci U S A 2005; 102(42): 15201–15206. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJoshi S, Platanias LC: Mnk Kinases in Cytokine Signaling and Regulation of Cytokine Responses. Biomol Concepts 2012; 3(2): 127–139. 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}
|
[
{
"id": "82648",
"date": "08 Apr 2021",
"name": "Kun Zhang",
"expertise": [
"Reviewer Expertise Medical Genetics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors report an interesting observation describing a patient with non-syndromic hearing loss caused by a de novo heterozygous variant of GJB2 c.262G>C. The authors identified the variant by whole exome sequencing and provided biological evidence of the variant by in vitro analysis.\nHere, several concerns were raised:\nThe number of de novo variants (23) seemed very high. De novo genetic variants are recently suggested to be important in human disease, one investigation of severe childhood cardiomyopathy identified a de novo variant in 46% of children with a pathogenic variant (Vasilescu et al., Genetics basis of severe childhood onset cardiomyopathies. Journal of the American College of Cardiology 2018), yet the overall frequency of de novo variants is largely unknown. Should the authors discuss more about the issue? It should be noted that one case here is limited.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "6699",
"date": "26 May 2021",
"name": "Sonia Liao",
"role": "Author Response",
"response": "Thanks a lot. We presented the suggested reference in the new version, please see the 4th paragraph of the discussion section.."
}
]
},
{
"id": "82018",
"date": "15 Apr 2021",
"name": "Yuande Tan",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper displays a variant profile of a Chinese family with a case of congenital nonsyndromic hearing loss using the whole-exome sequencing data. Authors attempted to utilize heterozygote of a de nova variant (c.262G>C) in gene GJB2 to explain case of nonsyndromic hearing loss occurring in an offspring individual. However, I have several major concerns to be addressed:\n\nThe results show among the total~47,000 variants, 143 were de novo occurring in the patient. According to definition of de nova from Wikipedia, a de nova variant is a variant occurring in offspring individuals, not in parents, that is, de nova variants results from mutation occurring in sperm or germ cells. However, 143/47000(0.304%) is too high. Since there is one offspring individual in this study, so, it is very difficult to determine whether these de nova variants are due to noise or true mutation. In addition,47,000 variants detected in the patient are also too many and most of these so-called variants may be noisy or result from sequencing error. Authors should discuss this issue.\n\nIf it is known that nonsyndromic hearing loss is due to mutation in gene GJB2, it is unnecessary to do the whole exom sequencing, that is to say, the whole variant profiles of parents and daughter (proband) do not provide useful information for interpreting the nonsyndromic hearing loss. The de nova variants listed in Table 2 also do not make sense because they are not used to explain occurrence of the nonsyndromic hearing loss.\n\nHow heterozygous c.262G>C missense variants works for occurrence of the nonsyndromic hearing loss is not clear. Since the farther and mother have homozygote c.262GG and have no nonsyndromic hearing loss and heterozygous c.262G>C variant was also found in healthy individuals, the proband with heterozygous c.262G>C variant at this position in gene GJB2 should be normal hearing. However, the proband had heterozygous variants c.79G>A and c.341A>G in gene GJB2 derived from her mother but her mother is normal hearing. Therefore, there may be interaction (dominant epistasis or receive epistasis) between c.262G>C and c.79G>A or c.341A>G. Author should discuss this possible heredity mechanism.\nMinor points:\nOn page 3, simple, monogenetic should be simple and monogenetic.\n\nOn page 3, “another was the c.263C>A (p.A88E) variant” should be “another case was the c.263C>A (p.A88E) variant”.\n\nOn page 3,\n\n“c.235delC5 ; and another was the c.263C>T (p.A88V) variant” should be\n\n“c.235delC5 and the other variant was the c.263C>T (p.A88V)”.\n\nOn page 3, “several clinical studies have found the p.[V27I; E114G] haplotype to be a risk factor” should be “several clinical studies have found that the p.[V27I; E114G] haplotype is a risk factor”.\n\nOn page 3, “Written informed consent was obtained” should be “An informed consent was obtained”.\n\nOn page 4, what is “size distribution and concentration”?\n\nOn page 5, “the affected infant is considered to be a sporadic case of NSHL”. I don’t think it is a sporadic case because you just found one case and you cannot determine it is a sporadic case or a pedigree case or a family case.\n\nOn page 5, what is “large deletions”?\n\nOn page 5, “The exome sequences revealed no known NSHL-causing variants” should be “The exome sequences revealed unknown NSHL-causing variants”.\n\nOn page 5, “whereas her parents were wild type” should be “whereas her parents were normal type”. I have never seen “wild type” in human.\n\nLegend Figure 1 is unclear. It does not state what is Figure 1A.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6698",
"date": "24 Aug 2021",
"name": "Sonia Liao",
"role": "Author Response",
"response": "1. The results show among the total~47,000 variants, 143 were de novo occurring in the patient. According to definition of de nova from Wikipedia, a de nova variant is a variant occurring in offspring individuals, not in parents, that is, de nova variants results from mutation occurring in sperm or germ cells. However, 143/47000(0.304%) is too high. Since there is one offspring individual in this study, so, it is very difficult to determine whether these de nova variants are due to noise or true mutation. In addition,47,000 variants detected in the patient are also too many and most of these so-called variants may be noisy or result from sequencing error. Authors should discuss this issue. Our answer: Thanks. We discussed that “sequencing errors remain one of the main obstacles in the identification of causative genetic variants and/or mutations” in the new version, please see the 4th paragraph of the discussion section. We may need to mention here, the genetic counseling center in our hospital, one of the earliest clinic genetic research groups in China, offers regular exome sequencing to identify and study disease-related genetic mutations for patients. For the quality of our exome sequencing in the current work, please refer to the chapter of Whole-exome and mitochondrial DNA sequencing in the materials and methods. And also, all sequence information is open at NCBI Gene: Exome sequencing of a Chinese family with a sporadic congenital NSHL. Accession number PRJNA688744. 2. If it is known that nonsyndromic hearing loss is due to mutation in gene GJB2, it is unnecessary to do the whole exom sequencing, that is to say, the whole variant profiles of parents and daughter (proband) do not provide useful information for interpreting the nonsyndromic hearing loss. The de nova variants listed in Table 2 also do not make sense because they are not used to explain occurrence of the nonsyndromic hearing loss. Our answer: Thanks. As we mentioned in the 1st paragraph of the introduction: “GJB 2 have been shown to be the leading genetic cause of NSHL (OMIM: 121011). GJB2-related autosomal recessive deafness can explain approximately 50% of congenital autosomal recessive deafness.” In fact, pathogenic variants were found in 49 genes according to GeneReviews of NSHL (https://www.ncbi.nlm.nih.gov/books/NBK1272/). In the current case of an NSHL newborn, we think that it is necessary to carry out the whole-exome sequencing to search for the genetic causes of the disease. In the new version, we added that “the pathogenic variants of non-syndromic sensorineural hearing loss (NSHL) (OMIM: 121011) were found in 49 genes (https://www.ncbi.nlm.nih.gov/books/NBK1272/)” in the 1st paragraph of the introduction, in order to emphasize that GJB2 variants are not the only genetic causes of NSHL, and also, we pointed out that “We carried out whole-exome sequencing, assessed the cytological/clinical characteristics of the genetic variants, specifically in the GJB2 genetic variants, and evaluated the possible cause of de novo pathogenic variants in the patient’s exome.” in the last paragraph of the introduction. 3. How heterozygous c.262G>C missense variants works for occurrence of the nonsyndromic hearing loss is not clear. Since the farther and mother have homozygote c.262GG and have no nonsyndromic hearing loss and heterozygous c.262G>C variant was also found in healthy individuals, the proband with heterozygous c.262G>C variant at this position in gene GJB2 should be normal hearing. However, the proband had heterozygous variants c.79G>A and c.341A>G in gene GJB2 derived from her mother but her mother is normal hearing. Therefore, there may be interaction (dominant epistasis or receive epistasis) between c.262G>C and c.79G>A or c.341A>G. Author should discuss this possible heredity mechanism. Our answer: Thanks. According to the definition of National Human Genome Research Insititute, epistasis refers to a circumstance where the expression of one gene is affected by the expression of one or more independently inherited genes (https://www.genome.gov/genetics-glossary/Epistasis). In the current study, both c.262G>C and the haplotype of c.79G>A and c.341A>G are in the exon2 of GJB2 gene, and encode amino acids which were tightly connected in this protein (for details please see the figure2). We do not think that it should be necessary to discuss about the independent heredity mechanism of these variants in the same gene. Additionally, in our study, we noticed the insufficient GJB2 function because of these variants, while we have not seen any report about the epistasis in this exact situation. Minor points: 1. On page 3, simple, monogenetic should be simple and monogenetic. Our answer: According to the suggestion, we modified the text. 2. On page 3, “another was the c.263C>A (p.A88E) variant” should be “another case was the c.263C>A (p.A88E) variant”. Our answer: The “case” was added in the context of the whole sentence. 3. On page 3, “c.235delC5 ; and another was the c.263C>T (p.A88V) variant” should be “c.235delC5 and the other variant was the c.263C>T (p.A88V)”. Our answer: Thanks. This sentence might be confusing due to the typesetting errors? “c.235delC5” was not correct here. Here, we listed that researchers have reported 3 p.A88 coding variants at the 263rd nucleotide: (1) c.263C>G (p.A88G) [reference4], (2) c.263C>A (p.A88E) in compound heterozygosity with c.235delC [reference5], (3) c.263C>T (p.A88V) [reference5]. Since there were totally 3 reported cases, the sentence we presented them like: “there are three pens, one is red, another is black, and another is green” 4. On page 3, “several clinical studies have found the p.[V27I; E114G] haplotype to be a risk factor” should be “several clinical studies have found that the p.[V27I; E114G] haplotype is a risk factor”. Our answer: We modified the text according to the suggestion. 5. On page 3, “Written informed consent was obtained” should be “An informed consent was obtained”. Our answer: Thanks. We found that “written informed consent” without any prefix ( “a” or “the”) was used in many research articles, and listed below 2 of these examples from the Pubmed for your reference. “Consent for publication Written informed consent was obtained from the patient for the publication of this report and any accompanying images.” Reich M, Cakir B, Cvetkoski S, Lang SJ, Stahl A, Ness T, Agostini H, Lange C. Acute unilateral maculopathy associated with adult onset of hand, foot and mouth disease: a case report. BMC Ophthalmol. 2019; 19(1):104. doi: 10.1186/s12886-019-1111-4. “Informed consent Written informed consent was obtained from the patient for publication of this case report.” Lieberman A, Curtis L.Severe Adverse Reactions Following Ketoconazole, Fluconazole, and Environmental Exposures: A Case Report. Drug Saf Case Rep. 2018 18;5(1):18. doi: 10.1007/s40800-018-0083-2. And also, there are the same sentence examples at the websites of English sources like: https://www.lawinsider.com/dictionary/informed-written-consent and https://ludwig.guru/s/written+informed+consent+was+obtained+from+all+subjects. 6. On page 4, what is “size distribution and concentration”? Our answer: Here the “size distribution and concentration” belong to the qPCR of the enriched DNA fragments; we changed it into “the size distribution and concentration of these DNA fragments were examined…” Please see the revised sentence in the new version. 7. On page 5, “the affected infant is considered to be a sporadic case of NSHL”. I don’t think it is a sporadic case because you just found one case and you cannot determine it is a sporadic case or a pedigree case or a family case. Our answer: Commonly for patients with birth defect, we investigated their family history for any inheritance diseases; if we got no report of such case in their family, we would consider that the new case could be isolated and sporadic. We think that, to an individual family with birth defect, this kind of considerations and the searching for genetic causes of the disease could be useful, especially when these families want to prevent and intervene more disease happening. We believe that current case report about the de novo pathogenic variants could provide new and useful information that lead to further and vital research. On page 5, what is “large deletions”? Our answer: According to the National Human Genome Research Institute: “deletion can be small, involving a single missing DNA base pair, or large, involving a piece of a chromosome”. Large deletions in genomic DNA have been reported to associate with many diseases. For an example: Yu CE, Dawson G, Munson J, D'Souza I, Osterling J, Estes A, Leutenegger AL, Flodman P, Smith M, Raskind WH, Spence MA, McMahon W, Wijsman EM, Schellenberg GD. Presence of large deletions in kindreds with autism. Am J Hum Genet. 2002; 1(1):100-15. doi: 10.1086/341291 In our study, because large deletions in mitochondrial DNA have been reported to associate with hearing loss [some related references were listed below], we stated our sequencing result as that “the mitochondrial sequencing showed no NSHL-causing variants or large deletions.” Souied EH, Salès MJ, Soubrane G, Coscas G, Bigorie B, Kaplan J, Munnich A, Rötig A. Macular dystrophy, diabetes, and deafness associated with a large mitochondrial DNA deletion. Am J Ophthalmol. 1998; 125(1):100-3. doi: 10.1016/s0002-9394(99)80243-8. Yin S, Yu Z, Sockalingam R, Bance M, Sun G, Wang. The role of mitochondrial DNA large deletion for the development of presbycusis in Fischer 344 rats. J. Neurobiol Dis. 2007; 27(3):370-7. doi: 10.1016/j.nbd.2007.06.006. 8. On page 5, “The exome sequences revealed no known NSHL-causing variants” should be “The exome sequences revealed unknown NSHL-causing variants”. Our answer: Here we want to say that “The exome sequences did not revealed any known NSHL-causing variants”, NOT about any unknown NSHL-causing variants. 9. On page 5, “whereas her parents were wild type” should be “whereas her parents were normal type”. I have never seen “wild type” in human. Our answer: Thanks. We searched “wild type in human” in the Pubmed and listed some results here for your reference: Serebryany E, King JA. Wild-type human γD-crystallin promotes aggregation of its oxidation-mimicking, misfolding-prone W42Q mutant. J Biol Chem. 2015; 290(18):11491-503. doi: 10.1074/jbc.M114.621581. Graffmo KS, Forsberg K, Bergh J, Birve A, Zetterström P, Andersen PM, Marklund SL, Brännström T. Expression of wild-type human superoxide dismutase-1 in mice causes amyotrophic lateral sclerosis. Hum Mol Genet. 2013; 22(1):51-60. doi: 10.1093/hmg/dds399. Friedman PN, Kern SE, Vogelstein B, Prives C. Wild-type, but not mutant, human p53 proteins inhibit the replication activities of simian virus 40 large tumor antigen. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9275-9. doi: 10.1073/pnas.87.23.9275. 10. Legend Figure 1 is unclear. It does not state what is Figure 1A. Our answer: Thanks. We made it clear now that figure1A shows the pedigree of the family in the new version."
}
]
}
] | 1
|
https://f1000research.com/articles/10-61
|
https://f1000research.com/articles/9-1501/v1
|
23 Dec 20
|
{
"type": "Research Article",
"title": "Chlorpyrifos and other pesticide exposure and suspected developmental delay in children aged under 5 years: a case-control study in Phitsanulok, Thailand",
"authors": [
"Yuwayong Juntarawijit",
"Uraiwan Chaichanawirote",
"Paphada Rakmeesri",
"Punaphop Chairattanasakda",
"Varintorn Pumyim",
"Chudchawal Juntarawijit",
"Yuwayong Juntarawijit",
"Uraiwan Chaichanawirote",
"Paphada Rakmeesri",
"Punaphop Chairattanasakda",
"Varintorn Pumyim"
],
"abstract": "Background: Developmental delay among children under 5 years of age is a serious global public health problem and much research has been carried out to find potential causes. Pesticides - especially organophosphates - are suspected to be one of the main causes of the problem. This study aimed to investigate the association between pesticide use by the mother during pregnancy and preschool children development using a case-control study. Methods: Data on prenatal and postnatal pesticide exposure of 442 children with suspected developmental delay, and 413 controls with normal development were included for analysis. The children were matched for gender, age, and residency. Data on pesticide exposure were collected via interview with the mother, and data on pregnancy outcomes abstracted from hospital records.\n\nResults: Chlorpyrifos exposure significantly increased the risk of developmental delay with an odds ratio (OR) of 3.71 (95% CI 1.03-13.36) for ever use of the pesticide, and an OR of 5.92 (95% CI 1.01-34.68) for postnatal exposure (p <0.05). Some other pesticides also had a positive association with developmental delay but none were statistically significant (p <0.05). Those pesticides were insecticide, fungicide, herbicide, and molluscicide. Individual pesticides with a positive association were glyphosate, paraquat, butachlor, methyl parathion (pholidon), savin, methomyl, endosulfan, carbosulfan, methamidophos, monochrotofos, mancozeb, and bordeaumixture. Conclusions: This case-control study found that chlorpyrifos and some other pesticide exposure during pregnancy was positively associated with developmental delay in children aged under 5 years. Further research should be conducted to better understand this potential effect of pesticides on child neurodevelopment, and the public - especially those who plan to have families - should be informed.",
"keywords": [
"Developmental disorder",
"child developmental delay",
"neurodevelopmental toxicity",
"pesticides neurotoxicity",
"chlorpyrifos"
],
"content": "Abbreviations\n\nADHD, attention deficit and hyperactivity disorder; ASD, autism spectrum disorders; CPF, chlorpyrifos; DAP, dialkylphosphate metabolites; DD, developmental delay; IQ, intelligence quotient; OP, organophosphate; Ever, either prenatal exposure or postnatal exposure; PostN, postnatal exposure; PreN, prenatal exposure; SDD, suspected developmental delay.\n\n\nIntroduction\n\nDevelopmental delay in young children is a global public health concern. A study of 35 low- and middle-income countries reported that one in every three children below five years of age fails to reach their developmental potential1. In Thailand, a national survey by the Ministry of Public Health reported that approximately 15% of children aged under 5 years are suspected to have a developmental delay (SDD)2. In addition to stunting, inadequate cognitive stimulation, iodine and iron deficiency, malaria, intrauterine growth restrictions, maternal depression, exposure to violence3, exposure to environmental toxicants including phthalates, bisphenol A, flame retardants, polycyclic aromatic hydrocarbon (PAHs), gas cooking4, and heavy metals3.\n\nPesticides of the acetylcholinesterase inhibitor group are another set of compounds suspected to affect neurodevelopment. In laboratory studies, this type of pesticide has been found to affect neuron cell and synaptic functions5. Young children are also at a higher risk of pesticide effects because their bodies are not yet fully developed, and they also have a higher chance of exposure to environmental pesticides from engagement in high-risk behaviors, e.g. crawling on the floor, object-to-mouth behaviors, and playing with items found in the environment6. A recent literature review indicated that 45 out of a total of 50 articles found a positive association between delayed neurodevelopment in young children and OP exposure7. The neurological and behavioral developmental outcomes induced by pesticides include slower neonatal reflexes, delayed psychomotor and mental development8, attention deficit9, lower IQ10, and autism spectrum disorder (ASD)11,12.\n\nRegarding individual pesticides, chlorpyrifos (CPF) is the only OP pesticide that has been extensively studied, with most studies finding a positive association between exposure to CPF and child developmental delay. In a study among inter-city minority communities in New York City, researchers reported a positive association between levels of CPF in umbilical cord plasma and neurodevelopmental delay13. Studies have also linked CPF exposure to poorer outcomes in working memory, visual motor coordination, color discrimination14, and verbal comprehension15, in addition to vision and hearing loss16, and lower IQ17. There is limited evidence that CPF exposure might also relate to ASD18. On the other hand, a study of 2-year-old Mexican-American children found no association between cognitive function and CPF exposure19, meaning this link is not yet conclusive.\n\nCurrently, in Thailand, the effects of CPF on child development have not been adequately studied. The objective of this case-control study was to analyze the association between suspected developmental delay (SDD) in children aged under 5 years living in Phitsanulok province, Thailand, and the use of CPF and other compounds during pregnancy. The results may be useful for SDD prevention, and for comparison to other similar studies in this field.\n\n\nMethods\n\nPhitsanulok province is in lower northern Thailand, located 370 km from Bangkok. It is a midsize province of 4,176 square miles, with nine districts, and a population of 866,891 people (density = 200 people per square mile). The capital city of the province is Muang district.\n\nThis study used a case-control design. Children diagnosed with suspected developmental delay (SDD) (cases) were compared with normal children (controls) with respect to pesticides exposure of the mother during pregnancy. The cases were children aged under 5 years who had participated in the National Child Developmental Screening Program (DSPM), and had been assigned as SDD. In Thailand, under the DSPM, every child is screened for development progress at the ages of 9, 18, 30, and 42 months using a modified Denver Development Screening Test II (DDST-II). The screening is carried out by a trained nurse or health personnel at a health promoting hospital. In accordance with the DSPM manual, the children are evaluated in five skills, namely 1) gross motor skills), 2) fine motor skills, 3) receptive language skills, 4) expressive language skills, and 5) personal and social skills. If a child fails one or more of these skills, they are classified as having SDD. Children classified as having SDD were the target population in this study and were randomly selected to take part. The controls were children who attended the same hospital for the screening program but passed all five skills and were therefore classified as having normal development. The case and control groups were matched for gender, age, and area residence at assessment. Children with congenital anomalies or head trauma were excluded from the study.\n\nParticipants were children who participated in the screening program in selected local hospitals in the Bang Rakam and Muang districts of Phitsanulok province, Thailand. These two of the nine districts in the province were purposively selected to represent a rural area (Bang Rakam district) and an urban area (Muang district) of the province. A total of 15 out of 21 local hospitals in the Bang Rakam district, and 10 out of 30 hospitals in the Muang district were randomly chosen using a simple lottery method. The mothers of every child with SDD who met the inclusion criteria from the selected hospitals were invited to take part in the study at their appointment. For each case, a child with normal development was randomly selected from the hospital database matching for gender, age, and area residence.\n\nThe sample size was calculated to be 816 (408 cases and 408 controls) using OpenEpi online using the following assumptions: confident interval = 95%, power of detection = 80%, ratio of case to control = 1:1, proportion of control with exposure = 40, odds ratio = 1.520.\n\nData on pesticide use and exposure during pregnancy was collected from the child’s mother using a constructed questionnaire (provided as Extended data in English)21. Besides demographic data, the children’s mothers were asked “yes” or “no” questions concerning prenatal and postnatal use of pesticides. The exposure period was classified as “ever” for any prenatal and/or postnatal exposure to pesticides, “prenatal” for prenatal exposure to pesticides, and “postnatal” for postnatal exposure to pesticides. Pesticides were categorized into insecticides, herbicides, fungicides, rodenticides, and molluscicides. Exposure data for 14 individual compounds that are commonly used in Thailand and around the world were also collected. There were also questions for potential confounding factors such as occupation, monthly income, education, cigarette smoking, and alcohol use of the mother. Data on health status and pregnancy outcomes including delivery method, gestation, birth order, birth weight, and breast-feeding history, were retrieved from the hospitals’ medical records. Data collection took place in the participants’ homes, and was conducted between January and May, 2019. Data were collected by 60 village health volunteers who were trained to use the questionnaire and conduct the interviews.\n\nThe questionnaire was constructed by literature reviewed. The content validity of the questionnaire was tested by three experts in pediatric, obstetrics and gynecology and family medicine, and occupational health nursing. The index of Item Objective Congruence (IOC) was between 0.67–1.00. The questions were also tested for sequencing and understanding with a group of 30 women with similar characteristics of the intended participants.\n\nDemographic characteristics were analyzed with descriptive statistics and the results presented as frequency, percentage, mean, and standard deviation. Differences between groups were compared via t-test for continuous variables, and chi-square test for categorical data. The association between developmental delay and pesticide exposure was analyzed using multivariable logistic regression with odds ratios (OR) and a 95 percent confidence interval (CI) adjusted for mother age when pregnant (continuous), education (no school, primary school, secondary school, college degree), occupation (farmer, own business, civil servant, employee [formal], employee [general work], housewife, retired, unemployed), income (<5000 baht, 5000–9999, 10000–14999, 15000 or more), chronic disease (yes, no), alcohol consumption (yes, no), gestation (<37 weeks, 37 or more weeks), birth order (1, 2, 3 or more), delivery method (vaginal delivery, caesarean section, assisted delivery), baby weight (<2500 grams, 2500 grams or more), and breast-feeding (yes, no). Data was analyzed using IBM SPSS (version 26) software. Statistical significance was set at p <0.05 (2-tailed test).\n\nEthical approval for this study was obtained from Naresuan University Institutional Review Board (Approval number 448/2019). Written informed consent to participate in the study and for attaining of their clinical details was obtained from the parents of the patients before data collection.\n\n\nResults\n\nFrom the dataset of 858 individuals, 855 records (413 cases, 442 controls) were used in the data analysis. Three records were not included for analysis because important information such as gender and age, was missing. Demographic data of the participants is shown in Table 1 and in the Underlying data22. Most of the mothers were in the youngest age group with an average age of about 25 years. Most of them finished secondary school and had a monthly income of about 10,000 Thai Baht (300 USD) which is the minimum wage for Thailand. Only about 10% of them were farmers, and therefore reported using pesticides. There was a significantly higher proportion of mothers working as private employees, housewives, and civil servants. Most of the participants were healthy and had never drunk alcohol. One participant reported smoking cigarettes, and thus, was excluded from the data analysis. Data from the child’s medical records revealed that most of them, with the same proportion of case to control were born with spontaneous vaginal delivery (n=303, 69.5% and n=274, 67.5%, respectively). Compared to the control group, there were a higher proportion of cases born preterm and being the second or third child of the family. There was also a significant difference in birth weight and breastfeeding between groups. Although a higher percentage of cases had a birth weight of below 2,500 grams (n=64, 14.5% vs n=31, 7.6%, respectively), a lower percentage of them were not breast fed (n=25, 7.7% vs n=43, 12.8%, respectively).\n\nValue expressed as number (percent) or mean ± standard error unless noted otherwise.\n\n* Statistically significant difference with p value <0.05.\n\nRoughly half of the participants had lived in the community for more than 10 years. With an equal proportion in the case and control groups, about 35% of participants had a family member working on a farm, 20% often entered farmland, and 14% stored pesticides in the house (Table 1), yet around 70% lived within 1.0 km of farm land.\n\nThere were only 47 (10.4%) case mothers and 46 (11.4%) control mothers who reported ever using any pesticides during pregnancy. Table 2 presented odds ratio of SDD by types of pesticides the children were exposed to during pregnancy. Types of pesticides and exposure periods that were positively associated with SDD were insecticides (PostN), fungicides (PreN), fungicides (PostN), herbicides (PostN), and molluscicides (PostN). However, none of these ORs were statistically significant (p <0.05).\n\nEver, either prenatal exposure or postnatal exposure; PreN, prenatal exposure; PostN, postnatal exposure.\n\n* Statistically significant with p value <0.05.\n\n**Adjusted for mother age when pregnant (continuous), education (no school, primary school, secondary school, college degree), occupation (farmer, own business, civil servant, employee [formal], employee [general work], housewife/ retired / unemployed, income (<5000 baht, 5000–9999, 10000–14999, 15000 or more), chronic disease (yes, no), alcohol consumption (yes, no), gestation (<37 weeks, 37 or more), birth order (1, 2, 3 or more), delivery method (vaginal delivery, caesarean section, assisted delivery), baby weight (<2500 grams, 2500 grams or more), and breast-feeding (yes, no).\n\nOf 14 individual pesticides, exposure to CPF during pregnancy was significantly associated with child developmental delay. The associated odds ratio was significant for CPF (Ever) (OR = 3.71, 95% CI 1.03-13.36), and CPF (PostN) (OR = 5.92, 95% CI 1.01-34.68) (Table 3). Risk of SDD were also increased with exposure to some other pesticides, including glyphosate(PostN), paraquat(PostN), butachlor(PostN), Methyl parathion/Pholidon(PostN), savin(PreN), savin (PostN), methomyl(PostN), endosulfan(PostN), carbosulfan(PostN), methamidophos(PreN), methamidophos(PostN), monochrotofos(PostN), mancozeb(PreN), mancozeb(PostN), bordeaumixture(PreN), and bordeaumixture(PostN); however, none were statistically significant.\n\nEver, either prenatal exposure or postnatal exposure; PreN, prenatal exposure; PostN, postnatal exposure.\n\n* Statistically significant with p value <0.05.\n\n**Adjusted for mother age when pregnant (continuous), education (no school, primary school, secondary school, college degree), occupation (farmer, own business, civil servant, employee [formal], employee [general work], housewife/ retired / unemployed, income (<5000 baht, 5000–9999, 10000–14999, 15000 or more), chronic disease (yes, no), alcohol consumption (yes, no), gestation (<37 weeks, 37 or more), birth order (1, 2, 3 or more), delivery method (vaginal delivery, caesarean section, assisted delivery), baby weight (<2500 grams, 2500 grams or more), and breast-feeding (yes, no).\n\n\nDiscussion\n\nThe results showed CPF exposure during pregnancy and childhood SDD, with an odds ratio of 3.71 (95% CI 1.03-13.36) for ever using the pesticide (either prenatal or postnatal exposure), 2.97 (95% CI 0.80-11.07) for prenatal exposure, and 5.92 (95% CI 1.01-34.68) for postnatal exposure (Table 3). Ever and postnatal exposure were found to be statistically significant. There was also a positive association, though not statistically significant, between SDD and other types of pesticides and individual compounds, including three herbicides [Glyphosate(PostN), Paraquat(PostN)), Butachlor(PostN)], two organophosphate insecticides [Pholidon (methyl parathion) (PostN), Tamaron (methamidophos)(PreN)], three carbamate insecticides [Savin(carbaryl), Methomyl(PostN), Carbosulfan(PostN)], and one organochlorine insecticide [Endosulfan(PostN)], and one fungicide [mancoceb(PreN)]. This is consistent with the literature: in an experimental study, CPF showed an ability to alter neuronal formation and structure in animal and human fetuses23,24.\n\nThe results of epidemiological studies into SDD and pesticides have found a range of outcomes. In a study of Mexican American children aged 6–24 months, prenatal or child exposure to CPF was not associated with mental development, pervasive developmental disorder (a group of disorders characterized by delays in the development of socialization and communication skills), or behavioral problems19. However, several other studies have found a positive association between prenatal exposure to CPF and neurodevelopmental problems. A cohort study of three-year-old children from minority communities in New York City, USA, reported a high exposure group (CPF levels of >6.17 pg/g in the mother’s plasma) to have a higher proportion of developmental delay, assessed by the psychomotor development index and the mental development index13. A more recent study in Costa Rica found 6–9-year-old children with higher CPF exposure to have several neurobehavioral problems, including poorer working memory, visual motor coordination, and color discrimination, as well as parent-reported cognitive problems/inattention, oppositional disorder, and attention deficit hyperactivity disorder14. A recent study of 9-month-old Thai infants reported an association between prenatal exposure to CPF and a reduction in grating visual acuity (OR = 0.64, 95% CI -1.22 to 0.06)16.\n\nOne study has also linked prenatal exposure to CPF to lower IQ levels in children17. Similarly, a study among children aged 5.9–11.2 years linked prenatal exposure to CPF to brain anomalies25. This result has been replicated in a study of an adolescent group26. Neurotoxic deficits have also been associated with CPF exposure in high-exposure occupations27.\n\nFor groups of pesticides, most literature has focused on OPs due to their neurological toxic effects. These studies, usually using a cross-sectional or a cohort study design, have found positive correlations between OP metabolite in the mother’s urine and neurodevelopmental problems in the child7,8. Studies in the USA have reported prenatal exposure to OPs to increase the risk of abnormal reflexes in neonatal children (OR = 2.24, 95% CI 1.55-3.24)28, and ADHD in male children at age five years (β = 1.3; 95% CI 0.4-2.1)9. Living in close proximity to agricultural areas using OPs and other pesticides during pregnancy has also been related to ASD and developmental delay29. A study in Taiwan using a case-control study design reported a dose-response relationship between OP metabolites in child urea and ADHD among children aged 4–15 years11. Studies have also linked OP, carbamate, and pyrethroid pesticide exposure to lower IQ10,15,30. A cohort study in Thailand also found lower motor and cognitive performance (using Bayley Scales of Infant and Toddler Development III [Bayley III]) among five-month old infants prenatally exposed to OP31.\n\nFor other pesticides, data is limited. A study in Costa Rica reported a positive association of prenatal mancozeb exposure and lower social-emotional scores (β per 10-fold increase = -7.4 points [95% CI -15.2 to 0.4][measured by Bayley III]) in one-year-old infants32. This is consistent with the present study which also found an elevated risk of SDD among those exposed to mancozeb, with odds ratio of 1.87 (95% CI 0.59-5.93) for prenatal exposure, and OR of 3.97 (95% CI 0.60-26.38) for postnatal exposure (Table 3). A cohort study in Brittany, France, reported a negative association with neurocognitive development of 6-year-old children with prenatal exposure to pyrethroid33. A cohort study in 4-year-old children in Greece reported the association between prenatal exposure to the organochlorine compounds and neurodevelopmental effects34. A recent study in Indonesia reported a higher risk of small head circumference at birth to antenatal exposure to household non-OP pesticides (OR = -22.1 mm, 95% CI -36.5 to -7.6)35.\n\nOverall, the literature is limited and inconsistent regarding the critical duration of pesticide exposure developmental effects. In the current study, both prenatal and postnatal exposure was related to an increased risk of SDD (Table 3), yet only postnatal exposure was significant. However, most of the previous studies on the prenatal and postnatal effects of CPF on neurodevelopmental, reported a positive effect only with prenatal exposure13,16,17,25. Unfortunately, only a limited number of studies have examined the effects of child neurodevelopment from both prenatal and postnatal exposure. One study that did36 report a negative association of children’s developmental quotients (DQ) - a numerical indicator of a child’s growth to maturity across a range of psychosocial competencies - with prenatal exposure to OP but not with postnatal exposure. On the other hand, a cohort study in China found both prenatal and postnatal OP exposure increased the risk of developmental delay especially in the adaptive development (self-care skills) , among two-year old boys37. In a laboratory study, CPF caused neurobehavioral impairment to a zebrafish when the exposure occurred in either the fertilization stage or embryonic stage38.\n\nIn the current study, there were some limitations that need to be mentioned. First, there was a smaller number of participants who had used pesticides during pregnancy than expected, which limits the power of association between the variables. In addition, it is difficult to study the effect of low-level pesticide exposure on growth and development because the outcomes can be affected by several factors including biological factors (e.g. stunting, infections, anemia, IUGR, preterm birth, birth weight, sex of the child, gestational age at delivery), psychosocial factors (e.g. inadequate cognitive stimulation, exposure to violence, maternal depression, household dysfunction), and maternal sociodemographic factors (e.g. poverty, low education, young age, smoking, drinking alcohol)39. There may also have been a problem with recall bias during the interviews where participants may not have recalled or did not know the name of the pesticides they’d used in the past. However, if this did occur, it would have happened equally between groups. It was also very likely that study participants were exposed to pesticides in the environment, and this information bias could lower the strength of the reported association.\n\n\nConclusion\n\nThis case-control study found a negative association between chlorpyrifos and some other pesticide exposure during pregnancy and preschool child development. This effect was found in both prenatal and postnatal exposure. More research, using a larger sample size, is still needed to identify more individual pesticides which may impact prenatal and postnatal growth and development of children. This potential effect of pesticides on child neurodevelopment should receive more attention by researchers, and the public, especially those who plan to have families, should be informed.\n\n\nData availability\n\nFigshare: child developmental delay and pesticide, Thailand. https://doi.org/10.6084/m9.figshare.13238501\n\nThis project contains the following underlying data:\n\nChild developmental delay and pesticide-database.csv (Collected demographic and child development data)\n\nData dictionary-child development.docx (Word document containing dictionary for study dataset)\n\nFigshare: Questionnaire-child developmental delay and pesticide, https://doi.org/10.6084/m9.figshare.13238507.v2\n\nThis project contains the following extended data:\n\nQuestionnaire-child development and pesticide.docx (Study questionnaire in English)\n\nQuestionnaire pesticide and development-Thai.docx (Study questionnaire in Thai)\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\nFirst, we must thank the study participants for the useful information they provided. We would like to also thank the staff at the health promoting hospitals for their support and coordination. Deep gratitude goes to the village health volunteers for data collection. Finally, we’d like to thank Dr. Saroj sentayakarn for his advice and Mr. Kevin Mark Roebl for English language editing of the manuscript.\n\n\nReferences\n\nMcCoy DC, Peet ED, Ezzati M, et al.: Early Childhood Developmental Status in Low- and Middle-Income Countries: National, Regional, and Global Prevalence Estimates Using Predictive Modeling. Tumwine JK ed. PLoS Med. 2016; 13(6): e1002034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorrison J, Chunsuwan I, Bunnag P, et al.: Thailand’s national universal developmental screening programme for young children: Action research for improved follow-up. BMJ Glob Heal. 2018; 3(1): e000589. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalker SP, Wachs TD, Gardner JM, et al.: Child development: risk factors for adverse outcomes in developing countries. Lancet. 2007; 369(9556): 145–157. PubMed Abstract | Publisher Full Text\n\nJurewicz J, Polańska K, Hanke W: Exposure to widespread environmental toxicants and children’s cognitive development and behavioral problems. Int J Occup Med Environ Health. 2013; 26(2): 185–204. PubMed Abstract | Publisher Full Text\n\nVester A, Caudle WM: The synapse as a central target for neurodevelopmental susceptibility to pesticides. Toxics. 2016; 4(3): 18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoya J, Bearer CF, Etzel RA: Children’s Behavior and Physiology and How It Affects Exposure to Environmental Contaminants. Pediatrics. 2004; 113(4 Suppl): 996–1006. PubMed Abstract\n\nSapamrer R, Hongsibsong S: Effects of prenatal and postnatal exposure to organophosphate pesticides on child neurodevelopment in different age groups: a systematic review. Environ Sci Pollut Res Int. 2019; 26(18): 18267–18290. PubMed Abstract | Publisher Full Text\n\nLiu J, Schelar E: Pesticide exposure and child neurodevelopment: Summary and implications. Workplace Health Saf. 2012; 60(5): 235–242; quiz 243. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarks AR, Harley K, Bradman A, et al.: Organophosphate pesticide exposure and attention in young Mexican-American children: The CHAMACOS study. Environ Health Perspect. 2010; 118(12): 1768–1774. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRowe C, Gunier R, Bradman A, et al.: Residential proximity to organophosphate and carbamate pesticide use during pregnancy, poverty during childhood, and cognitive functioning in 10-year-old children. Environ Res. 2016; 150: 128–137. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYu CJ, Du JC, Chiou HC, et al.: Increased risk of attention-deficit/hyperactivity disorder associated with exposure to organophosphate pesticide in Taiwanese children. Andrology. 2016; 4(4): 695–705. PubMed Abstract | Publisher Full Text\n\nShelton JF, Geraghty EM, Tancredi DJ, et al.: Neurodevelopmental disorders and prenatal residential proximity to agricultural pesticides: The charge study. Environ Health Perspect. 2014; 122(10): 1103–1109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRauh VA, Garfinkel R, Perera FP, et al.: Impact of prenatal chlorpyrifos exposure on neurodevelopment in the first 3 years of life among inner-city children. Pediatrics. 2006; 118(6): e1845–59. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan Wendel de Joode B, Mora AM, Lindh CH, et al.: Pesticide exposure and neurodevelopment in children aged 6– 9 years from Talamanca, Costa Rica. Cortex. 2016; 85: 137–150. PubMed Abstract | Publisher Full Text\n\nWang N, Huang M, Guo X, et al.: Urinary metabolites of organophosphate and pyrethroid pesticides and neurobehavioral effects in Chinese children. Environ Sci Technol. 2016; 50(17): 9627–9635. PubMed Abstract | Publisher Full Text\n\nSilver MK, Shao J, Ji C, et al.: Prenatal organophosphate insecticide exposure and infant sensory function. Int J Hyg Environ Health. 2018; 221(3): 469–478. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBouchard MF, Chevrier J, Harley KG, et al.: Prenatal exposure to organophosphate pesticides and IQ in 7-year-old children. Environ Health Perspect. 2011; 119(8): 1189–1195. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSagiv SK, Harris MH, Gunier RB, et al.: Prenatal organophosphate pesticide exposure and traits related to autism spectrum disorders in a population living in proximity to agriculture. Environ Health Perspect. 2018; 126(4): 047012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEskenazi B, Marks AR, Bradman A, et al.: Organophosphate pesticide exposure and neurodevelopment in young Mexican-American children. Environ Health Perspect. 2007; 115(5): 792–798. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHorton MK, Kahn LG, Perera F, et al.: Does the home environment and the sex of the child modify the adverse effects of prenatal exposure to chlorpyrifos on child working memory? Neurotoxicol Teratol. 2012; 34(5): 534–541. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJuntarawijit C, Juntarawijit Y: Questionnaire-Child Developmental Delay and Pesticide. 2020. http://www.doi.org/10.6084/m9.figshare.13238507.v2\n\nJuntarawijit C, Juntarawijit Y: Child Developmental Delay and Pesticide Thailand. 2020. http://www.doi.org/10.6084/m9.figshare.13238501.v1\n\nEaton DL, Daroff RB, Autrup H, et al.: Review of the toxicology of chlorpyrifos with an emphasis on human exposure and neurodevelopment. Crit Rev Toxicol. 2008; 38(Suppl 2): 1–125. PubMed Abstract | Publisher Full Text\n\nPotera C: Newly discovered mechanism for cchlorpyrifos eeffects on neurodevelopment. Environ Health Perspect. 2012; 120(7): a270. Publisher Full Text\n\nRauh VA, Perera FP, Horton MK, et al.: Brain anomalies in children exposed prenatally to a common organophosphate pesticide. Proc Natl Acad Sci U S A. 2012; 109(20): 7871–7876. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSagiv SK, Bruno JL, Baker JM, et al.: Prenatal exposure to organophosphate pesticides and functional neuroimaging in adolescents living in proximity to pesticide application. Proc Natl Acad Sci U S A. 2019; 116(37): 18347–18356. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnger WK, Farahat FM, Lein PJ, et al.: Magnitude of behavioral deficits varies with job-related chlorpyrifos exposure levels among Egyptian pesticide workers. Neurotoxicology. 2020; 77: 216–230. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEngel SM, Berkowitz GS, Barr DB, et al.: Prenatal organophosphate metabolite and organochlorine levels and performance on the Brazelton Neonatal Behavioral Assessment Scale in a multiethnic pregnancy cohort. Am J Epidemiol. 2007; 165(12): 1397–1404. PubMed Abstract | Publisher Full Text\n\nShelton JF, Geraghty EM, Tancredi DJ, et al.: Neurodevelopmental disorders and prenatal residential proximity to agricultural pesticides: The charge study. Environ Health Perspect. 2014; 122(10): 1103–1109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGunier RB, Bradman A, Harley KG, et al.: Prenatal residential proximity to agricultural pesticide use and IQ in 7-year-old children. Environ Health Perspect. 2017; 125(5): 057002. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKongtip P, Techasaensiri B, Nankongnab N, et al.: The impact of prenatal organophosphate pesticide exposures on thai infant neurodevelopment. Int J Environ Res Public Health. 2017; 14(6): 570. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMora AM, Córdoba L, Cano JC, et al.: Prenatal mancozeb exposure, excess manganese, and neurodevelopment at 1 year of age in the infants’ environmental health (ISA) study. Environ Health Perspect. 2018; 126(5): 057007. PubMed Abstract | Publisher Full Text | Free Full Text\n\nViel JF, Warembourg C, Le Maner-Idrissi G, et al.: Pyrethroid insecticide exposure and cognitive developmental disabilities in children: The PELAGIE mother-child cohort. Environ Int. 2015; 82: 69–75. PubMed Abstract | Publisher Full Text\n\nKyriklaki A, Vafeiadi M, Kampouri M, et al.: Prenatal exposure to persistent organic pollutants in association with offspring neuropsychological development at 4 years of age:The Rhea mother-child cohort, Crete, Greece. Environ Int. 2016; 97: 204–211. PubMed Abstract | Publisher Full Text\n\nSoesanti F, Idris NS, Klipstein-Grobusch K, et al.: The effect of non-organophosphate household pesticides exposure during pregnancy on infants birth sizes and growth rate: A cohort study. BMC Pregnancy Childbirth. 2020; 20(1): 476. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang Y, Zhang Y, Ji L, et al.: Prenatal and postnatal exposure to organophosphate pesticides and childhood neurodevelopment in Shandong, China. Environ Int. 2017; 108: 119–126. PubMed Abstract | Publisher Full Text\n\nLiu P, Wu CH, Chang XL, et al.: Prenatal and postnatal exposure to organophosphate pesticides and child neurodevelopment in an agricultural area of Jiangsu province, China: a cohort study. Lancet. 2015; 386: S83. Publisher Full Text\n\nSledge D, Yen J, Morton T, et al.: Critical duration of exposure for developmental chlorpyrifos-induced neurobehavioral toxicity. Neurotoxicol Teratol. 2011; 33(6): 742–751. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcDonald S, Kehler H, Bayrampour H, et al.: Risk and protective factors in early child development: Results from the All Our Babies (AOB) pregnancy cohort. Res Dev Disabil. 2016; 58: 20–30. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "76367",
"date": "18 Jan 2021",
"name": "Zhijun Zhou",
"expertise": [
"Reviewer Expertise Children environmental health",
"toxicology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript reported the association between pesticide exposure of pregnant women and the suspected developmental delay of their children. It is interesting, but the quality of exposure assessment (description) is in question, only the questionnaire was used and there was obvious recall bias. How we can ensure the reality of pesticide exposure history? The authors should add more information on this point.\nBesides, several pesticide exposures were reported to have association with suspected developmental delay, what about the biological mechanism? Please add more literature on animal studies to support your results. Currently, only the similar studies were mentioned.\nFurthermore, the following minor comments should also be considered:\nThe description that “Three records were not included for analysis because important information such as gender and age, was missing” in the section of results (Page 4) can’t be understood, since you have data of all cases firstly, then select the reference.\n\nAccording to the description in the section of Sampling and sample size, all cases, including cases and controls, were from the database of children in the screening program. It is not case-control study, but cross-sectional study.\n\nAbout pesticide exposure history - is there data (records) of use of pesticides (types, amounts, use way, etc.) in these areas during the period when the mother were in pregnancy? It is important to use such data to confirm the answer of these mothers, specifically the use stage (pre-N, or post-N).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6327",
"date": "12 Feb 2021",
"name": "Chudchawal Juntarawijit",
"role": "Author Response",
"response": "Reviewer I 1. This manuscript reported the association between pesticide exposure of pregnant women and the suspected developmental delay of their children. It is interesting, but the quality of exposure assessment (description) is in question, only the questionnaire was used and there was obvious recall bias. How we can ensure the reality of pesticide exposure history? The authors should add more information on this point. The risk of health effects associated with long-term exposure to pesticides is difficult to assess in epidemiologic studies. Direct measurement of exposure is often not feasible in large studies. Also, measurement of a biomarker in blood or urine is costly and represent a short-term exposure. For long-term exposure, using a questionnaire collecting data on duration and intensity of pesticide use might be more appropriate. This practice was found in a large study like Agricultural Health Study in the United State1. It may inappropriate to discuss issue in the paper. Besides, several pesticide exposures were reported to have association with suspected developmental delay, what about the biological mechanism? Please add more literature on animal studies to support your results. Currently, only the similar studies were mentioned. Thanks for reminding the point. More information on biological mechanism has been added. 2. The description that “Three records were not included for analysis because important information such as gender and age, was missing” in the section of results (Page 4) can’t be understood, since you have data of all cases firstly, then select the reference. The information was missing during data entry. The problems occur with only a few cases thus it should not significantly affect the result. 3. According to the description in the section of Sampling and sample size, all cases, including cases and controls, were from the database of children in the screening program. It is not case-control study, but cross-sectional study. Yes, all cases were from the same database. However, the study designed is a case-control study because case and control groups were selected based on their disease status (developmental delay). Then, pesticide exposure data in the past of the two groups were collected. If it was a cross-sectional study, all children should have been randomly selected, regardless of their developmental status, and the data on either diseases or exposure should have been collected simultaneously. 4. About pesticide exposure history - is there data (records) of use of pesticides (types, amounts, use way, etc.) in these areas during the period when the mother were in pregnancy? It is important to use such data to confirm the answer of these mothers, specifically the use stage (pre-N, or post-N). We agree that the data will be useful. Unfortunately, there was no such data in the area, especially data of individual pesticides. As we mentioned before, using a questionnaire may be the best and the only way to collect data on long-term historical exposure of pesticides. References: [1] Coble J, Thomas KW, Hines CJ, Hoppin JA, Dosemeci M, Curwin B, Lubin JH, Freeman LEB, Blair A, Sandler DP, Alavanja MCR. An Updated Algorithm for Estimation of Pesticide Exposure Intensity in the Agricultural Health Study. International Journal of Environmental Research and Public Health. 2011; 8(12):4608-4622. https://doi.org/10.3390/ijerph8124608"
}
]
},
{
"id": "76458",
"date": "19 Jan 2021",
"name": "Ru-Lan Hsieh",
"expertise": [
"Reviewer Expertise Rehabilitation medicine",
"pediatric rehabilitation",
"developmental delay"
],
"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 aimed to evaluate the association between pesticide use by mothers during pregnancy and preschool children development using a case-control design in Thailand. They concluded that chlorpyrifos exposure during pregnancy was positively associated with developmental delay in children less than 5 years. I have some comments as listed below:\n\nThe cases of children included in the present study were “suspected developmental delay” rather than “confirmed developmental delay”. Therefore, it would severely affect the results.\n\nAs the authors pointed out, there were only 47 (10.4%) of case mothers and 46 (11.4%) of control mothers reported ever using any pesticide during pregnancy. The case numbers were too small for comparison.\n\nThere were only 11 (2.7%) case mothers and 13 (2.9%) of control mothers had ever exposed to chlorpyrifos. Therefore, using these very small numbers of exposure to chlorpyrifos to evaluate the risk of developmental delay of children is not adequate at all. The results would severely mislead the readers.\n\nThe age ranges of mothers were between 13-42 and 13-46 in the control group and case group, respectively. Please re-analyze the mother’s age by below 18 (or 20) vs. above 18 (or 20).\n\nThe only significant variable to developmental delay was the exposure to chlorpyrifos, and other variables were not statistically significantly associated with developmental delay. The authors calculated the crude odds ratios of chlorpyrifos ever exposure was 2.88, prenatal exposure was 2.34, and postnatal exposure was 4.18 as shown in Table 3. However, I found that it should be 1.10 in ever exposure, 1.02 in prenatal exposure, and 1.87 in postnatal exposure. Please recheck all variables’ odds ratios carefully.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "6328",
"date": "12 Feb 2021",
"name": "Chudchawal Juntarawijit",
"role": "Author Response",
"response": "Reviewer II This study aimed to evaluate the association between pesticide use by mothers during pregnancy and preschool children development using a case-control design in Thailand. They concluded that chlorpyrifos exposure during pregnancy was positively associated with developmental delay in children less than 5 years. I have some comments as listed below: 1. The cases of children included in the present study were “suspected developmental delay” rather than “confirmed developmental delay”. Therefore, it would severely affect the results. We agree with the reviewer that using confirm developmental delay may be the best outcome variable for studying conclusion. However, a number of children with developmental delay in the study area was so small, we have to rely on Suspected Developmental Delay (SDD). SDD is an important outcome variable and it has been used widely either in public health surveys for early identification of the prevalence rate, or to study risk factors. For example, a large study in 8 counties of rural China by Yang et al. (2019)1 published in BMC Pediatrics, use SDD variables to evaluate the effects of care quality and development of children aged 1-59 months. Another study by Valla and team (2015)2 also used SDD to study prevalence rates of developmental delay in Norwegian infants. 2. As the authors pointed out, there were only 47 (10.4%) of case mothers and 46 (11.4%) of control mothers reported ever using any pesticide during pregnancy. The case numbers were too small for comparison. Yes, we admitted that sample size is the study’s limitations. The number of mothers ever using pesticides is actually the exposure of interest. In this study, we collected data from about 800 participants, the minimum sample size required for this type of study, under the following assumption: 95% confident interval, power of detection = 80%, case to control = 1:1, odds ratio = 1.5, and control with exposure = 40% (as presented in the methods section). Unfortunately, only about ten percent of the mother had experience using pesticides. The problem was beyond our control, and with some other constraints, we have to report the result as such. We did not completely agree that the sample size was ‘too small’. The issue is rather subjective, and it should depend mainly on the purpose of the study, and the statistics used for the analysis. The problem of using a small sample size is the lack of power of detection and precision. As seen in the study results, OR and other statistical parameters will not be significant. A small sample size will not completely destroy the usefulness of the study if it was analyzed with proper statistics and clearly presented. According to the following article (DOI: 10.22004/ag.econ.103771), sample size should not be a main concern for logistic regression. Thus, we believed the result is good enough to be presented to research community. As said by P. Mean. “A small sample size does not mean that your results are \"wrong\". It means that the data is consistent with a wide range of possible hypotheses.” (http://www.pmean.com/11/WideInterval.html) 3. There were only 11 (2.7%) case mothers and 13 (2.9%) of control mothers had ever exposed to chlorpyrifos. Therefore, using these very small numbers of exposure to chlorpyrifos to evaluate the risk of developmental delay of children is not adequate at all. The results would severely mislead the readers. As mentioned before, the minimum sample size depends on the kind of statistic used for data analysis. If the sample size is too small, the OR obtained was not significant, as seen in many individual pesticides. This confirmed that the study results will not mislead the readers. We do the best to present study results. Data was analyzed with appropriate statistic, and the results were widely discussed. Therefore, readers can justify by themselves the reliability of the results. It is not uncommon for studies to rely on small number of outcomes or exposure of interest, especially for rare diseases, e.g. developmental delay. For example, a study published in the Environmental Health Perspectives by Lui, et al. (2016), also included only 310 mother-infant pairs when studying the effects of organophosphate exposure and developmentally delayed. In this study, it reported OR between 9.75 (95% CI: 1.28, 73.98, p = 0.028) and 12.00 (95% CI: 1.23, 117.37, p = 0.033), notice a wide confidence interval. This conclusion came from the data nearly all with <10 number of cases in each group of exposure of interest (please see the manuscript and its supplemental materials https://doi.org/10.1289/EHP196). The following are a list of some other studies that have a small sample size but yet provide useful information: Geetha, B., Sukumar, C., Dhivyadeepa, E. et al. Autism in India: a case–control study to understand the association between socio-economic and environmental risk factors. Acta Neurol Belg 119, 393–401 (2019). https://doi.org/10.1007/s13760-018-01057-4 Rocha SGMO, Correia LL, Da Cunha AJLA, et al. Zika Virus Infection and Microcephaly: A Case-Control Study in Brazil. Ann Glob Health. 2019;85(1):116. Published 2019 Aug 28. doi:10.5334/aogh.2394 El-Baz F., Ismael, NA., and El-Din, SMN. (2011). Risk factors for autism: An Egyptian study. Egyptian Journal of Medical Human Genetics. 12(1). DOI: 10.1016/j.ejmhg.2011.02.011 4. The age ranges of mothers were between 13-42 and 13-46 in the control group and case group, respectively. Please re-analyze the mother’s age by below 18 (or 20) vs. above 18 (or 20). Thank you for suggestions, it is a good point. At first, we considered the best age to have a healthy baby is between 25 and 35 years of age, and thus using 25 as a cut point. However, actually, there is no scientific data to support the idea. So, we agree and decide to recategorize the age group to be <20, 20-25, 26-30, 31-35, and ≥36 years, as suggested. 5. The only significant variable to developmental delay was the exposure to chlorpyrifos, and other variables were not statistically significantly associated with developmental delay. The authors calculated the crude odds ratios of chlorpyrifos ever exposure was 2.88, prenatal exposure was 2.34, and postnatal exposure was 4.18 as shown in Table 3. However, I found that it should be 1.10 in ever exposure, 1.02 in prenatal exposure, and 1.87 in postnatal exposure. Please recheck all variables’ odds ratios carefully. Thank you so much for your effort to identify the problem. All the data was checked and the error was found only with the crude OR. Data in Table 2 and Table 3 has been revised. Sorry for the mistake. References: Yang, C., Liu, X., Yang, Y. et al. Quality of care and suspected developmental delay among children aged 1–59 months: a cross-sectional study in 8 counties of rural China. BMC Pediatr 19, 41 (2019). https://doi.org/10.1186/s12887-019-1406-x Valla, L., Wentzel-Larsen, T., Hofoss, D. et al. Prevalence of suspected developmental delays in early infancy: results from a regional population-based longitudinal study. BMC Pediatr 15, 215 (2015). https://doi.org/10.1186/s12887-015-0528-z de Moura DR, Costa JC, Santos IS, Barros AJD, Matijasevich A, Halpern R, Dumith S, Karam S, Barros FC. Risk factors for suspected developmental delay at age 2 years in a Brazilian birth cohort. Paediatric and Perinatal Epidemiology 2010; 24: 211–221."
}
]
}
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https://f1000research.com/articles/9-1501
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https://f1000research.com/articles/10-237/v1
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24 Mar 21
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{
"type": "Brief Report",
"title": "Contextualizing adolescents’ self-awareness of problematic mobile phone use: a preliminary study",
"authors": [
"Andrew Karnaze",
"Katherine Grevelding",
"Traci Marquis-Eydman",
"Douglas McHugh",
"Andrew Karnaze",
"Katherine Grevelding",
"Traci Marquis-Eydman"
],
"abstract": "Adolescents engage cognitively, emotionally, and behaviorally with smartphones. Growing evidence suggests they struggle to interact with them in moderation, which has been framed in relation to behavioral addiction as problematic mobile phone use. This study contextualized 13-15 year-old adolescents’ self-awareness of problematic mobile phone use. Focus groups were conducted with 11 adolescents who assessed themselves using the problematic use of mobile phones scale. The authors used interpretative phenomenological epistemology as a guiding framework. Audio recordings were analyzed qualitatively using a constant comparison approach. Students agreed or strongly agreed with multiple dimensions of the problematic mobile phone use construct. Four major themes emerged in relation to circumstances, factors, processes, constraints, and opportunities: drivers of excessive smartphone use, with family or friends, barriers to healthier smartphone use, and nighttime habits. Adolescents’ assessment of perceived proper versus problematic mobile phone can inform hypotheses targeted at improving overall wellness and developing healthy habits in adolescence that carry over into young adulthood and beyond.",
"keywords": [
"Public Health",
"Health Behavior",
"Adolescents",
"Problematic Smartphone Use",
"Mobile Phones",
"Cell Phones",
"Social Media",
"Qualitative Methods"
],
"content": "Introduction\n\nFollowing the release of the iPhone in 2007, estimated smartphone ownership in the United States has steadily increased to 81% in 2019 and 96% for 18-29 year-olds (www.pewresearch.org/internet/fact-sheet/mobile/#mobile-phone-ownership-over-time). Mobile phone dependency (a.k.a. problematic mobile phone use) has grown prevalent in keeping with this surge1–2, and has been framed in relation to behavioral addiction.3 For the purposes of this study, we used the definition “problematic mobile phone use is a habitual drive or compulsion to continue to repeat a human-technology interaction despite its negative impact on one’s well-being.”3 Among the general population, determinants and effects of problematic phone use have been studied, screening tools developed, and prevalence of mobile dependency measured.2,4–5 While the detrimental effects of problematic mobile phone use on sleep, stress, anxiety, and depression can occur at various ages2, adolescents comprise a notably vulnerable age group. This relates to decreased levels of self-control and low resistance to peer pressure. Steinberg and Monahan (2007) noted “susceptibility to peer pressure in adolescence follows an inverted U-shaped curve, increasing during early adolescence, peaking around age 14, and declining thereafter.”6\n\nWe searched the PubMed database using the query “((Smartphone OR mobile phone OR cell phone) AND (dependency OR dependence OR problematic)) AND (adolescent OR adolescence OR teenage OR youth)” and found with regard to adolescents that studies are limited to reports of prevalence and associations with adverse wellness. More specifically: cross-sectional studies have measured prevalence of mobile phone dependency1,7–8; mobile phone dependence correlated positively with unintentional injuries (odds ratio = 1.452)9; depressive symptoms, higher interpersonal anxiety, and lower self-esteem have been correlated with problematic cell phone use10–12; and Walsh et al (2008) held qualitative focus groups with Australian 16-24 year-olds and found extreme attachment to phones with symptoms of behavioral addiction evident in participants' descriptions.13 Adolescent-specific investigations are limited to mobile phone dependency prevalence1,7; and to correlation with depression, interpersonal anxiety, lower self-esteem, and symptoms of behavioral addiction evident.10,13 Adolescents are knowledgeable agents capable of representing and articulating the different aspects of how they interact with smartphones. Yet little work has been devoted to exploring how adolescents experience mobile phone dependency and what meanings and interpretations they attach to it.\n\nThis preliminary study sought to contextualize 13-15 year-old adolescents’ self-awareness of problematic mobile phone use by exploring interconnections between mobile phone dependency phenomena, the context in which they occur (i.e., circumstances, factors, processes, constraints, or opportunities), and participants’ subjective experiences and interpretations. We believe this to be a crucial step towards generating hypotheses targeted at improving overall wellness and developing healthy habits in adolescence that can carry over into young adulthood and beyond.\n\n\nMethods\n\nQuinnipiac University’s Institutional Review Board approved this study (protocol #01018; 9 February 2018).\n\nEleven 13-15 year-old adolescents were recruited by convenience sampling to participate: six from Morgan High School (School #1; five females, one male) in Clinton, CT, USA and five from Dodd Middle School (School #2; three females, two male) in Cheshire, CT, USA. Email invitations were sent to eligible participants by School Guidance Counsellors. Inclusion criteria: age 13-15; uses a smartphone; speaks English; and parental consent was obtained. No participants dropped out of the study.\n\nThis study was conducted through a constructivist lens using an interpretative phenomenological epistemology.14 We chose a phenomenological approach to better understand participants’ interpretation of the contexts in which they interact with their smartphones. Phenomenology may help us learn from others’ experiences by describing what was experienced and how it was experienced.14 We selected a constructivist lens to align with our phenomenological methodology based on the assumption that internal and external constructs influence an individuals’ knowledge and experience.15\n\nIn order to establish evidence of mobile phone dependency, participants assessed themselves using hardcopies of the problematic use of mobile phones (PUMP) survey22. Merlo et al. (2013) developed this 20-item instrument as a self-reported measure of the 10-dimension construct problematic mobile phone use, based upon the diagnostic and statistical manual of mental disorders 4th edition (DSM-IV) criteria for substance use disorders4. They published validity evidence supporting PUMP’s use with English speakers; namely it demonstrated: 1) a single-factor structure via principal components analysis; 2) excellent internal consistency (Cronbach α = 0.94); 3) convergent validity when compared to the existing cellular phone dependence tendency questionnaire, cell phone usage data (duration and frequency measurements), and self-perceptions of addiction; and 4) discriminant validity when compared to length of time a phone has been owned and money spent monthly on mobile phone minutes4.\n\nAuthor K.G., facilitated the focus group sessions; she is an assistant professor with an educational doctorate (EdD) and expertise in qualitative research methodology and focus group facilitation. K.G. had no established relationship with any of the participants prior to study commencement. Participants knew about K.G.’s qualifications and the general purpose of the research study from the informed consent documents. Two 90-minute focus groups were held, one for the Clinton High School cohort on June 18, 2018 and one for the Dodd Middle School cohort on July 12, 2018, in a reservable meeting room of the Henry Carter Hull Library in Clinton, CT. Author A.K. was present as a non-participatory observer. They began with 60 minutes of facilitated, semi-structured discussion, then participants watched an eight-minute video clip on social media app development before discussion resumed (CBSNews.com. Brain Hacking. www.youtube.com/watch?v=awAMTQZmvPE&t=1s time: 0-5:30, 8:45-11:30). K.G. wrote field notes after each focus group to reflect on the participants’ observations, K.G.’s growing insights, and how her facilitator-outsider role informed the research process.16 Audio recordings were transcribed verbatim then subject to de-identified inductive qualitative analysis using a constant comparison approach.17 De-identified transcripts were read, then hand-coded by assigning first-stage preliminary codes. A.K. and D.M. then met together to group similar codes into categories and identify major concepts while referencing K.G.’s memos and field notes. Iteratively, major concepts were further organized and expressed as themes and subthemes.\n\n\nResults\n\nOne or more participants agreed or strongly agreed with items representing nine of the ten dimensions of the PUMP construct. Longer than intended, great deal of time spent, activities given up or reduced, and use despite physical or psychological problems were most frequently agreed with; use in physically hazardous situations, withdrawal, and craving least frequently (Figure 1).\n\nParticipants possessed a notable awareness of problematic smartphone use in themselves and their peers. Four main themes with associated subthemes emerged: drivers of excessive smartphone use, with family or friends, barriers to healthier smartphone use, and nighttime habits; Illustrative quotes are identified by anonymous participant codes. All perspectives were shared by both female and male participants alike with the exception of the sleepover comments for theme 2A, which were limited to female participants.\n\nThere was consensus among participants that a few social media apps (e.g., Instagram, Snapchat) and texting were among the predominant drivers of excessive smartphone use. They or others had observed they were spending a great deal of time, or longer than intended, interacting with their smartphone, which kept them from other important work (e.g., schoolwork). Participants interacted and re-interacted with these apps habitually, even when there was no longer unknown, new, or updated content. Notifications (i.e., visual, audible, or tactile alerts) bolstered excessive use by prompting phone-checking and re-prioritization of current activities. Delaying or avoiding unpleasant tasks or managing stress were also connected with extended phone use.\n\nTheme 1A: A few smartphone apps take up the majority of adolescents’ time\n\n“I’ll have lots of apps on my phone, but really it’s two or three that I’ll actually be using. And those apps alone are just driving the time up … To just be scrolling through Instagram, to just be on, just texting non-stop. And that’s not really a good habit.” (School #1 student C, female, 15)\n\n“Specifically with Snapchat, I remember deleting it for an amount of time and I felt really, I was never on my phone and it was all because of this one app.” (School #2 student B, female, 13)\n\nTheme 1B: Reiterative use of apps despite an awareness of the lack of fresh content\n\n“I don’t even have a reason to go on my phone. I just go on it, even if nothing’s new and it’s like five seconds later, I just switch between [social media] apps and even if it’s completely the same as I saw five seconds ago.” (School #2 student C, female, 15)\n\n“I’m aware most of the time I’m not gaining anything from using it.” (School #2 student A, male 15).\n\nTheme 1C: Notifications lead inevitably to checking of apps\n\n“I check my phone at least 50 times a day, at least … whenever I hear a ring on Snapchat or whatever, I’m like “Ooh, who’s texting me? It triggers me and I’m like “who’s texting me?, and then I have to check, right?” (School #2 student E, male 15)\n\n“I'll get 30 Snapchat in an hour or something … so I just turn the notifications off so I don't have that tendency to just keep checking and re-checking every time I see someone has sent me something.” (School #2 student D, female 13)\n\n“A lot of times I'll get notifications … then I just start thinking, ‘Oh, what if something is really important happened? I really need to know. Or, what if something changed in my schedule.’ If I don't look right now then that could impact my day.” (School #1 student D, female, 13)\n\nTheme 1D: Phone interactions facilitate delaying or managing something unpleasant\n\n“Phone use is clearly a procrastination/dealing with stress tool.” (School #2 student A, male 15)\n\n“When there's a big test the next day and you come home from school … you don't wanna work at school and then come straight home and start working again. It's not what I do, at least. I take a little break, but sometimes I'm on my phone for a long period of time watching TV or on the internet for a long period of time. I'm procrastinating, procrastinating, procrastinating, making myself more stressed for this test that I still have to study for.” (School #2 student B, female, 13)\n\nParticipants were prepared to forego access to their phones in favor of spending quality time with close family, but not to de-prioritize phone interactions when gathered with close friends. Perceived hypocrisy with regard to family members’ phone use was also noted.\n\nTheme 2A: Phone interactions prioritized over friend interactions\n\n“I’ll be at a sleepover with one of my friends or like a group sleepover and you can look around the room and every single person’s on their phone and you’re all together. Most of the time, it's all the people that you talk to, and everyone's on their phone. Like, who are you talking to? Because all your friends are here. So, I don't know what's going on but that's causing everybody not to really talk and it's all just on your phone. People are just scrolling through Instagram or just going through random stuff, even though nobody has posted anything.” (School #2 student C, female, 15)\n\nI have noticed that sometimes I'll be with friends and I'll be literally Snapchatting them as they sit right next to me. And it makes no sense, but it's just a habit. I don't even know why, it just happens. (School #2 student B, female, 13)\n\nWalking around the school, people aren't even looking up from their phones to say hi to their friends. Or during lunch where it's quality time that you're supposed to [spend] talking to your friends, they use that time to go on their phones or just not talk to anyone next to them and be on Snapchat or Instagram. (School #2 student C, female, 15)\n\nTheme 2B: Impacts quality time with family\n\n“I'm not allowed to use my phone when I'm on family vacations or spending time with my grandparents because my mom wants me to enjoy every moment that I have with them. It feels good. I just feel happier that I'm with my family, I'm not worried about who's texting me or what somebody's doing or anything like that.” (School #1 student F, male, 15)\n\n“My grandparents are getting old and they have Parkinson's and they're kind of deteriorating. And I'm on my phone and I feel so guilty because I'm like I only have 'em for a couple more years, so honestly, my texting other people can wait and stuff like that.” (School #2 student E, male, 15)\n\nTheme 2C: Poor role-modeling\n\n“My mom always claims that I’m addicted. But then, so when I get off my phone, I always find that she’s on her phone or my sister’s on her phone … it might seem that it's just the kids, but it's also the adults at times, too.” (School #2 student D, female, 13)\n\nWhen asked to identify obstacles that prevented them from reducing smartphone use, participants noted peer pressure, social media etiquette, and competitive approval seeking.\n\nTheme 3A: Peer pressure\n\n“It’s actually making people feel pressured … like you have to reply back. Gotta keep the [Snapchat] streak, gotta keep the friendship alive …” (School #2 student D, female, 13)\n\n“There's so much pressure to be on all the social media's. To be checking on people. If someone posts something, then everyone will start texting, ‘Look what this person posted.’ People saying, ‘You've got to join this app, you've got to join this app, you've got to get the newest phone.’ It's just so much pressure, and sometimes you just don't want to do that.” (School #1 student C, female, 15)\n\nTheme 3B: Social media etiquette\n\n“I definitely think there’s an etiquette when it comes to social media, especially Instagram. A lot of the girls I know, if your best friend posts, you have to comment something on it.” (School #1 student D, female, 13)\n\n“I feel like there's kind of these rules. Just hidden little things that everyone needs to know about. Whoever gets the most likes, that's a big thing. ‘Oh, 200, 300 people liked this’. All the rules are different for every grade. No one really knows who started the rules, but one person would say something, and it'll get passed on. And pretty soon the whole grade will be following one rule or multiple rules about social media. And there's no real clear, this person spread it. It's just kind of just something that's taking form, and everyone should know, and everyone needs to adapt to essentially.” (School #1 student C, female, 15)\n\nTheme 3C: Competition and approval seeking\n\n“Things become a competition, so when you’re on your phone you see someone post something and think, “Wow, that’s really cool, I have to do that, because that would make me so cool.” So then, everyone just keeps posting [their own version]. Trying to have the best post, and everyone like it. See who can get the most likes. It's just a big competition that it's not really a healthy environment to be in.” (School #1 student B, female, 15)\n\nBedtime routines in relation to continued smartphone access arose in relation to sleep hygiene, wellness, and school.\n\nTheme 4A: Sleep Hygiene and Putting Phones Away\n\n“Going to sleep... the phone makes that harder, definitely … just talking to people especially on Snapchat, that can just extend your time before you go to sleep by a lot without you realizing it.” (School #2 student A, male, 15)\n\n“I've kind of gotten into the habit of I go to sleep at 9:00pm every night because I've been on my phone all day and I put it far away from my bed where I don't have the energy to get up and grab it. So, I put it there and it feels actually nice when I put it down because I feel like I'm just disconnected and I can be soothing and I don't have to worry about people texting me all the time. So, it feels pretty good.” (School #2 student C, female, 15)\n\n“There's other people at my school whose parents don't take away their phones at 10:00pm, so they'll be up to 2:00am or sometimes there's kids who are up all night, just on their phone for no reason. And that's super-unhealthy for their physical state when they're super-tired during school, they're not paying attention, they're not into it. They're sitting there falling asleep in school and they look terrible. They shouldn't be up all night on their phones. It's just unhealthy for them.” (School #2 student B, female, 13)\n\n\nDiscussion\n\nNine and six of the eleven participants agreed or strongly agreed with items representing the PUMP dimensions of longer than intended and great deal of time spent, respectively. We found that these phenomena occurred for our 13-15 year-olds when they were interacting with only a select number of social media or texting apps, and this was facilitated by habitual processes of evaluating and responding to notifications or checking and re-checking app content. This infers it is not the phone that drives problematic behavior, it is the apps. A significant reason that adolescents are attracted to social media apps is that they increase a sense of social inclusion and connectedness.8 Social media tech companies have capitalized on this for the sake of monetization. They compete with one another for finite attention in a zero-sum game. One example of this is Snapchat, an app where users snap each other (i.e., send pictures or videos with overlying captions, emojis, or animations); as of March 2020, Snapchat had 229 million daily active users and 4 billion+ snaps are sent each day (Snap Inc. First Quarter 2020 Financial Results https://investor.snap.com/news-releases/2020/04-21-2020-210949737). A design feature called Snapstreak involves two users seeing how many days in a row they can maintain snapping each other. Snapstreaks are considered an indicator of success and are viewed by adolescents as proof of friendship (Lorenz T. 17 teens take us inside the world of Snapchat streaks, where friendships live or die. Mic. https://www.mic.com/articles/173998/17-teens-take-us-inside-the-world-of-snapchat-streaks-where-friendships-live-or-die). Adolescents are often sensitive and acutely aware of their own, and peers’, social dynamics; therefore, having tangible evidence of committed friendships that endure over time can be a meaningful source of acceptance and recognition. One of our participants shared, “I'll get 30 Snapchat in an hour or something”. Adolescents can be devasted if months- or year-long snapstreaks lapse that they have poured an immoderate amount of time, energy, and self-validation into. Tristan Harris has stated, “Snapstreak is driving some teenagers nuts—to the point that before going on vacation, they give friends their log-in information and beg them to snap in their stead” (Harris T. What’s Now San Francisco with Tristan Harris. https://youtu.be/YQh2FQ7MZdA). Harris refers to the persuasive tactics behind Snapstreaks as hijacking techniques intended to maximize viewership and consequently advertisement revenue. In addition to these conditions and processes, peer pressure, emergent social media etiquette, and competition for approval were factors that also fed into and shaped the relevant context here. These represent reinforcers; an operant conditioning term referring to anything that strengthens or increases a behavior. Our participants recognized the pressure to conform and do what their peers are doing to be powerful and hard to resist. This manifested in the form of coercion to maintain Snapstreaks and have an active presence with multiple prevailing social media apps. Social media etiquette, in setting conventions and expectations for behavior, connects to adolescents’ group identity. This reinforcer increased app engagement by threatening a person’s sense of belonging and how they feel about themselves in relation to their peer group. In this sense, creating and posting a distinct version of a notable social media post and competing with peers for ‘likes’ is normalized and offers raised perceived social status as a reward.\n\nAlmost half of the participants agreed or strongly agreed with items representing the PUMP dimensions of activities given up or reduced and use despite physical or psychological problems. With regard to these phenomena, adolescents’ experiences were shaped by both constraints and opportunities. Problematic use of smartphones was limited when some participants were gathered socially with close family; they acceded to restrictions placed on their phone access. In contrast, when gathered for social activities with close friends, phone interactions were prioritized and quality time forfeited. Participants could not fully rationalize this behavior. Physical restrictions on the proximity of smartphones to adolescents’ beds at night was another relevant constraint that directly impacted sleep hygiene, wellness, and next day preparedness for education. Likewise, Smetaniuk (2014) studied 301 undergraduates and found that more than 20% deprived themselves of sleep due to late-night phone use.5 Smartphone interactions provided adolescents with opportunities to delay or avoid something unpleasant (e.g., putting off studying for a test) or to manage stress. One of our participants noted, “You don't wanna work at school and then come straight home and start working again … I take a little break, but sometimes I'm on my phone for a long period of time … . I'm procrastinating, procrastinating, procrastinating, making myself more stressed for this test that I still have to study for.” This is consistent with the understanding that we mis-regulate ourselves by believing task avoidance will make us feel better.18 By engaging with their smartphones as a coping mechanism, adolescents choose to focus on feeling good in the moment, in the now.\n\nImplications for Research and Practice\n\nThe 21st century has seen the convergence of widely accessible software apps, participatory media, and internet connectivity such that virtual learning and online coaching are no longer uncommon. Having reflected on our findings, we suggest that future studies explore the effectiveness of app-based digital coaching and management techniques to scaffold adjustments to adolescents’ habits in favor of a healthy phone-life balance. For example, Moment (Moment Health Inc., Burlingame CA) offers features suited to the contexts described here including goal-setting and guided coaching to: track phone and app usage, establish phone-free times with friends and family, stop sleeping with your phone, reduce distractions, role-model accountability, and stop aimless browsing. This could affect a novel approach to reducing mobile phone use that would place some of the impetus for change upon the adolescent and facilitate conversations between teens, parents, and care providers.\n\nLimitations\n\nThis preliminary study was limited in that it involved only two adolescent cohorts from one geographical region of the United States. A minimum sample size of twelve participants is recommended for qualitative studies to reach data saturation (i.e., the point where redundancy signals to researchers that data collection may cease).19–21 Given this, our sample of eleven participants isn’t quite sufficient for us to assert that our qualitative data achieved thematic saturation. The timeline of recruitment, data collection, and data analysis for this study necessarily followed the availability of the first author A.K. while he was in medical school. The authors had intended to recruit a third group of adolescents in 2020 to increase the participant number above twelve but the SARS-CoV-2 coronavirus pandemic prevented this.\n\nIn addition, no cut-point(s) for the PUMP scale have been established, preventing us from making more concrete judgments about the problematic mobile phone use construct with regard to our participants.\n\n\nConclusions\n\nSmartphones have ensconced themselves into the everyday lives of consumers around the globe. The prevalence of problematic phone use amongst adolescents and its connection with adverse wellness is a growing public health concern because harmful behaviors established in childhood can shape one’s subsequent life course. Context is important for most phenomena of health care and health. This preliminary study supplies a contextualized glimpse into the adolescent assessment of perceived proper versus problematic smartphone use, potentially allowing parents, educators, and clinicians to reframe their approach to this critically important topic with the adolescents themselves.\n\n\nEthics statement\n\nThis study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Human Experimentation Committee/Institutional Review Board of Quinnipiac University (#01018; 9 February 2018).\n\n\nConsent statement\n\nWritten informed consent for publication of the participants’ details was obtained from the participants and parents/guardian/relative of the participant.\n\n\nData availability statement\n\nThe Quinnipiac University Institutional Review Board (IRB) required that the audio recordings of our focus groups not be made publicly available because 1) the participants were minors (adolescents 13-15 years old) and may accidentally use their real names rather than their assigned anonymous designations; e.g., “participant A” or “participant C” … etc and 2) that our small sample size increased the risk of them being identified if their voices were to be heard in conjunction with the names and locations of their Schools and dates of the study being publicly available. This requirement shaped our informed consent documents which stated that the original audio recording would not be made publicly available, but de-identified transcripts of the focus group sessions would be available upon request of the corresponding author/principle investigator.\n\nDue to the age of the participants in this study, their parents/guardians did not agree for the original audio files to be shared publicly, so these data are not available to be shared. The de-identified focus group transcript data that support the findings of this study are available from the corresponding author, DM, upon request. Readers may apply for access to the de-identified transcripts by emailing the corresponding author at Douglas.McHugh@quinnipiac.edu.\n\nRestrictions apply to the availability of these transcript data; disqualifying criteria for access consist of the following: data will not be available to any person under the age of 18 years old; and data will not be available to any person who currently is (or formerly was) a student, teacher, or employee of the schools from which participants in this study were recruited.\n\nZenodo: Contextualizing adolescents' self-awareness of problematic mobile phone use: a preliminary study - PUMP Survey and PUMP Raw Data. https://doi.org/10.5281/zenodo.457101322.\n\nThis project contains the following underlying data:\n\n• Dodd PUMP Survey Raw Data.pdf\n\n• Morgan PUMP Survey Raw Data.pdf\n\nZenodo: Contextualizing adolescents' self-awareness of problematic mobile phone use: a preliminary study - PUMP Survey and PUMP Raw Data. https://doi.org/10.5281/zenodo.457101322.\n\nThis project contains the following extended data:\n\n• Karnaze PUMP Survey.docx\n\nCOREQ checklist for “Contextualizing adolescents’ self-awareness of problematic mobile phone use: a preliminary study”. https://doi.org/10.3886/E131701V223.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International (CC-BY 4.0) License.",
"appendix": "References\n\nNikhita CS, Jadhav PR, Ajinkya SA: Prevalence of mobile phone dependence in secondary school adolescents. J Clin Diagn Res. 2015; 9: VC06–VC09. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDe-Sola Gutiérrez J, Rodríguez de Fonseca F, Rubio G: Cell-phone addiction: A review. Front Psychiatry. 2016; 7: 175PubMed Abstract | Publisher Full Text | Free Full Text\n\nGriffiths MD: Does Internet and computer “addiction” exist? Some case study evidence. CyberPsychologyBehavior. 2000; 3: 211–218. Publisher Full Text\n\nMerlo LJ, Stone AM, Bibbey A: Measuring problematic mobile phone use: Development and preliminary psychometric properties of the PUMP scale. J Addict. 2013: 912807–7. Publisher Full Text\n\nSmetaniuk P: A preliminary investigation into the prevalence and prediction of problematic cell phone use. J Behav Addict. 2014; 3: 41–53. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSteinberg L, Monahan KC: Age differences in resistance to peer influence. Dev Psychol. 2007; 43: 1531–1543. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCabré-Riera A, Torrent M, Donaire-Gonzalez D, et al.: Telecommunication devices use, screen time and sleep in adolescents. Environ Res. 2019; 171: 341–347. PubMed Abstract | Publisher Full Text\n\nJamir L, Duggal M, Nehra R, et al.: Epidemiology of technology addiction among school students in rural India. Asian J Psychiatr. 2019; 40: 30–38. PubMed Abstract | Publisher Full Text\n\nZhang SC, Yang R, Li DL, et al.: Zhonghua Liu Xing Bing Xue Za Zhi. 2018; 39(12): 1549–1554. Publisher Full Text\n\nYang R, Li DL, Wan YH, et al.: Association of the Health Literacy and the Incidence of Injuries Among Chinese Middle School Students in Five Provinces. Zhonghua Yu Fang Yi Xue Za Zhi. 2019; 53: 279–283. PubMed Abstract | Publisher Full Text .\n\nHa JH, Chin B, Park DH, et al.: Characteristics of Excessive Cellular Phone Use in Korean Adolescents. CyberPsychologyBehavior. 2008; 11(6): 783–784. PubMed Abstract | Publisher Full Text\n\nOh J, Depressive Symptoms AJ, Aggression E, et al.: Mobile Phone Dependency Among Adolescents with Allergic Diseases in South Korea. J Pediatr Nurs. 2019; 47: e24–e29. PubMed Abstract | Publisher Full Text .\n\nWalsh SP, White KM, Young RM: Over-connected? A qualitative exploration of the relationship between Australian youth and their mobile phones. J Adolesc. 2008; 31: 77–92. PubMed Abstract | Publisher Full Text\n\nNeubauer BE, Witkop CT, Varpio L: How phenomenology can help us learn from the experiences of others. Perspect Med Educ. 2019; 8(2): 90–97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO’Brien BC, Harris IB, Beckman TJ, et al.: Standards for Reporting Qualitative Research: A Synthesis of Recommendations. Acad Med. 2014; 89(9): 1245–1251. PubMed Abstract | Publisher Full Text\n\nDwyer SC, Buckle JL: The Space Between: On Being an Insider-Outsider in Qualitative Research. I J Qualitative Methods. 2009; 8(1): 54–63. Publisher Full Text\n\nButler-Kisber L: Constant comparison inquiry. In: Qualitative Inquiry. Butler-Kisber L, Ed.;Lon-don, UK:SAGE Publications Ltd;2018; pp. 41–59.\n\nSirois F, Pychyl T: Procrastination and the Priority of Short-Term Mood Regulation: Consequences for Future Self. Soc Personal Psychol Comp. 2013; 7: 115–127. Publisher Full Text\n\nGuest G, Bunce A, Johnson L: How many interviews are enough? An experiment with data saturation and variability. Field Methods. 2006; 18(1): 59–82. Publisher Full Text\n\nBraun V, Clarke V: (Mis) conceptualising themes, thematic analysis, and other problems with Fugard and Potts’ (2015) sample-size tool for thematic analysis. Int J Soc Res Methodol. 2016; 19(6): 739–43. Publisher Full Text\n\nFugard AJ, Potts HW: Supporting thinking on sample sizes for thematic analyses: a quantitative tool. Int J Soc Res Methodol. 2015; 18(6): 669–84. Publisher Full Text\n\nKarnaze A, Grevelding K, Marquis-Eydman T, et al.: Contextualizing adolescents' self-awareness of problematic mobile phone use: a preliminary study - PUMP Survey and PUMP Raw Data [Data set]. Zenodo. 2021. Publisher Full Text\n\nMcHugh D: COREQ checklist: Contextualizing adolescents’ self-awareness of problematic mobile phone use: a preliminary study. Ann Arbor, MI: Inter-university Consortium for Political and Social Research [distributor] 2021-02-04. Publisher Full Text"
}
|
[
{
"id": "82756",
"date": "26 Apr 2021",
"name": "Folashade Tawakalitu Alloh",
"expertise": [
"Reviewer Expertise Mental health",
"qualitative research",
"quantitative research",
"minority health",
"health inequality."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 explored the experiences of adolescence in managing smartphone use. This is an interesting and valuable research area in the context of the pandemic and mental health impact on adolescents. Qualitative data collection was gathered from adolescents using interpretive phenomenology to guide the research process.\n\nIntroduction A justification of why the study was implemented among students in the chosen schools can be helpful for readers. The authors mentioned reviewing the literature and the search terms used but has not clearly presented the outcome of the review or how this contributed to the study design.\n\nMethod What is the impact of watching the Youtube clip before discussion with participants? Authors did not clarify why this is needed and how it contributed to responses from participants. Developing themes, how is the data analysis phase influenced by phenomenology approach adopted for the study, this needs to be further discussed; how does this influence the findings?\nResults Similarly, to the methods section, the result from the study should be presented within the framework of phenomenology approach.\n\nDiscussion A limitation of the study has been discussed due to the limited participants recruited for the study. However, the discussion can be improved by discussing the impact of smartphone use on mental health of adolescents.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\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": "7046",
"date": "20 Sep 2021",
"name": "Douglas McHugh",
"role": "Author Response",
"response": "Response to Reviewer - Folashade Tawakalitu Alloh Author response: Thank you for your comments and feedback. I wish to acknowledge the value of your contributions to improving this article. My co-authors and I are grateful for peer-reviewers who contribute to assuring that scholarship entering the field is of high quality and grounded in previous findings and appropriate methodologies. Reviewer suggested revisions: The manuscript explored the experiences of adolescence in managing smartphone use. This is an interesting and valuable research area in the context of the pandemic and mental health impact on adolescents. Qualitative data collection was gathered from adolescents using interpretive phenomenology to guide the research process. Introduction 1. A justification of why the study was implemented among students in the chosen schools can be helpful for readers. Author response: Thank you for this prompt to clarify why we targeted adolescents in this study. We wrote in the introduction the following to draw readers’ attention to research on problematic mobile phone use that has involved the general population and why adolescents in particular represent a vulnerable age group, “Among the general population, determinants and effects of problematic phone use have been studied, screening tools developed, and prevalence of mobile dependency measured. [2,4-5] While the detrimental effects of problematic mobile phone use on sleep, stress, anxiety, and depression can occur at various ages [2], adolescents comprise a notably vulnerable age group. This relates to decreased levels of self-control and low resistance to peer pressure. Steinberg and Monahan (2007) noted “susceptibility to peer pressure in adolescence follows an inverted U-shaped curve, increasing during early adolescence, peaking around age 14, and declining thereafter.” [6] This together with the findings of our literature review of problematic mobile phone use is the justification for our focus on 13-15 year-olds as study participants. 2. The authors mentioned reviewing the literature and the search terms used but has not clearly presented the outcome of the review or how this contributed to the study design. Author response: We conducted a comprehensive review of the literature pertaining to adolescents and problematic mobile phone use in order to make readers of aware of what was available and to highlight the lack of qualitative data for those aged 13-15. The second paragraph of the introduction describes both how we conducted the literature review and a succinct summary of its findings (highlighted in bold below), consistent with the Brief Report category of F1000 Research. The lack of qualitative data for adolescents informed our choice to pursue a qualitative research question and study design that sought to explore the context of problematic mobile phone use with 13-15 year-olds.. “We searched the PubMed database using the query “((Smartphone OR mobile phone OR cell phone) AND (dependency OR dependence OR problematic)) AND (adolescent OR adolescence OR teenage OR youth)” and found with regard to adolescents that studies are limited to reports of prevalence and associations with adverse wellness. More specifically: cross-sectional studies have measured prevalence of mobile phone dependency [1,7-8]; mobile phone dependence correlated positively with unintentional injuries (odds ratio = 1.452) [9]; depressive symptoms, higher interpersonal anxiety, and lower self-esteem have been correlated with problematic cell phone use [10-12]; and Walsh et al (2008) held qualitative focus groups with Australian 16-24 year-olds and found extreme attachment to phones with symptoms of behavioral addiction evident in participants' descriptions. [13] Adolescent-specific investigations are limited to mobile phone dependency prevalence [1,7]; and to correlation with depression, interpersonal anxiety, lower self-esteem, and symptoms of behavioral addiction evident. [10,13] Adolescents are knowledgeable agents capable of representing and articulating the different aspects of how they interact with smartphones. Yet little work has been devoted to exploring how adolescents experience mobile phone dependency and what meanings and interpretations they attach to it.” Method 3. What is the impact of watching the Youtube clip before discussion with participants? Authors did not clarify why this is needed and how it contributed to responses from participants. Author response: In short, this was to help elicit participants’ views on Snapstreaks. It is not uncommon in humanities or sociology qualitative research for researchers to employ the use of artifacts (i.e., something created by humans which gives information) for participants to react or respond to (Crotty, 1998; Edwards et al, 2015). These artifacts are used, along with an episodic semi-structured interviewing style, to elicit participants’ views about the subject under investigation. The nature of this type of research is inherently subjective in contrast to basic science or clinical research where data can be objectively measured. In our case, the artifact was a YouTube-hosted CBS News interview with Tristan Harris the CEO of the social media app Snapchat which uses Snapstreaks. The adolescent participants are knowledgeable agents capable of representing and articulating what they think and believe (or don’t think or don’t believe) about the content of the video. In so doing, we as researchers were able to better explore from the qualitative data collected, how the use of social media apps may increase excessive mobile phone use in adolescents. Our citation of the video means that readers of the article can watch it and make their own judgments. We have added the following to the Data Collection and Analysis section of the Methods to clarify our rationale: “This video clip artifact was employed to help elicit participants’ views on Snapstreaks. It is not uncommon in humanities or sociology qualitative research for researchers to employ the use of artifacts (i.e., something created by humans which gives information) for participants to react or respond to (Crotty, 1998; Edwards et al, 2015). These artifacts are used, along with an episodic semi-structured interviewing style, to elicit participants’ views about the subject under investigation.” References: Edwards R, Fenwick T, Sawchuk P. Emerging Approaches to Educational Research: Tracing the Socio-Material. London: Routledge; 2015 Crotty M. The foundations of social research: meaning and perspective in the research process. London: Sage Publications, 1998 4. Developing themes, how is the data analysis phase influenced by phenomenology approach adopted for the study, this needs to be further discussed; how does this influence the findings? Author response: Thank you for prompting us to better describe our data analysis processes in relation to phenomenology.We have added the following to the Data Collection and Analysis section of the Methods (new content highlighted in bold): “The primary goal of researchers during the data analysis process in a phenomenological study is to deduce meaning out of the themes identified through organizing the data, coding the data, deducing categories, identifying common themes, making interpretations, and maintaining a reflective journal. The latter is an important step on phenomenological study to address researcher bias and overall credibility. It involves maintaining field notes detailing researchers’ choices and decision-making; it serves to keep the themes generation and interpretation transparent, coherent, and simple (Chenai 2011). K.G. wrote field notes after each focus group to reflect on the participants’ observations, K.G.’s growing insights, and how her facilitator-outsider role informed the research process. [16] Audio recordings were transcribed verbatim then subject to de-identified inductive qualitative analysis using a constant comparison approach. [17] De-identified transcripts were read, then hand-coded by assigning first-stage preliminary codes. A.K. and D.M. then met together to group similar codes into categories and identify major concepts while referencing K.G.’s memos and field notes. Iteratively, major concepts were further organized and expressed as themes and subthemes.” Results 5. Similarly, to the methods section, the result from the study should be presented within the framework of phenomenology approach. Author response: We have added the following to the Qualitative Findings section of the Results to make more explicit the connection between our research approach and the presentation of our findings (new content highlighted in bold). The results of data explication of phenomenological studies is ultimately theme generation and interpretation of the participants’ experiences of the phenomenon being investigated: “Phenomenological data explication involves researchers’ inferring the meaning behind participants’ words and articulating experiences through thematic statements (Bassett 2004). Participants possessed a notable awareness of problematic smartphone use in themselves and their peers. Four main themes with associated subthemes emerged from our phenomenological data analysis processes: drivers of excessive smartphone use, with family or friends, barriers to healthier smartphone use, and nighttime habits; Illustrative quotes are identified by anonymous participant codes.” Discussion 6. A limitation of the study has been discussed due to the limited participants recruited for the study. However, the discussion can be improved by discussing the impact of smartphone use on mental health of adolescents. Author response: Thank you for this welcome recommendation to include a short discussion of the impact of problematic smartphone use on adolescents’ mental well-being. We have added the following to the end of the first paragraph in the Discussion section: “Problematic smartphone use has been negatively associated with adolescents’ mental well-being. Souza Pereiva et al (2020), in a study of 359 female and 308 male students aged 13-18 years, associated it adversely with physical activity levels, personal interactions, academic performance, and mood disturbances. Abi-Jaoude et al (2020) also report, “Evidence from a variety of cross-sectional, longitudinal and empirical studies implicate smartphone and social media use in the increase in mental distress, self-injurious behaviour and suicidality among youth; there is a dose–response relationship, and the effects appear to be greatest among girls.” As we also noted from our participants’ responses, Abi-Jaoude et al describe smartphone app-facilitated social comparisons among adolescents that negatively affected their self-view and led to increased cyberbullying and promotion of self-harming behaviors. They call for an increase in public awareness of problematic smartphone use. The contexts highlighted by our study may help inform social policy interactions aimed at promoting safe, inclusive, and nourishing home or educational environments.”"
}
]
},
{
"id": "82119",
"date": "07 May 2021",
"name": "Marquisette Glass Lewis",
"expertise": [
"Reviewer Expertise Healthcare",
"uterine artery embolization",
"HIV",
"uterine fibroids",
"COVID-19",
"diabetes",
"fibroids."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 was an easy read and written well. There are few things that I believe would be valuable.\nWhat specific websites were mostly reviewed or downloaded from boys and girls?\n\nWhen watching the films were the subjects talking or watching the movie?\n\nWhat games were used the majority of the time?\n\nHow often did the subjects upgrade their phone and who purchased it?\n\nDid any of the participants spend time looking up school work?\n\nDid any of the participants have a house phone?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7027",
"date": "13 Aug 2021",
"name": "Douglas McHugh",
"role": "Author Response",
"response": "Response to Reviewer - Marquisette Glass Lewis Author response: Thank you for your comments and feedback, and I wish to acknowledge the value of your contributions to improving this article. My co-authors and I are grateful for peer-reviewers who contribute to assuring that scholarship entering the field is of high quality and grounded in previous findings and appropriate methodologies. Reviewer suggested revisions: The manuscript was an easy read and written well. There are few things that I believe would be valuable. 1. What specific websites were mostly reviewed or downloaded from boys and girls? 2. When watching the films were the subjects talking or watching the movie? 3. What games were used the majority of the time? 4. How often did the subjects upgrade their phone and who purchased it? 5. Did any of the participants spend time looking up school work? 6. Did any of the participants have a house phone? Author response: These are excellent questions that target the details of what specific content the adolescent participants were accessing on their smartphones as well as when and how often, and further contextualize smartphone upgrades and the presence of landline phones. Unfortunately, these questions are outside the scope of the data we collected for this preliminary study. Therefore, we will not be able to accommodate this requested revision simply because we do not have the relevant information. We agree that asking and gathering answers to these questions would be important to collect for future, generalizable quantitative studies. Thank you for this suggested improvement."
}
]
}
] | 1
|
https://f1000research.com/articles/10-237
|
https://f1000research.com/articles/8-2050/v1
|
03 Dec 19
|
{
"type": "Case Report",
"title": "Case Report: Occupational therapy in a patient with an overgrowth syndrome that restricts movement",
"authors": [
"Luca Coppeta",
"Sandro Gentili",
"Francesca Papa",
"Ludovico Maria De Zordo",
"Stefano Mugnaini",
"Antonio Pietroiusti",
"Sandro Gentili",
"Francesca Papa",
"Ludovico Maria De Zordo",
"Stefano Mugnaini",
"Antonio Pietroiusti"
],
"abstract": "Background: Overgrowth syndromes are a heterogeneous group of conditions characterized by excessive body growth - localized or generalized - commonly associated with various malformities and an increased oncological risk. Case report: Here we present the case of a 57-year old man, employed in an office, who suffers from an asymmetric overgrowth of the lower limbs. Currently the patient presents malformations of the lower left arm (hip, knee and ankle), evident on the articular and periarticular level, where there are diffuse exostoses. This case discusses the main occupational concerns relating to the patient’s workspace at a high floor level that could create critical issues in the event of an emergency exodus. Given the impossibility of placing the patient in heavy manual activities, employment is limited to office activities. Adjustments were carried out at the patient’s workstation, and thus the patient has been recognized as fit to work. Increased frequency of breaks were prescribed in order to allow the physiological alternation of postures. Conclusions: In cases of overgrowth syndromes, the exact identification of the limitations presented by the patient and observations about ambulatory functions must be carefully evaluated in order to modulate the work environment.",
"keywords": [
"Proteus syndrome",
"SEMG",
"overgrowth",
"ergonomics"
],
"content": "Introduction\n\nOvergrowth syndromes are a heterogeneous group of conditions characterized by excessive body growth - localized or generalized - commonly associated with various abnormalities and an increased oncological risk1. The classification of this group of disorders has proved to be very complex, both due to the extensive overlap of their clinical characteristics and to the fact that the causative molecular anomalies are not fully known2. Although rapid progress has been made in delineating the causal molecular defects of the most common overgrowth syndromes in the last decade1, there is still much to be done and numerous conditions still need to be carefully understood both phenotypically and genetically.\n\nIt is important to underline that most of the overexploited syndromes continue to be diagnosed on the basis of clinical criteria and the genetic identification of typical molecular alterations represent a diagnostic confirmation3. Rapid technological progress currently being made with genetic analysis will probably allow doctors to use more genetic data in the diagnostic approach in the future, and therefore improve the classification of these disorders4.\n\nOvergrowth syndromes are characterized by an increased body size in terms of stature, whether it is generalized or localized, and if there is an increase of the cranial circumference (macrocephaly). To distinguish overgrowth from certain endocrinological (hormonal) disorders, both acquired and genetic, which may induce an increase in growth rate (such as pituitary gigantism, caused by excess growth hormone), the hyperaccumulation syndrome remains by definition non-hormonal. There may also be mental retardation, although cognitive delay is not a constant feature of the syndrome,. as well as dysmorphisms.\n\nThe simplest and most practical classification model is based on the type of excessive growth, general and localized, and the part of the body the overgrowth is located on. For example, generalized overgrowth may relate to Beckwith-Wiedemann syndrome, Simpson-Golabi-Behmel, or Perlman, while overgrowths associated with macrocephaly could be Sotos syndrome, and Bannayan-Riley-Ruvalcaba. Hyper-fattening limited to a segment of the body is referred to as isolated hyperplasia.\n\nHere, we report a clinical case regarding the occupational issue and ergonomics adjustments for a patient affected by a rare form of overgrowth syndrome with asymmetric growing of the lower limbs.\n\n\nCase report\n\nOur patient is a man aged 59 years, and is currently employed in an office, who suffers from an asymmetric overgrowth of the lower limbs. This pathology is benign and localized. The abnormal growth process of the left leg began at the age of 18 months and led to the amputation of the distal phalanx of the second finger, which was repeated for recurrence at the age of 4 years. At 35 years the patient underwent subtotal amputation of the first finger and the removal of calcification of the back of the left foot. At the age of 40, he underwent surgical revision of the first finger and amputation of the distal third and fourth finger phalanges.\n\nOver the years, cerebriform connective tissue nevi (CCTNs) has developed on the left upper limb and has undergone surgical treatment of the suspected malignant nevi.\n\nThe patient’s speech is fluent and his understanding complete. He presents with good personal and social fulfillment (there are no malformations that can disturb the aesthetic appearance of the face). General conditions of the patient are good, from the diagnostic tests performed (medical visit, E.K.G., ultrasonography, spirometry) there are no alterations of the cardio-circulatory system, pulmonary or sensory apparatus. Laboratory tests are normal.\n\nCurrently the patient presents with malformations of the lower left arms (hip, knee and ankle), evident on the articular and periarticular level, where there are diffuse exostoses. At the hip level, the exostotic formations do not result in reductions of the joint range of motion (ROM). More serious is the situation proceeding distally, where the knee malformations reduce the ROM in a range between 27 and 90 degrees in flexion-extension. At the level of the medial tibial segment a bone exostosis is found on the deep planars, ~4 cm of diameter (Figure 1, Figure 2).\n\nIn 1989 the tibial area was the site of surgical removal of an intra and extra capsular fibrolipomatous bulk, about 5 cm in diameter, excision of an intra-articular mobile body, medial transposition of the patellar tendon with insertion of metal plaque and transposition of the tendon insertion of the vast medial. The ankle condition appeared even more severe, with full ankylosis in plantar flexion of 32 degrees. Both the ankle and the foot appeared to be twice the size of the contralateral limb for bone hyperplasia and connective tissue (Figure 3, Figure 4).\n\nMovement of the patient. The patient has a gait abnormality (limp, asymmetrical, slower than normal), which currently does not require aids on level ground. Uphill movement causes bending of the torso with increased effort, therefore where the risk of falling increases (e.g. while descending the stairs) support with a stick is required.\n\nThe patient, due to the high risk of falling while using the stairs, has to be highly concentrated and a handrail is required. The deficit is increased by the sharp decrease in proprioceptive and exteroceptive sensitivity of the left foot plantar, which is housed in custom-made orthopedic footwear.\n\nThe impairment of walking leads to functional overload of the lower right limb with episodes of low back pain and homolateral coxalgia.\n\nOur patient reported that based on the clinical characteristics, a diagnosis of proteus syndrome was issued at 18 months.\n\nHowever, a recent genetic study performed in the patient at the age of 54 years highlighted the absence of the characteristic mutation present in proteus syndrome, suggesting a different diagnosis. The detection of the PIK3CA gene mutation (c.3140A> G), together with the clinical aspects of the patient, suggests a diagnosis of fibro-adipose hyperplasia syndrome (FHS), characterized by a congenital, progressive and localized overgrowth of fibrous and adipose tissue and bone. The FHS is part of the broader category of syndromes termed PIK3CA-related overgrowth spectrum (PROS), which includes LOVES, FHS, macrodactyly and megalocephaly syndrome. To date, the only treatment expected to slow down uncontrolled tissue growth is surgical resection. The aim of genetic research is to use ‘target therapies’, such as molecular inhibitors of the PI3K/AKT /mTOR pathway, currently used in oncology, which may slow down if not reverse the characteristic hyper-growth of these syndromes. Objective assessment of neuromuscular function can help the occupational medicine specialist to better evaluate global impairment and the presence of symptoms5.\n\nWe performed no therapeutic intervention since no health issue was present at the clinical evaluation. However, since the patient’s job had recently changed from administrative tasks to an activity characterized by more frequent contact with the public (more standing up and moving around for the worker), we ergonomically evaluated and adjusted the patient’s workplace.\n\nThe patient’s work environment consists of an office on the second floor where the patient carries out activities on a PC connected to the administration of the library where he works. His work chair is comfortable, allows height adjustment and an inclination of the backrest; the desk is spacious, ergonomically organized and allows comfortable housing of the legs of the subject. To allow the comfortable support of the foot, a stool was provided to the patient.\n\nMovements at the workplace are very limited and of short duration; however, given the limitations of the patient’s movement, the use of the stairs must be limited and the use of a dedicated elevator is required. Therefore, to allow travel to and from the workplace, the patient was reserved a flat parking space, and an elevator located at the parking level to his workstation was provided, as well as to the entire library area and related offices.\n\nThe main occupational concern that could create critical issues with patients with this type of syndrome with restricted movement would be in the event of an emergency exodus, e.g. fire. Therefore, various measures and simulations were put in place to assess and reduce the risk for this patient in an event such as this.\n\nFor our patient, the maximum distance between a safe place to go to in event of an evacuation (as determined by the fire department, which was on a level) and the patient’s workstation or other places of work the patient occasionally frequented, such as reading room and book store, was <30 meters. A simulation was carried out at the patient’s workplace by the patient to assess the time taken for arrival at the safe place from the usual workstation (30 seconds) and from a more distant location (45 seconds), which seem to be acceptable times for the worker to keep in safe.\n\nThe presence of an automatic fire detection and extinguishing system may constitute a risk element for our patient as it maked the floors more slippery, increasing the risk of falls. Therefore, a training plan aimed at emergency evacuation and a specific exercise was planned for the entire staff. In addition, two work colleagues were trained specifically for the assistance of the patient, and a tested evacuation and transport chair (model PRO-SKID by SPENCER) was purchased to descend the external fire escape stairs.\n\nWe assessed the outcomes of the change in workstation at 6 months. The patient reported increased work comfort and a regular use of the elevator located at the parking level to reach his workstation. He reported no falls during the last 6 months and no accidents have occurred.\n\n\nDiscussion\n\nOvergrowth syndrome is a clinical condition characterized by progressive and uncontrolled growth of different parts of the body. It can affect the skeleton, skin, subcutaneous tissue, and central nervous system. The onset is mostly between 6 and 18 months of life, with asymmetric overgrowth, usually of the hands and feet. Macrodactyly and hemi-hypertrophy of bone and connective tissue are the most common onset symptoms.\n\nIn 1998 the National Institutes of Health (Bethesda, MD, USA) defined guidelines to base the diagnosis of this syndrome on clinical criteria. In order for the diagnosis of proteus syndrome to be considered valid, the following must be present (Table 1): all three general criteria plus a criterion relating to category A; two criteria of category B; three criteria of category C. The absence of such requirements can lead to the diagnosis of proteus-like syndrome. In the case of our patient, the clinical diagnosis was carried out in accordance with the general criteria, with the specific criteria of class A and a criterion of class B. For the diagnostic confirmation it is necessary to identify the mutation of the gene responsible for the syndrome. Proteus syndrome is an extremely rare and complex disease (1/1,000,000 newborns) and currently only 120 cases in the world are recognized2.\n\nRecent studies have shown that proteus syndrome is caused by a mutation of the pathway of the phosphatidylinositol-3-kinase signal (PI3K)-AKT6. Patients are affected by somatic activating mutation of the oncogene AKT1, present in the form of mosaicism. AKT (also known as protein-kinase B or PKB) is a cytosolic protein that plays a key role in the PI3K\\Akt pathway. Its activity consists of the phosphorylation of various protein substrates in the serine and threonine residues, often leading to their inactivation. The activation of this oncogene triggers biochemical pathways that lead to cell proliferation and resistance to apoptosis.\n\nTreatment of overgrowth syndrome requires a multidisciplinary approach. Interventions for the control of overgrowth are epiphysiodesis and amputation in severe cases. Physiotherapy and occupational therapy are very important to avoid joint ankylosis and to maintain an adequate self-functional autonomy. Orthoses and custom-made shoes may be needed.\n\nFor CCTNs, which are a typical manifestation of this syndrome, dermatological treatment is required; the lesions must be removed surgically in the case of suspected malignancy or if the deformities and/or pain are significant. In the case of deep venous thrombosis and pulmonary embolism, guidelines for anticoagulant therapy should be applied promptly. Regular screening tests must be performed due to a predisposition to neoplasms.\n\nPatients and their families can benefit from psychosocial counseling. Annual physical and radiological examination is recommended. Given the consequent impossibility of placing the patients in heavy manual activities, the employment of these patients is limited to office activities. In cases of overgrowth syndromes, the exact identification of the limitations presented by the patient and observations about ambulatory functions must be carefully evaluated in order to modulate the work environment.\n\n\nEthical approval\n\nThe occupational therapy protocol was approved by the local ethical committee of Tor Vergata Policlinic and written informed consent was obtained by the patient for their participation in the study.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
"appendix": "References\n\nLindhurst MJ, Sapp JC, Teer JK, et al.: A mosaic activating mutation in AKT1 associated with the Proteus syndrome. N Engl J Med. 2011; 365(7): 611–619. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCohen MM Jr: Proteus syndrome review: molecular, clinical, and pathologic features. Clin Genet. 2014; 85(2): 111–9. PubMed Abstract | Publisher Full Text\n\nFerence T, Fertig RM, Feldman M, et al.: Rehabilitation of a Patient with Proteus Syndrome: Case Report and Literature Review. J Clin Med Ther. 2(2): 16. Reference Source\n\nOu M, Sun Z, Zhu P, et al.: Proteus syndrome: A case report and review of the literature. Mol Clin Oncol. 2017; 6(3): 381–383. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoppeta L, Gentili S, Mugnaini S, et al.: Neuromuscular Functional Assessment in Low Back Pain by Surface Electromyography (SEMG). Open Pub Health J. 2019; 12(1): 61–67. Publisher Full Text\n\nMichael CM, Cohen MM: Proteus syndrome review: molecular, clinical, and pathologic features nothing to declare. Clin Genet. 2014; 85: 111–119."
}
|
[
{
"id": "57442",
"date": "04 Dec 2019",
"name": "Nicola Magnavita",
"expertise": [
"Reviewer Expertise occupational health"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is interesting because, beyond the description of the case which is infrequent in itself, it offers interesting hints about ergonomic interventions that can be useful to improve the employment conditions of those suffering from this disease. Since the pathology is progressive and the worker will also undergo periodic checks at the workplace in the future, the authors could say whether, from a total worker health perspective, they have planned interventions aimed at increasing physical activity, avoiding weight accumulation, improve joint mobilisation.\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": "90062",
"date": "02 Aug 2021",
"name": "Enrico Maria Staderini",
"expertise": [
"Reviewer Expertise Biomedical technology",
"medicine",
"cardiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNice report of a quite rare case of overgrowth syndrome quite severely involving lower limbs. Very good description of the case and scientific framing of the syndrome. The description of the original workplace intervention may be of interest to other readers.\nA few points to modify:\nIn various parts of the text \"lower left arm\" is indicated while it should be much more appropriated to write \"lower left leg\" or \"lower left limb\" instead (please fix this point).\n\nIn the abstract the age of the patient is given as 57 years old, while in the text (first line Case report Patient information paragraph) the age of the same patient is given a 59 years old (please fix this point).\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": "6985",
"date": "23 Aug 2021",
"name": "luca coppeta",
"role": "Author Response",
"response": "Thank you for your suggestions. We have provided to corrections the text."
}
]
}
] | 1
|
https://f1000research.com/articles/8-2050
|
https://f1000research.com/articles/10-419/v1
|
25 May 21
|
{
"type": "Systematic Review",
"title": "The role of single nucleotide polymorphisms of IL-1A -889C>T (rs1800587), TNF-A -238G>A (rs361525), and VDR TaqI (rs731236) on susceptibility to herniated nucleus pulposus",
"authors": [
"Azharuddin Azharuddin",
"Muhammad Ilmawan",
"Jonny Karunia Fajar",
"Marhami Fahriani",
"Sukamto S. Mamada",
"Helnida Anggun Maliga",
"Firzan Nainu",
"Kuldeep Dhama",
"Harapan Harapan",
"Rahadyan Magetsari",
"Muhammad Ilmawan",
"Jonny Karunia Fajar",
"Marhami Fahriani",
"Sukamto S. Mamada",
"Helnida Anggun Maliga",
"Firzan Nainu",
"Kuldeep Dhama",
"Harapan Harapan",
"Rahadyan Magetsari"
],
"abstract": "Background: The objective of this study was to determine the role of single nucleotide polymorphisms (SNPs) in interleukin 1 alpha (IL-1A), tumor necrosis factor-alpha (TNF-A), and vitamin D receptor (VDR) genes on the susceptibility to herniated nucleus pulposus (HNP). Methods: Four databases (PubMed, Embase, Cochrane, and Web of Science) were searched as of April 1st, 2021. Authors, publication year, targeted genes, genotype and allele frequency in each case and control groups were collected. Newcastle-Ottawa scale was used to evaluate the publication quality. The pooled estimates of association of IL-1A -889C>T (rs1800587), TNF-A -238G>A (rs361525), and VDR TaqI (rs731236) and susceptibility to HNP were assessed using Z test and presented as odd ratio (OR) and 95% confidence intervals (95%CI). Results: We screened 3,067 unique studies for eligibility and three, two and nine studies on IL-1A -889C>T, TNF-A -238G>A, and VDR TaqI were included, respectively, in our meta-analysis. The studies consisting 369 HNP cases and 433 controls for IL-1A -889C>T, 252 cases and 259 controls for TNF-A -238G>A and 1130 cases and 2096 controls for VDR TaqI. Our pooled estimates indicated that there was no significant association of those SNPs with the susceptibility to HNP in any genotype, dominant model, recessive model, or allele comparations. Conclusion: Although individual studies suggested the important role of gene expression dysregulation associated with SNPs in IL-1A, TNF-A, and VDR, our data indicated that IL-1A -889C>T, TNF-A -238G>A, and VDR TaqI had weak association with HNP susceptibility in both genotypes and allele distributions. However, since heterogeneity was identified among studies included in this meta-analysis, further meta-analysis with a larger population and subgroup analysis on specific population are warranted to support this finding.",
"keywords": [
"Spinal disc herniation",
"SPN",
"IL-1A",
"TNF-A",
"VDR"
],
"content": "Introduction\n\nHerniated nucleus pulposus (HNP) or disc herniation is the most common spinal degenerative disease associated with lower back pain and radicular pain of the lower extremities due to nerve compression.1 HNP is also the most common cause of persistent sciatic pain due to displacement of the nucleus pulposus beyond the intravertebral disc space.2 The most prevalent HNP locations are between the L4 and L5 vertebrae and between the L5 and S1 vertebrae3 whilst the highest incidence is observed amongst people aged 30-50 years old.4 Diabetes,5 smoking,5,6 obesity,5-7 type of occupation,8 age,7 and gender4,9 have all been associated with a high risk of developing disc degenerative diseases. However, it has been suggested that genetic factors also play a vital role in susceptibility to disc degenerative diseases. A study showed that individuals aged younger than 30 years who have a family history of disc herniation have a 14.5 times higher risk of developing disc protrusion than individuals who have no family history.8 Family history is also attributed to a 5.1 times higher risk of disc herniation in people aged between 30-50 years old.8 The Twin Spine Study found that heredity substantially influences disc degeneration by 43-77%.10,11\n\nThe intervertebral disc (IVD) consists of two different components: the nucleus pulposus (NP) and the annulus fibrosus (AF),12 where proteoglycans (mostly found in NP) acts as an internal semi-fluid mass and collagen (mostly found in AF) acts as a laminar fibrous container.13 Genes encoding components of IVD such as collagens I,14 collagens IX,15 collagens XI,16 aggrecan,17 cartilage intermediate layer protein (CILP),18 and vitamin D receptor (VDR)19 have previously been studied to determine susceptibility to lumbar disc diseases. Other factors such as increased production of extracellular matrix-degrading enzymes (encoded by matrix metalloproteinase 3 gene (MMP-3) and MMP-920 and increased expression of inflammatory cytokines such as interleukin-1 alpha (IL-1A), IL-18,21 IL-6, and tumor necrosis factor-alpha (TNF-α)22) are commonly found in disc degeneration. Excessive synthesis, secretion, and biological activity of these inflammatory mediators are associated with tissue destruction and are therefore commonly found in inflammatory disorders including disc degeneration.23\n\nOne of the mechanisms that alters the production of protein mediators in the human body are single-nucleotide polymorphisms (SNPs). These genetic variations, single nucleotide changes at specific positions in a gene, may influence gene expression and hence associate to particular disease. A three-fold increase in susceptibility of disc degeneration was observed in individuals with a TT genotype compared to those without the allele (CC genotype) on SNP IL-1A -889C>T (rs1800587).24 People with minor allele of IL-1A -889C>T (T allele) also had a 2.4-fold increased risk of disc bulges24 and a 2.5-fold increased risk of endplate modic change.25 A study in an Iranian population found that among nine SNPs on pro-inflammatory cytokine genes (IL-1, IL-6 and TNF-A), no association to IVD degeneration was found except for two SNPs in the TNF-A gene (TNF-A−308 G/A and TNF-A −238 G/A).19 TNF-α plays important role in the pathophysiology of HNP such as upregulating the activity and the gene expression of MMP, stimulating other cytokines such as IL-1, IL-6, and IL-8, stimulating cell migration, altering endothelial permeability, and decreasing the synthesis of collagen and proteoglycan.26 A study reported that G allele and GG genotype of TNF-A 238G>A (rs361525) were 2.51 times and 2.98 times, respectively, more prevalent in patients with HNP compared to healthy controls.19\n\nSeveral roles of VDR such as regulating chondrocyte proliferation and differentiation, bone mineralization and remodeling, and matrix production have previously been demonstrated.27 VDR's role in spinal degenerative disorder has been studied in Italian,28 Turkish,29 and Southern European populations.30 A study in a Chinese population suggested that subjects with the t allele of VDR TaqI (rs731236) had a 2.61 times higher risk to have degenerative disc disease.31 Moreover, individuals aged younger than 40 years who had the t allele were almost six times more likely to develop disc degeneration and 7.17 times more likely to develop disc bulge compared to those without the t allele.31 However, studies in Danish32 and Mexican populations33 contradict previous results suggesting a role of VDR TaqI in disc degenerative disease. This conflicting role of SNPs inIL-1A, TNF-A and VDR on HNP therefore needs to be further evaluated. This study sought to determine the association of IL-1A -889C>T (rs1800587), TNF-A 238G>A (rs361525), and VDR TaqI (rs731236) in susceptibility to HNP.\n\n\nMethods\n\nA systematic review and meta-analysis were conducted to assess the association of three SNPs, IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236), on susceptibility to HNP. The outcome variable of this study was the risk or susceptivity to have HNP while the response variables were the SNPs in three genes: IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236). We searched databases for relevant studies, then extracted and analyzed data from those studies to achieve the pooled odds ratios (ORs) and 95% confidence interval (95%CI) using a random or fixed effect model depending on the data. This study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guideline.34,35 The protocol of this study has been registered in PROSPERO (reg. number CRD42021249187).\n\nThe literature searches were conducted on PubMed, Embase, Cochrane, and Web of Science. The searches were conducted using the keywords:‘degenerative disc disease’ AND (‘IL-1A’ OR ‘rs1800587’ OR ‘-889C>T’) OR (‘TNF-A’ OR ‘rs361525’ OR ‘-238G>A’) OR (‘VDR’ OR ‘rs731236’ OR ‘TaqI’) AND ‘gene polymorphism’, including all results up to April 1st, 2021. The keywords were adapted from Medical Subject Heading (MeSH). Additional studies were also retrieved from the references of relevant papers. If two or more studies with the same study data were identified, the most recent study was used. The processes were conducted by three independent authors (JKF, MI, HAM).\n\nTo be eligible for the meta-analysis, a study had to meet all the inclusion criteria below: (1) the study design should be case-control, cross-sectional, or cohort design; (2) the study should evaluate the association of IL-1 (rs1800587), TNF-A (rs361525), or VDR (rs731236) on HNP and have case and control groups; and (3) studies should present genotype frequency or minor allele frequency (MAF). All studies with duplicate records, poor quality or which had deviation from Hardy-Weinberg Equilibrium (HWE) were excluded.36\n\nImportant information from the studies such as first author name, year of publication, names of targeted gene and the SNP, genotype frequency, or MAF from case and control groups were collected. The allele frequency and MAF were recalculated using Mendel’s law. Data extraction processes were conducted by three independent authors (JKF, MI, HAM) and consensus established together with senior authors (AA, HH) if discrepancies were found.\n\nThe quality of the included studies was evaluated using Newcastle-Ottawa Score (NOS)37 by three independent authors (JKF, MI, HAM). This evaluation was conducted to ensure the quality of three fundamental methodological parameters of the studies: patient selection (four points), comparability of the groups (two points), and ascertainment of exposure (three points); NOS ranged from 0 to 9. Each study was then categorized based on the NOS: (1) good quality (NOS ≥ 7); (2) moderate quality (NOS ≥ 5); or (3) poor quality (NOS < 5). Consensus was established if discrepancies were found.\n\nTo assess the association of IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236) on HNP, a Z-test was employed. The Egger test was used to evaluate the publication bias and a p < 0.05 indicated the possibility of publication bias in each calculated result. The Q test was used to evaluate the heterogeneity and decide between random and fixed-effect models for OR calculation. If heterogeneity was indicated (p-value less than 0.10), the random effect model was used; otherwise, the fixed-effect model was used. All analyses were performed using ‘meta’,38 ’ metafor’,39 and ‘dmetar’40 packages in R version 4.0.4.41\n\n\nResults\n\nThe literature searches yielded 3,199 articles of which 3,067 references were retained after removing duplicates. Screening of the titles and abstracts excluded 2,965 articles as they did not meet the inclusion criteria. After a further screening of full text, an additional 90 studies were excluded due to lack of relevance (n = 90), incomplete data (n = 5), and HWE deviation (n = 6) (Figure 1). 12 studies were included in the meta-analysis: three studies for IL-1A (rs1800587),19,42,43 two studies for TNF-A (rs361525),19,44 and nine studies for VDR (rs731236).28,42,45-51 The summary of studies included in the meta-analysis is presented in Table 1.\n\nOur data indicated that the TT genotype of IL-1A -889C>T was 1.37 more frequent in HNP patients than in controls, while the distribution of alleles and other genotypes were similar between patients and healthy controls. CT genotype and T allele of TNF-A 238G>A were both 1.6 times more frequent in healthy controls than in HNP cases. No difference in the distribution of alleles or genotypes between HNP and controls was observed in VDR TaqI (Table 1).\n\nOur pooled estimates suggested that no IL-1A -889C>T genotypes were associated with the risk of HNPs with CC vs. CT+TT (OR: 0.82, 95%CI: 0.62, 1.09), CT vs. CC+TT (OR: 0.07; 95%CI: 0.81, 1.42), and TT vs. CT+CC (OR: 1.20; 95%CI: 0.13, 11.37) (Table 2 and Figure 2). The pooled data also suggested that allele frequency of IL-1A -889C>T had no significant association with the susceptibility to HNP with OR: 0.83; 95%CI: 0.67, 1.02 for C allele compared to T allele.\n\n(A) CC vs CT+TT (OR: 0.82; 95%CI: 0.62, 1.09); p-value0.170, p-Het 0.867, and p-Egger 0.193, (B) CT vs CC+TT (OR1.07; CI95%: 0.81, 1.42); p-value 0.637; p-Het 0.373; p-Egger 0.675, (C) TT vs CT+CC (OR: 1.20; CI95%: 0.13, 11.37); p-value 0.764, p-Het 0.039, p-Egger 0.177, (D) C vs T (OR0.83; 95%CI: 0.67, 1.02); p-value 0.081; p-Het 0.369; p-Egger 0.221), and (E) T vs C (OR: 1.21; CI95%: 0.98, 1.50); p-value 0.081; p-Het 0.369; p-Egger 0.221.\n\nPooled estimates for allele and genotype distribution of the TNF-A 238G>A also had no significant association with the risk for HNP. No association was observed between genotype models and the risk of HNP: GG vs. GA+AA (OR: 1.60; 95%CI: 0.00, 12882.74), GA vs. GG+AA (OR: 0.63; 95%CI: 0.00, 4211.31), and AA vs. GG+GA (OR: 1.34; 95%CI: 0.16, 6712.96) (Table 2 and Figure 3). Distribution of the allele also had no strong association with HNP susceptibility.\n\n(A) GG vs GA+AA (OR1.60; CI95%: 0.00, 12882.74); p-value 0.628, p-Het 0.034, p-Egger 0.889, (B) GA vs GG+AA (OR0.63; CI95%: 0.00, 4211.31); p-value 0.629, p-Het 0.038, p-Egger 0.864, (C) AA vs GG+GA (OR1.05; CI95%: 0.16, 6712.96); p-value 0.955, p-Het 0.587, p-Egger <0.001, (D) G vs A (OR1.49; 95%CI: 0.00, 3473.60); p-value 0.629, p-Het 0.034, p-Egger 0.744, (E) A vs G (OR: 0.67; 95%CI:0.00, 1555.67); p-value 0.629, p-Het 0.056, p-Egger 0.744.\n\nOur estimates for genotypes of VDR TaqI (rs731236) suggested that none of the genotypes were associated with susceptibility to degenerative disc disease HNP with OR: 2.65; 95%CI: 0.60, 11.85 for TT vs. TC+CC, OR: 1.01; 95%CI: 0.55, 1.85 for TC vs. TT+CC and OR: 0.94; 95%CI: 0.69, 1.28 (Table 2 and Figure 4). None of the alleles of VDR TaqI (rs731236) were associated with HNP; people with T allele had OD 1.06 with 95%CI: 0.91, 1.22 for HNP.\n\n(A) TT vs TC+CC (OR: 2.65; CI95%: 0.60, 11.85); p-value 0.172, p-Het <0.001, p-Egger 0.986, (B) TC vs TT+CC (OR1.01; CI95%: 0.55, 1.85); p-value 0.964, p-Het 0.041, p-Egger 0.791, (C) CC vs TC+TT (OR 0.94; CI95%: 0.69, 1.28); p-value 0.688, p-Het 0.970, p-Egger 0.387, (D) T vs C (OR: 1.06; CI95%: 0.91, 1.22); p-value 0.775, p-Het 0.023, p-Egger 0.874), (E) C vs T (OR: 0.92; 95%CI: 0.50, 1.72); p-value 0.775, p-Het 0.023, p-Egger 0.874.\n\n\nDiscussion\n\nHNP occurs when the central part of the intervertebral disc, the nucleus pulposus, herniates through the surrounding part of the disc, the annulus fibrosus. The damage to the annulus fibrosus resulting in the herniated disc may be associated with factors such as gender, age, certain activities such as lifting of weights and carrying, and being overweight.52 For example, the degeneration of disc organization could occur during aging as the regulation of the extracellular matrix (ECM), a major component of the disc, is damaged during the aging process.52 The herniated disc or HNP may occur as a result of several pathological mechanisms. Those mechanisms ultimately cause imbalances in disc composition that are directly linked to the quality of the ECM.52 Therefore, the balance between the ECM and its degrading enzymes, such as matrix metalloproteases (MMPs), seems to be the key to maintaining normal disc function. Interestingly, of several mechanical pathways, the regulation of the ECM and the MMPs could also be determined by the occurrence of single nucleotide polymorphisms in genes responsible for ECM regulation as explained below.53\n\nTwo major structural proteins that are important in the matrix structure of the disc are collagen and proteoglycan.52 The main proteoglycan found in the normal intervertebral disc is aggrecan.54 Although both annulus fibrosus and nucleus pulposus are mainly composed of water, proteoglycan, and collagen, the level of those contents differ between the structures. The annulus fibrosus consists of 70% water, 15% collagen, and 5% proteoglycan, while the composition in the nucleus pulposus is 77% water, 4% collagen, and 14% proteoglycan.52 Any event causing disturbances in those ratios and/or in synthesis and/or degradation of those structural proteins could lead to herniated disc problems. For example, hypoxic and acidic conditions could repress the synthesis of the matrix leading to the dysfunctionalities of the cells of the disc.55,56\n\nThe role of inflammation in predisposing the disc to damage has also been revealed. Specifically, proinflammatory cytokines are found to play a specific role in herniated and degenerated discs.54,57-59 A controlled immunohistochemical study observed the accumulation of inflammatory cells, mainly macrophages, in herniated disc cells indicating the role of proinflammatory cytokines in the disease.58 For example, IL-1β could induce the annulus fibrosus to generate inflammatory factors leading to the impairment of proteoglycan aggregation.59 Another cytokine, TNF-α, is also involved in the development of intervertebral disc problems.60 However, it seems that its effect is less significant than IL-1.61 This finding may be related to its relatively lower expression compared to IL-1 in the normal and healthy disc.52,62\n\nPenetration of those inflammatory cells or proteins could be caused by matrix loss. In normal conditions, aggrecan should prevent the penetration of various compounds, especially serum proteins and cytokines.63 Therefore, in addition to its pivotal role in maintaining sufficient hydration to the disc, proteoglycan loss could stimulate the movement of cytokines towards the disc activating the inflammation cascade.52\n\nOne of the mechanisms by which the proinflammatory cytokines, such as IL-1α and TNF-α, generate problems in the intervertebral disc is related to their effect on inducing MMP production.64-67 The exaggerated activity of MMPs causes excessive degradation of collagen and proteoglycan.54 Another mechanism is associated with the activity of the cytokines in inhibiting tissue inhibitors of MMPs (TIMPs) which are responsible for terminating the action of MMPs.54 Taken together, those actions ultimately impair disc functionality.\n\nAs the normal intervertebral disc is relatively avascular and aneural,52 the nutritional supply to the disc depends on the ability of the nutrients to diffuse from the closest vascularized structure outside the disc which are the vertebral bodies.68 The nutrients then penetrate the cartilaginous endplate and finally reach the annulus fibrosus and nucleus pulposus.68,69 Accordingly, calcification of the endplate would diminish diffusion of vital nutrients, leading to the death of the disc cells.70 Therefore, VDR plays a critical role as this ligand-dependent transcription factor is involved in regulating calcium homeostasis and bone mineralization in the body, including in the intervertebral disc.71,72 It has been known that genetic polymorphisms occurring in genes encoding VDR are associated with intervertebral disc problems,72 including herniated disc.\n\nIn conclusion, our results suggest that well-regulated IL-1A, TNF-A, and VDR are important for normal intervertebral discs and that dysregulation of these could negatively affect the intervertebral discs. Some individual studies found that SNPs in IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236) were associated with the susceptibility to HNP, however, our meta-analysis suggested that the effects are not robust. There are some possible reasons for this finding. First, HNP is a complex disease and is cause by multiple factors. Thus, no single factor such as a single SNP is responsible for the whole pathogenesis. Second, large variations in the number of samples or allele frequencies among studies in our meta-analysis also contribute to the findings. This probably relates to differences in populations where study data were collected. Finally, the small number of samples significantly influenced the results of our meta-analysis. Therefore, studies with larger sample sizes and sub-analyses for different populations such as Asian, Caucasian, and other populations are warranted whenever more data are available.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: PRISMA checklist for ‘The role of single nucleotide polymorphisms of IL-1A -889C>T (rs1800587), TNF-A -238G>A (rs361525), and VDR TaqI (rs731236) on susceptivity of herniated nucleus pulposus’, https://doi.org/10.7910/DVN/RBU2VR73",
"appendix": "References\n\nKim DH, Lee SH, Kim KT, et al.: Association of interleukin-1 receptor antagonist gene polymorphism with response to conservative treatment of lumbar herniated nucleus pulposus. Spine. 2010 Jul 15; 35(16): 1527–31. PubMed Abstract | Publisher Full Text\n\nDe Cicco FL, Willhuber GOC: Nucleus pulposus herniation. StatPearls [Internet]. 2020.\n\nJordan J, Konstantinou K, O'Dowd J: Herniated lumbar disc. BMJ Clin Evid. 2009; 2009: 1118. eng. PubMed Abstract | Free Full Text\n\nFjeld OR, Grøvle L, Helgeland J, et al.: Complications, reoperations, readmissions, and length of hospital stay in 34 639 surgical cases of lumbar disc herniation. Bone Joint J. 2019; 101-B(4): 470–7. PubMed Abstract | Publisher Full Text\n\nJakoi AM, Pannu G, D'Oro A, et al.: The clinical correlations between diabetes, cigarette smoking and obesity on intervertebral degenerative disc disease of the lumbar spine. Asian Spine J. 2017; 11(3): 337–47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLener S, Wipplinger C, Hartmann S, et al.: The impact of obesity and smoking on young individuals suffering from lumbar disc herniation: a retrospective analysis of 97 cases. Neurosurg Rev. 2020; 43(5): 1297–303. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTeraguchi M, Yoshimura N, Hashizume H, et al.: Prevalence and distribution of intervertebral disc degeneration over the entire spine in a population-based cohort: the Wakayama Spine Study. Osteoarthritis Cartilage. 2014; 22(1): 104–10. PubMed Abstract | Publisher Full Text\n\nY-g Z, Sun Z, Zhang Z, et al.: Risk factors for lumbar intervertebral disc herniation in Chinese population: A case-control study. Spine. 2009; 34(25). PubMed Abstract | Publisher Full Text\n\nWang YXJ, Griffith JF, Ma HT, et al.: Relationship between gender, bone mineral density, and disc degeneration in the lumbar spine: a study in elderly subjects using an eight-level MRI-based disc degeneration grading system. Osteoporosis Int. 2011; 22(1): 91–6. PubMed Abstract | Publisher Full Text\n\nBattié MC, Videman T, Kaprio J, et al.: The Twin Spine Study: Contributions to a changing view of disc degeneration. Spine J. 2009; 9(1): 47–59. PubMed Abstract | Publisher Full Text\n\nBattié MC, Videman T, Gibbons LE, et al.: Determinants of lumbar disc degeneration: A study relating lifetime exposures and magnetic resonance imaging findings in identical twins. Spine. 1995; 20(24): 2601–12. Publisher Full Text\n\nNiosi CA, Oxland TR: Degenerative mechanics of the lumbar spine. Spine J. 2004; 4(6): S202–S8. PubMed Abstract | Publisher Full Text\n\nYoon ST, Patel NM: Molecular therapy of the intervertebral disc. Eur Spine J. 2006; 15 Suppl 3(Suppl 3): S379–S88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPluijm SMF, van Essen HW, Bravenboer N, et al.: Collagen type I α1 Sp1 polymorphism, osteoporosis, and intervertebral disc degeneration in older men and women. Ann Rheum Dis. 2004; 63(1): 71–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnnunen S, Paassilta P, Lohiniva J, et al.: An allele of COL9A2 associated with intervertebral disc disease. Science. 1999; 285(5426): 409. PubMed Abstract | Publisher Full Text\n\nMio F, Chiba K, Hirose Y, et al.: A functional polymorphism in COL11A1 which encodes the alpha 1 chain of type XI collagen, is associated with susceptibility to lumbar disc herniation. Am J Hum Genet. 2007; 81(6): 1271–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKawaguchi Y, Osada R, Kanamori M, et al.: Association between an aggrecan gene polymorphism and lumbar disc degeneration. Spine. 1999; 24(23): 2456–60. PubMed Abstract | Publisher Full Text\n\nSeki S, Kawaguchi Y, Chiba K, et al.: A functional SNP in CILP, encoding cartilage intermediate layer protein, is associated with susceptibility to lumbar disc disease. Nat Genet. 2005; 37(6): 607–12. PubMed Abstract | Publisher Full Text\n\nAbdollahzade S, Hanaei S, Sadr M, et al.: Significant association of TNF-α, but not other pro-inflammatory cytokines, single nucleotide polymorphisms with intervertebral disc degeneration in Iranian population. Clin Neurol Neurosurg. 2018; 173: 77–83. PubMed Abstract | Publisher Full Text\n\nTakahashi M, Haro H, Wakabayashi Y, et al.: The association of degeneration of the intervertebral disc with 5a/6a polymorphism in the promoter of the human matrix metalloproteinase-3 gene. J Bone Joint Surg Br. 2001; 83-B(4): 491–5. PubMed Abstract | Publisher Full Text\n\nVideman T, Saarela J, Kaprio J, et al.: Associations of 25 structural, degradative, and inflammatory candidate genes with lumbar disc desiccation, bulging, and height narrowing. Arthritis Rheum. 2009; 60(2): 470–81. PubMed Abstract | Publisher Full Text\n\nYang Q, Liu Y, Guan Y, et al.: Vitamin D Receptor gene polymorphisms and plasma levels are associated with lumbar disc degeneration. Sci Rep. 2019; 9(1): 7829. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKalb S, Martirosyan NL, Kalani MYS, et al.: Genetics of the degenerated intervertebral disc. World Neurosurg. 2012; 77(3): 491–501. PubMed Abstract | Publisher Full Text\n\nSolovieva S, Kouhia S, Leino-Arjas P, et al.: Interleukin 1 polymorphisms and intervertebral disc degeneration. Epidemiology. 2004; 15(5): 626–33. PubMed Abstract | Publisher Full Text\n\nKarppinen J, Solovieva S, Luoma K, et al.: Modic changes and interleukin 1 gene locus polymorphisms in occupational cohort of middle-aged men. Eur Spine J. 2009; 18(12): 1963–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeiler C, Nerlich AG, Bachmeier BE, et al.: Expression and distribution of tumor necrosis factor alpha in human lumbar intervertebral discs: a study in surgical specimen and autopsy controls. Spine. 2005; 30(1): 44–53. PubMed Abstract | Publisher Full Text\n\nZwerina K, Baum W, Axmann R, et al.: Vitamin D receptor regulates TNF-mediated arthritis. Ann Rheum Dis. 2011; 70(6): 1122–9. PubMed Abstract | Publisher Full Text\n\nColombini A, Brayda-Bruno M, Lombardi G, et al.: BsmI, ApaI and TaqI polymorphisms in the vitamin D receptor gene (VDR) and association with lumbar spine pathologies: an Italian case-control study. PloS one. 2016; 11(5): e0155004. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHekimoglu B, Eraltan H, Sari H, et al.: Investigation of the vitamin D receptor (VDR) gene polymorphisms in lumbar disc herniation in Turkish patients. Experimed. 2020; 9: 93–8. Publisher Full Text\n\nToktaş ZO, Ekşi MŞ, Yılmaz B, et al.: Association of collagen I, IX and vitamin D receptor gene polymorphisms with radiological severity of intervertebral disc degeneration in Southern European Ancestor. Eur Spine J. 2015; 24(11): 2432–41. PubMed Abstract | Publisher Full Text\n\nCheung KMC, Chan D, Karppinen J, et al.: Association of the Taq I allele in vitamin D receptor with degenerative disc disease and disc bulge in a Chinese population. Spine. 2006; 31(10): 1143–8. PubMed Abstract | Publisher Full Text\n\nEskola PJ, Kjaer P, Daavittila IM, et al.: Genetic risk factors of disc degeneration among 12-14-year-old Danish children: a population study. Int J Mol Epidemiol Genet. 2010; 1(2): 158–65. PubMed Abstract | Free Full Text\n\nCervin Serrano S, González Villareal D, Aguilar-Medina M, et al.: Genetic polymorphisms of interleukin-1 alpha and the vitamin D receptor in Mexican Mestizo patients with intervertebral disc degeneration. Int J Genomics. 2014; 2014: 302568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoher D, Liberati A, Tetzlaff J, et al.: Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. Plos Med. 2009 Jul; 6(7): e1000097. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPage MJ, Moher D, Bossuyt PM, et al.: PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. BMJ. 2021: 372. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodriguez S, Gaunt TR, Day IN: Hardy-Weinberg equilibrium testing of biological ascertainment for Mendelian randomization studies. Am J Epidemiol. 2009; 169(4): 505–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIlmawan M, Satriawan AG, Purnamasari Y, et al.: The association between glutathione S-transferase P1 105IIe>Val gene polymorphism and the risk of bladder cancer: A meta-analysis. Türkiye Klinikleri Tip Bilimleri Dergisi. 2020; 40(2): 250–9. Publisher Full Text\n\nBalduzzi S, Rücker G, Schwarzer G: How to perform a meta-analysis with R: a practical tutorial. Evid Based Ment Health. 2019; 22(4): 153–60. PubMed Abstract | Publisher Full Text\n\nViechtbauer W: Conducting meta-analyses in R with the metafor package. J Stat Softw. 2010; 36(3): 1–48. Publisher Full Text\n\nHarrer M, Cuijpers P, Furukawa T, et al.: dmetar: Companion R Package For The Guide 'Doing Meta-Analysis in R'. R package version 00. 2019; 9000.\n\nR Core Team: R: A language and environment for statistical computing. R Foundation for Statistical Computing. Vienna, Austria; 2020. Reference Source\n\nCervin Serrano S, González Villareal D, Aguilar-Medina M, et al.: Genetic polymorphisms of interleukin-1 alpha and the vitamin d receptor in mexican mestizo patients with intervertebral disc degeneration. Int J Genomics. 2014; 2014: 302568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen Y, Ma H, Bi D, et al.: Association of interleukin 1 gene polymorphism with intervertebral disc degeneration risk in the Chinese Han population. Biosci Rep. 2018; 38(4). PubMed Abstract | Publisher Full Text | Free Full Text\n\nAparicio JP, Bances IF, Fernández EL-A, et al.: The IL-1 β (+ 3953 T/C) gene polymorphism associates to symptomatic lumbar disc herniation. Eur Spine J. 2011; 20(3): 383–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen W, Li G, Sun H, et al.: Association of vitamin D receptor gene polymorphism in Han people with lumbar degenerative disc disease. Afr J Pharm Pharmacol. 2012; 6(16): 1211–5. Publisher Full Text\n\nCheung KM, Chan D, Karppinen J, et al.: Association of the Taq I allele in vitamin D receptor with degenerative disc disease and disc bulge in a Chinese population. Spine. 2006; 31(10): 1143–8. PubMed Abstract | Publisher Full Text\n\nEser B, Cora T, Eser O, et al.: Association of the polymorphisms of vitamin D receptor and aggrecan genes with degenerative disc disease. Genet Test Mol Biomark. 2010; 14(3): 313–7. PubMed Abstract | Publisher Full Text\n\nLi L, Ni D, Zhu F, et al.: No association between VDR gene polymorphisms and lumbar disc herniation in a Chinese population. Int J Clin Exp Med. 2018; 11: 1009–14.\n\nOishi Y, Shimizu K, Katoh T, et al.: Lack of association between lumbar disc degeneration and osteophyte formation in elderly Japanese women with back pain. Bone. 2003; 32(4): 405–11. PubMed Abstract | Publisher Full Text\n\nOmair A, Lie BA, Reikeras O, et al.: An association study of interleukin 18 receptor genes (IL18R1 and IL18RAP) in lumbar disc degeneration. Open Orthop J. 2012; 6: 164. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYuan H-Y, Tang Y, Liang Y-X, et al.: Matrix metalloproteinase-3 and vitamin d receptor genetic polymorphisms, and their interactions with occupational exposure in lumbar disc degeneration. J Occup Health. 2010; 52(1): 23–30. PubMed Abstract | Publisher Full Text\n\nRaj PP: Intervertebral disc: anatomy-physiology-pathophysiology-treatment. Pain Pract. 2008 Jan-Feb; 8(1): 18–44. PubMed Abstract | Publisher Full Text\n\nCervin Serrano S, González Villareal D, Aguilar-Medina M, et al.: Genetic polymorphisms of interleukin-1 alpha and the vitamin d receptor in mexican mestizo patients with intervertebral disc degeneration. Int J Genomics. 2014; 2014: 302568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMayer JE, Iatridis JC, Chan D, et al.: Genetic polymorphisms associated with intervertebral disc degeneration. Spine J. 2013 Mar; 13(3): 299–317. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIshihara H, Urban JP: Effects of low oxygen concentrations and metabolic inhibitors on proteoglycan and protein synthesis rates in the intervertebral disc. J Orthop Res. 1999 Nov; 17(6): 829–35. PubMed Abstract | Publisher Full Text\n\nOhshima H, Urban JP: The effect of lactate and pH on proteoglycan and protein synthesis rates in the intervertebral disc. Spine. 1992 Sep; 17(9): 1079–82. PubMed Abstract | Publisher Full Text\n\nAkyol S, Eraslan BS, Etyemez H, et al.: Catabolic cytokine expressions in patients with degenerative disc disease. Turk Neurosurg. 2010 Oct; 20(4): 492–9. PubMed Abstract | Publisher Full Text\n\nGrönblad M, Virri J, Tolonen J, et al.: A controlled immunohistochemical study of inflammatory cells in disc herniation tissue. Spine (Phila Pa 1976). 1994 Dec 15; 19(24): 2744–51. PubMed Abstract | Publisher Full Text\n\nRannou F, Corvol MT, Hudry C, et al.: Sensitivity of anulus fibrosus cells to interleukin 1 beta. Comparison with articular chondrocytes. Spine (Phila Pa 1976). 2000 Jan; 25(1): 17–23. PubMed Abstract | Publisher Full Text\n\nHong J, Yan J, Chen J, et al.: Identification of key potential targets for TNF-α/TNFR1-related intervertebral disc degeneration by bioinformatics analysis. Connect Tissue Res. 2020 Aug 26: 1–11. PubMed Abstract | Publisher Full Text\n\nLe Maitre CL, Hoyland JA, Freemont AJ: Catabolic cytokine expression in degenerate and herniated human intervertebral discs: IL-1beta and TNFalpha expression profile. Arthritis Res Ther. 2007; 9(4): R77. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLe Maitre CL, Freemont AJ, Hoyland JA: A preliminary in vitro study into the use of IL-1Ra gene therapy for the inhibition of intervertebral disc degeneration. Int J Exp Pathol. 2006 Feb; 87(1): 17–28. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaroudas A: Biophysical chemistry of cartilaginous tissues with special reference to solute and fluid transport. Biorheology. 1975 Jun; 12(3–4): 233–48. PubMed Abstract | Publisher Full Text\n\nEl-Omar EM, Carrington M, Chow WH, et al.: Interleukin-1 polymorphisms associated with increased risk of gastric cancer. Nature. 2000 Mar 23; 404(6776): 398–402. PubMed Abstract | Publisher Full Text\n\nNee LE, McMorrow T, Campbell E, et al.: TNF-alpha and IL-1beta-mediated regulation of MMP-9 and TIMP-1 in renal proximal tubular cells. Kidney Int. 2004 Oct; 66(4): 1376–86. PubMed Abstract | Publisher Full Text\n\nShingu M, Nagai Y, Isayama T, et al.: The effects of cytokines on metalloproteinase inhibitors (TIMP) and collagenase production by human chondrocytes and TIMP production by synovial cells and endothelial cells. Clin Exp Immunol. 1993 Oct; 94(1): 145–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWisithphrom K, Murray PE, Windsor LJ: Interleukin-1 alpha alters the expression of matrix metalloproteinases and collagen degradation by pulp fibroblasts. J Endod. 2006 Mar; 32(3): 186–92. PubMed Abstract | Publisher Full Text\n\nFournier DE, Kiser PK, Shoemaker JK, et al.: Vascularization of the human intervertebral disc: A scoping review. JOR Spine. 2020; 3(4): e1123. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUrban JP, Smith S, Fairbank JC: Nutrition of the intervertebral disc. Spine. 2004 Dec 1; 29(23): 2700–9. PubMed Abstract | Publisher Full Text\n\nRoberts S, Urban JP, Evans H, et al.: Transport properties of the human cartilage endplate in relation to its composition and calcification. Spine. 1996 Feb 15; 21(4): 415–20. PubMed Abstract | Publisher Full Text\n\nKongsbak M, Levring T, Geisler C, et al.: The Vitamin D Receptor and T Cell Function. Front Immunol. 2013 2013-June-18; 4(148). PubMed Abstract | Publisher Full Text | Free Full Text\n\nVideman T, Leppävuori J, Kaprio J, et al.: Intragenic polymorphisms of the vitamin D receptor gene associated with intervertebral disc degeneration. Spine. 1998 Dec 1; 23(23): 2477–85. PubMed Abstract | Publisher Full Text\n\nHarapan H: The role of single nucleotide polymorphisms of IL-1A -889C>T (rs1800587), TNF-A -238G>A (rs361525), and VDR TaqI (rs731236) on susceptivity of herniated nucleus pulposus. figshare. Figure. 2020. Publisher Full Text"
}
|
[
{
"id": "86114",
"date": "01 Jun 2021",
"name": "Ismail Hadisoebroto Dilogo",
"expertise": [
"Reviewer Expertise Stem cell and Tissue Engineering"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 remark:\nThe title is descriptive about the manuscript, however, please state the study design on the title.\n\nTo draw the interest of the reader, is it possible if the authors simplified the title from “IL-1A-889C>T(rs1800587)\" to “IL-1A”, and also the same for TNF-A and VDR?\n\nAbstract:\nLine 31, please state the problem that this review will answer.\n\nLine 35, in the methods section, please state the study design of included samples in this study to show the level of evidence of this meta-analysis.\n\nLine 58, for the conclusion, please kindly state the answer and summary of the research question, instead of restating limitation and result.\n\nIntroduction:\nThe Introduction is already well written. It gives enough information for the reader to understand the context. It also clearly explains why the study was necessary.\n\nMaterials and Methods:\nAs all the studies included in this review are a case-control, though it is uncommon for a systematic review meta-analysis to use a case control as a sample, please clarify and state that there is no Randomized Controlled Trial and Cohort study about this topic.\n\nI noticed the authors used Newcastle Ottawa Score, please kindly check https://ebm.bmj.com/content/23/2/60 to review the methodological quality of a case series.\n\nPlease define the primary outcome in this review.\n\nResult and discussion:\nThe results are presented clearly and accessibly, and it also supports the main conclusion. The discussion, has to be more detailed, from line 203- 244, the discussion mainly discusses the pathogenesis of the herniated nucleus pulposus. Please kindly deepen the discussion based on the result of this review, compare it with previous study(s), and explain the finding from the authors' point of view.\n\nFigures and Tables:\nFigures and Tables are adequately explained.\n\nConclusion:\nThe limitations are well stated, however, line 286-288 “Therefore, studies with larger sample sizes and sub-analyses for different populations such as Asian, Caucasian, and other populations are warranted whenever more data are available.” Please put in one paragraph before the conclusion to make the conclusion from your review stronger.\n\nOverall comments:\nThis manuscript may be considered for indexing after Major revisions.\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? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "6990",
"date": "06 Aug 2021",
"name": "Azharuddin Azharuddin",
"role": "Author Response",
"response": "#Reviewer 1 Abstract: Line 31, please state the problem that this review will answer. Response: We have added the problem that underly our study in abstract: “The pathogenesis of herniated nucleus pulposus (HNP) is complex, and may involve the wide variety of gene polymorphism. However, the reports from the existing evidence revealed inconclusive findings.” Abstract: Line 35, in the methods section, please state the study design of included samples in this study to show the level of evidence of this meta-analysis. Response: the study design of included articles has been added in the results section of abstract: “We screened 3,067 unique studies for eligibility and three, two and nine case-control studies on IL-1A -889C>T, TNF-A -238G>A, and VDR TaqI were included, respectively, in our meta-analysis.” Abstract: Line 58, for the conclusion, please kindly state the answer and summary of the research question, instead of restating limitation and result. Response: The main findings of our study has been outlined in the conclusion section of abstract: “our data indicated that IL-1A -889C>T, TNF-A -238G>A, and VDR TaqI had weak association with HNP susceptibility in both genotypes and allele distributions.” However, we also described about the clinical implication, limitation and future research direction to prevent the miss-understanding in interpretating the findings of our study. Introduction: The Introduction is already well written. It gives enough information for the reader to understand the context. It also clearly explains why the study was necessary. Response: thank you. Materials and Methods: As all the studies included in this review are a case-control, though it is uncommon for a systematic review meta-analysis to use a case control as a sample, please clarify and state that there is no Randomized Controlled Trial and Cohort study about this topic. Response: We agree that case-control studies are uncommon to include in meta-analysis. However, in the meta-analysis, we cannot manage the findings (the findings of article searching) as we expected if they are not supported by the available data. And unfortunately, in the searching strategy, we only found case-control studies. This point has also been included in the limitations of our study. Materials and Methods: I noticed the authors used Newcastle Ottawa Score, please kindly check https://ebm.bmj.com/content/23/2/60 to review the methodological quality of a case series. Response: We thank you for the suggestion. Case report and or case series studies may be possible to include in systematic review. However, they are not possible to include in meta-analysis (double arm calculation, as reported in our current study) because they do not have control. Materials and Methods: Please define the primary outcome in this review. Response: The primary outcomes have been provided in the Method section: “Covariates and sub-group analysis. The outcome measure in our study was the incidence of HNP while the predictor covariates were the gene polymorphisms of IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236). All genetic models were applied to describe the role of each gene variant in the pathogenesis of HNP. For IL-1A (rs1800587), the allele models were C vs. T and T vs. C; and the genotype models were CC vs. CT + TT, CT vs. CC + TT, and TT vs. CC + CT. For TNF-A (rs361525), the allele models were G vs. A and A vs. G; and the genotype models were GG vs. GA + AA, GA vs. GG + AA, and AA vs. GG + GA. For VDR (rs731236), the allele models were T vs. C and C vs. T; and the genotype models were TT vs. TC + CC, TC vs. TT + CC, and CC vs. TT + TC.” Result and discussion: The results are presented clearly and accessibly, and it also supports the main conclusion. Response: Thank you. The discussion, has to be more detailed, from line 203- 244, the discussion mainly discusses the pathogenesis of the herniated nucleus pulposus. Please kindly deepen the discussion based on the result of this review, compare it with previous study(s), and explain the finding from the authors' point of view. Response: The explanation on our main findings and the holistic comparison including the possible reason of our findings has been provided: “Our present study failed to clarify the role of IL-1A (rs1800587), TNF-A (rs361525), and VDR (rs731236) in the pathogenesis of HNP. To the best of our knowledge, our current study is the first study providing the holistic gene polymorphism in the case of HNP. Therefore, the comprehensive comparison in the context of methodological quality between our study and previous studies was unable to perform. However, several possible reason for the negative findings in our study might be proposed. First, HNP is a complex disease and is cause by multiple factors. Thus, no single factor such as a single SNP is responsible for the whole pathogenesis. Second, large variations in the number of samples or allele frequencies among studies in our meta-analysis also contribute to the findings. This probably relates to differences in populations where study data were collected. Finally, the small number of samples significantly influenced the results of our meta-analysis. Therefore, studies with larger sample sizes and sub-analyses for different populations such as Asian, Caucasian, and other populations are warranted whenever more data are available.” Figures and Tables: Figures and Tables are adequately explained. Response: Thank you. Conclusion: The limitations are well stated, however, line 286-288 “Therefore, studies with larger sample sizes and sub-analyses for different populations such as Asian, Caucasian, and other populations are warranted whenever more data are available.” Please put in one paragraph before the conclusion to make the conclusion from your review stronger. Response: The conclusion has been revised as suggested. Overall comments: This manuscript may be considered for indexing after Major revisions. Response: Thank you."
}
]
},
{
"id": "87698",
"date": "19 Jul 2021",
"name": "Mahir Gachabayov",
"expertise": [
"Reviewer Expertise Clinical outcomes research and evidence synthesis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 of reviewing this manuscript.\n\nThis is a systematic review and meta-analysis aiming at evaluating the impact of SNPs on susceptibility to HNP.\n\nThe research question makes sense. The gap in the literature was well presented and the objective of the review was well formulated.\n\nThe protocol of the systematic review was prospectively developed and registered in PROSPERO.\n\nThe search strategy was comprehensive.The screening and study selection process were well described and illustrated in a PRISMA flow diagram. Methodology of quality assessment and statistical analysis was adequate.\n\nThe results are well presented, summarized in tables, and illustrated in forest plots.\n\nThe Discussion is comprehensible, well-describes the findings of this systematic review in comparison with the current body of evidence.\n\nConclusions are justified by the findings.\n\nI have one minor comment:\nIt seems like the limitations were presented in the conclusion. I would separate them from the conclusions and move them as the last paragraph of the Discussion.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "6989",
"date": "06 Aug 2021",
"name": "Azharuddin Azharuddin",
"role": "Author Response",
"response": "#Reviewer 2 I have one minor comment: It seems like the limitations were presented in the conclusion. I would separate them from the conclusions and move them as the last paragraph of the Discussion. Response: The limitation has been provided in the end of discussion section. The conclusion has been revised as suggested."
}
]
}
] | 1
|
https://f1000research.com/articles/10-419
|
https://f1000research.com/articles/10-330/v1
|
29 Apr 21
|
{
"type": "Method Article",
"title": "A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases",
"authors": [
"Tiana M. Scott",
"Sam Jensen",
"Brett E. Pickett",
"Tiana M. Scott",
"Sam Jensen"
],
"abstract": "Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent of coronavirus disease-2019 (COVID-19), is a novel Betacoronavirus that was first reported in Wuhan, China in December of 2019. The virus has since caused a worldwide pandemic that highlights the need to quickly identify potential prophylactic or therapeutic treatments that can reduce the signs, symptoms, and/or spread of disease when dealing with a novel infectious agent. To combat this problem, we constructed a computational pipeline that uniquely combines existing tools to predict drugs and biologics that could be repurposed to combat an emerging pathogen. Methods: Our workflow analyzes RNA-sequencing data to determine differentially expressed genes, enriched Gene Ontology (GO) terms, and dysregulated pathways in infected cells, which can then be used to identify US Food and Drug Administration (FDA)-approved drugs that target human proteins within these pathways. We used this pipeline to perform a meta-analysis of RNA-seq data from cells infected with three Betacoronavirus species including severe acute respiratory syndrome coronavirus (SARS-CoV; SARS), Middle East respiratory syndrome coronavirus (MERS-CoV; MERS), and SARS-CoV-2, as well as respiratory syncytial virus and influenza A virus to identify therapeutics that could be used to treat COVID-19. Results: This analysis identified twelve existing drugs, most of which already have FDA-approval, that are predicted to counter the effects of SARS-CoV-2 infection. These results were cross-referenced with interventional clinical trials and other studies in the literature to identify drugs on our list that had previously been identified or used as treatments for COIVD-19 including canakinumab, anakinra, tocilizumab, sarilumab, and baricitinib. Conclusions: While the results reported here are specific to Betacoronaviruses, such as SARS-CoV-2, our bioinformatics pipeline can be used to quickly identify candidate therapeutics for future emerging infectious diseases.",
"keywords": [
"bioinformatics",
"repurposing",
"coronavirus",
"SARS-CoV-2",
"COVID-19",
"virus",
"infection",
"therapeutic",
"target"
],
"content": "Introduction\n\nCoronaviruses consist of a lipid envelope that contains a single-stranded positive-sense RNA genome that is approximately 30 kilobases in length. Prior to 2019, six human coronavirus species had been discovered including HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, and MERS-CoV. Four of these coronavirus species are endemic in humans and typically cause mild respiratory tract infections that present with cold-like symptoms but can cause more severe symptoms in immunocompromised individuals or infants1,2. Two of these four endemic virus species are members of the Alphacoronavirus genus (HCoV-229E and HCoV-NL63), while the other two species are members of the Betacoronavirus genus (HCoV-HKU1 and HCoV-OC43). The remaining two novel human coronavirus species discovered during this time are severe acute respiratory syndrome coronavirus (SARS-CoV; SARS) and Middle East respiratory syndrome coronavirus (MERS-CoV; MERS), which were emergent Betacoronaviruses responsible for epidemics in 2003 and 2012 respectively1,3. Human coronaviruses generally emerge from other animal hosts such as bats or mice, and typically pass through an intermediate host (e.g. civet cats for SARS and dromedary camels for MERS) before infecting a human host1,3.\n\nIn December 2019, a novel coronavirus was reported in Wuhan city, Hubei province, China and has since been named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 is highly similar to other SARS-like viruses that have been isolated from bats previously, especially BatCoV RaTG13 with which it shares 96.3% identity4,5. Initial infections with SARS-CoV-2 were traced back to the Huanan Seafood Wholesale Market and likely infected humans via a pangolin intermediate6. The global COVID-19 pandemic, as of February 14, 2021, has resulted in over 108 million cases and over 2.3 million deaths worldwide. Approximately 7.6 million of the cases and over 500,000 deaths have occurred in the United States of America7.\n\nCommon symptoms of COVID-19 include fever, dry cough, dyspnea, sore throat, myalgia, fatigue, and in some cases diarrhea4,5,8–11. SARS-CoV-2 is spread through aerosols, droplets, direct contact between people, and fomites4,12. Other studies suggest a fecal-oral transmission route is possible due to the presence of SARS-CoV-2 in stool samples of infected patients12,13. SARS-CoV-2 infects cells by binding to the membrane-associated Angiotensin-converting enzyme 2 (ACE2) receptor, which generally plays a role in the renin-angiotensin-aldosterone system to regulate blood pressure and fluid balance in the body14,15. ACE2 receptors are known to be expressed in lung, renal, cardiac, vascular, intestinal, and placental tissues14,15.\n\nBoth the widespread effects of COVID-19 and the initial highly susceptible population emphasized the need to identify potential drug treatments for emerging diseases--particularly before vaccines become available. The aim of many recent and ongoing clinical trials is to quantify the efficacy of various therapeutics for COVID-1916. Many vaccines are in various stages of preclinical (at least 139) or clinical (at least 25) development17, as well as some that have gained emergency use authorization by the US Food and Drug Administration (FDA).\n\nThe COVID-19 pandemic, caused by the SARS-CoV-2 virus, has highlighted the need to quickly and accurately identify therapeutics that can be repurposed to combat the signs, symptoms, and spread of disease. One method for predicting potential therapeutics is to identify host pathways that are dysregulated by infections and then find existing drugs that target those pathways. Programs to perform this analysis include DrugThatGene and GPSnet, which have both been used to identify potential drugs to target cancers18,19. The aim of this study was to construct a bioinformatics workflow that uniquely combines existing tools, databases, and programming libraries with custom scripts to predict potential human therapeutic targets for multiple members of the Betacoronavirus genus, which includes the SARS-CoV, SARS-CoV-2, and MERS-CoV species. Our unique combination of tools consists of a consistent and robust RNA-seq preprocessing workflow as well as an intracellular signaling pathway perturbation method that enables us to account for the role of protein-protein interaction networks instead of merely enriching for differentially expressed genes. We then applied this workflow to a use case involving a meta-analysis of coronaviruses and other respiratory viruses. This workflow first performs an analysis of human genes and significant signaling pathways that play a role in infection and pathogenesis. The pathway information is then used to predict relevant human drug targets and the associated small molecules or biologics that bind to the target of interest.\n\nThe rationale for identifying drug targets from multiple intersecting signaling pathways is based on the theory that a protein which participates in multiple affected pathways during viral infection has a higher likelihood of playing an important role in viral pathogenesis and replication. Targeting one or more of these proteins that act as “key hubs” with a therapeutic would therefore have a higher chance of reducing viral processes and the ensuing disease. Similarly, host proteins that participate in multiple pathways across various related viruses likely represent an evolutionarily conserved host-pathogen interaction that can be therapeutically modulated. We expect virus resistance to these host-based drugs to be relatively infrequent since they target relevant host processes. Our workflow could therefore be applicable not only to improving therapeutic treatment during infection with existing or emerging coronaviruses, such as SARS-CoV-2, but to rapidly identifying potential treatments for pathogens that may emerge in the future.\n\n\nMethods\n\nA search of the Gene Expression Omnibus (GEO) database, hosted at the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov/geo/)20, was performed in mid-2020 to find RNA-sequencing datasets for various viruses including “MERS”, “SARS”, and “coronavirus”. The corresponding sequencing data for four GEO series were retrieved from the Sequence Read Archive (SRA; https://www.ncbi.nlm.nih.gov/sra) at NCBI21: GSE122876, GSE56192, GSE147507, GSE13951622–24. These datasets were generated from cell cultures or patients infected with one of: respiratory syncytial virus (RSV), influenza A virus (IAV), MERS, SARS, and SARS-CoV-2. The SRA files were downloaded and converted to fastq format using version 2.10.1 of the NCBI sratools software package (https://github.com/ncbi/sra-tools).\n\nThe Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data (ARMOR) workflow was used to preprocess and analyze the fastq files against the Ensembl reference transcriptome for Homo sapiens build GRCh38, release 98 [GCA_000001405.15]25. Briefly, this automated snakemake-based workflow performs quality control of the reads with fastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/), trims the adapters and poor-quality regions with TrimGalore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), maps & quantifies reads to the human transcriptome using Salmon26, performs differential expression using edgeR27, identifies differential transcript usage with DRIMseq28, and enriches on Gene Ontology terms29 and Hallmark gene sets30 using the Camera algorithm to adjust for inter-gene correlation31. Differential expression was performed by calculating log2 fold-change and the associated p-values from infected samples versus mock-infected samples. The significance threshold for differential gene expression and Gene Ontology enrichment was defined as an false discovery rate (FDR)-corrected p-value < 0.05. Gene Ontology enrichment results from all datasets were then combined to identify shared terms.\n\nOnce the differentially expressed gene lists were constructed, the Ensembl identifiers for these human gene lists were mapped to the corresponding NCBI Entrez Gene identifiers using BioMart and Bioconductor32,33 prior to pathway enrichment using Signaling Pathway Impact Analysis (SPIA)34. Briefly, this pathway analysis combines robust statistics and bootstrapping to identify enriched pathways from lists of genes by incorporating the directionality of expression. Public pathway databases in the Graphite package in R Bioconductor were used by SPIA for enrichment with those surpassing a Bonferroni-corrected p-value < 0.05 being retained35. These databases include: KEGG36, Reactome37, Panther38, NCI39, and BioCarta. All pathways from each dataset were then compared to identify those that were shared among the various datasets, as well as those that were unique only to infection with SARS-CoV-2.\n\nThe output from the SPIA pathway enrichment were then used as input for a custom bioinformatics pipeline to identify existing drugs and biologics that could be repurposed to reduce signs, symptoms, and/or replication of coronaviruses. Specifically, this pipeline iteratively 1) retrieves the genes that participate in each statistically significant signaling pathway, 2) maps the gene identifiers to the corresponding UniProt protein identifier40, 3) searches the opentargets resource (www.opentargets.org41) to identify known drug targets and therapeutics, and 4) generates a table with various attributes of the target and small molecule/biologic treatment. These data were then integrated with the pathway comparisons across the various datasets and analyzed to determine what drugs would affect the pathways dysregulated in the greatest number of viruses and could be used as potential therapeutics for SARS-CoV-2 infection. The results were ranked by how many times a given protein target appeared in the results across the relevant virus taxa. The top ranked small molecules/biologic treatments were analyzed to determine which were predicted to reverse the effects of the viral infection on a given pathway. Manual review of high-ranking hits was then performed to determine the existing indication(s) for each treatment, followed by a literature search to determine which, if any, of the therapeutics identified had previously been used or considered for the treatment of COVID-19. Code for this workflow can be found on GitHub: https://github.com/bpickett/Pathway2Targets.\n\n\nResults\n\nEach of the algorithmic components of our computational workflow was dependent on first calculating differentially expressed (DE) genes for each of the datasets. We consequently began by using the same computational workflow to generate the DE genes from the raw transcriptomic data for human cells infected with one of: RSV, IAV, MERS, SARS, and SARS-CoV-2. Each set of results was specific to the comparison that was performed (e.g. mock-infected vs. infected) and included both log2 fold-change values and FDR-corrected p-values. We then integrated and compared the differential expression results across all virus comparisons to facilitate downstream comparisons.\n\nWe began by identifying genes that were either up- or down-regulated across a large number of studies. Specifically, we calculated the number of DE genes (FDR-corrected p-value < 0.05) that significantly changed during infection with influenza A (4205 genes), RSV (3661 genes), MERS (range across studies: 1222-13006 genes), SARS-CoV (range across studies: 2130-5557 genes), or SARS-CoV-2 (range across studies: 427-6933 genes). Out of the 15 studies evaluated, we observed 11 genes that displayed increased expression across 10-13 study comparisons including: TRIM25, C3, NCOA7, PTAFR, TNFAIP3, EIF2AK2, HELZ2, HBEGF, NFKB2, REL and VEGFC. We found an additional 18 genes that were upregulated across 9 of the 15 comparisons including: IFIT2, EGFR, and FOSL1. In contrast, we identified 14 genes that showed decreased expression across 11-12 comparisons including: EIF4H, APH1A, NME2, SEC61B, TUBB4B, CHCHD2, TUBA1C, TP53I3, H2AFZ, PEBP1, HOXB6, TPM2, CBR1, and SIVA1.\n\nWe next analyzed the DE lists to identify significant genes that were shared across infections involving only the Betacoronaviruses including SARS-CoV, MERS-CoV, and SARS-CoV-2. This analysis revealed 12 genes that were upregulated in at least nine of thirteen comparisons including: TRIM25, REL, DNASE1, C3, NCOA7, PTAFR, EIF2AK2, HELZ2, NFKB2, ZNF385C, ZC3H12A, and OR7E122P. In contrast, the 10 genes that were found to be downregulated in ten of the thirteen comparisons involving any of the Betacoronaviruses included: CHCHD2, SMIM3, EIF4H, NME2, CBR1, SPARC, DSTN, CDC123, TIMM17A, and PDAP1.\n\nWe then performed a similar analysis to identify the five statistically significant DE genes (FDR-corrected p-value < 0.05) that displayed the highest and lowest average fold-change values during infection across all comparisons of SARS-CoV-2, Betacoronaviruses, or all viruses (Figure 1). This analysis showed that a subset of the genes such as CXCL11, which is induced by interferon and is involved in T-cell signaling, displayed similar fold-change values across multiple comparisons. This finding was somewhat expected since certain genes involved in the host innate immune response are expected to be modulated during virus infection. However, we also observed that genes such as MUC3A, PCSK5, MRC1, and CLEC3B displayed somewhat different average fold-change values across the included comparisons. This observation was also expected given the diverse virus replication requirements and the resulting host intracellular transcriptional response that occurs during infections with human viral pathogens.\n\nThe five genes with the highest and lowest log2 fold-change values for each virus comparison were identified and compared against expression in the other datasets. Squares in red or blue represent genes that are upregulated or downregulated (respectively) in the relevant comparison.\n\nGiven the number of DE genes involved in the analysis, manual interpretation of the results would be intractable. We therefore performed an analysis to determine which Gene Ontology (GO) terms and Hallmark gene sets were specifically enriched to better understand which biological processes and molecular functions were represented by the genes in each of the DE gene lists. Overall, we observed a superset of 580 terms that were enriched in any of the included viral infections. The enrichment results for each taxon of virus were then reviewed to identify annotated terms that were shared between multiple types of viral infections, shared amongst coronaviruses, or specific to SARS-CoV-2.\n\nWe found several notable terms that were shared among the results obtained from infection of multiple unrelated taxa of viruses. These terms referred to functions such as the host interferon response, regulation of virus response, chemokine activity, and immune cell migration that were positively enriched in both the RSV infection of A549 cells and the SARS-CoV-2 infection of either A549 or NHBE cells. As expected, the statistical significance of these terms supports the important role that the human immune system plays in response to virus infection, which is an expected result and validates the upstream DE gene analysis.\n\nOur method identified no significant GO terms that were shared across all Betacoronavirus comparisons. Interestingly, we found that each coronavirus species had its own set of uniquely enriched terms. In MERS-CoV, “negative regulation of inclusion body assembly” was positively enriched in four of the seven comparisons, while “aggrephagy” and “regulation of nucleotide binding oligomerization domain containing 2 signaling pathway” were positively enriched in three of the seven comparisons. The SARS-CoV samples had very few significantly enriched annotation terms including the “signal peptidase complex” and “cyclin dependent protein serine threonine kinase activator activity” terms that were each negatively enriched in only one of the four SARS-CoV comparisons.\n\nWe also identified 290 terms that were uniquely present among the SARS-CoV-2 comparisons, although no significant terms were identified in comparisons involving either the human post-mortem biopsies or the infected Calu-3 cells. The shared significant terms that we identified in the NHBE- and A549-infected cells included “response to chemokine”, “antimicrobial humoral response”, and “humoral immune response.” Enriched terms in the NHBE-infected cells alluded to the role of the inflammatory response, interleukin-1, interleukin-6, neuroinflammation, arachidonic acid binding, and T-cell activation.\n\nWe then wanted to calculate which intracellular signaling pathways were significantly modulated during viral infection, based on the DE genes identified above. The pathway information used for this analysis was obtained from public databases that manually curate the proteins that participate in conveying a signal from receptors on the cell membrane to transcription factors within the nucleus in order to respond to a stimulus.\n\nWe used the results of the differential gene expression analysis as input to the SPIA algorithm. The robust bootstrap-based approach of this method identified 249 pathways that were significantly perturbed across at least one viral comparison. We subsequently analyzed the lists of significantly perturbed pathways for each comparison to determine those that were shared across virus taxa (e.g. influenza A, respiratory syncytial, MERS-CoV, SARS-CoV, and SARS-CoV-2), shared among coronaviruses, and unique to SARS-CoV-2. This analysis revealed a subset of the total number of pathways to be dysregulated across many of the viral taxa studied. These pathways included translation (affected in 12/17 comparisons and 4/5 viral taxa), cytokine-cytokine receptor interaction (modulated in 11/17 comparisons and 4/5 viral taxa), as well as rRNA processing (modulated in 10/17 comparisons and 3/5 viral taxa). We also observed that some of these pathways were predicted to be activated during infection with certain viral taxa in specific cell types, while inhibited in others.\n\nWe did not observe any signaling pathways that were significantly and consistently affected during infection by the individual coronavirus species examined. However, we did detect relevant pathways across multiple virus taxa. Interestingly, we found that the direction (i.e. activated or inhibited) was occasionally dependent on virus taxa or timepoint of infection. For example, the cytokine-cytokine receptor interaction pathway was predicted to be activated during infection with RSV, a subset of comparisons involving MERS-CoV, and many SARS-CoV-2 infections; while the same pathway was predicted to be inhibited during infection with SARS-CoV.\n\nWe predicted a total of 38 pathways that were uniquely affected during SARS-CoV-2 infection (Table 1). We noted that 35 of these pathways were only found to be significant in one SARS-CoV-2 comparison and included “NF-kB signaling pathway”, “Interleukin-1 signaling”, “IL6-mediated signaling events”, “PI3K-Akt signaling pathway”, “Jak-STAT signaling pathway”, “Apoptosis”, “Complement and coagulation cascades”, and other processes associated with either the immune system or infectious diseases. The remaining three pathways that were predicted as affected during at least two SARS-CoV-2 comparisons were “Cytokine signaling in Immune system”, “Tuberculosis”, and the “Innate immune system”. In short, these findings indicate a set of signaling pathways that are strongly associated with virus infection and/or immune activation in the host, some of which are uniquely detected during SARS-CoV-2 infection. The “Cytokine Signaling in Immune System” pathway is stored in the Reactome database and consists of interferon alpha/beta and gamma signaling, interleukin 1, 2, 6, and 10 signaling, and other components37. To better understand the impact of SARS-CoV-2 on interleukin-6 signaling, we overlaid the differential expression data on a representation of the signaling pathway (Figure 2). This analysis revealed six of the eleven total proteins in the pathway were upregulated, while another protein was downregulated during SARS-CoV-2 infection.\n\nU: upregulated pathway; D: downregulated pathway\n\nThis signaling pathway is a component of the larger Cytokine Signaling in Immune System pathway in Reactome. Each node represents a protein in the network, while each edge represents a characterized interaction between the proteins. Higher log2 fold-change values (up-regulation) are represented by increasing saturation of red, while more negative log2-fold-change values (down-regulation) are colored with increased saturation of blue. White nodes indicate no measured log2-fold change.\n\nWe next wanted to determine whether any of the significantly affected signaling pathways contained known drug targets that could be modulated to reduce infection, virus replication, and/or clinical signs and symptoms associated with infection by a panel of Betacoronaviruses or by SARS-CoV-2 alone. To do so we cross-referenced the results from our significant pathways analysis with the drug-target information accessible through an application programming interface (API) to the opentargets.org database, which yielded 179 potential human drug targets (Table 2). We ranked the predicted drugs and their associated targets according to how many coronaviruses shared the same drug target across the various datasets included in our analysis. We performed a separate ranking based on the data obtained solely from the SARS-CoV-2 studies.\n\n**KEY: 1 = target was present in comparison, 0 = target was NOT present in comparison\n\nAfter reviewing the results of this analysis, we identified 38 potential human protein targets to counteract MERS-CoV, SARS-CoV, and/or SARS-CoV-2. Specifically, 38 targets were predicted to be relevant in at least 10 of the 15 coronavirus comparisons (Table 3). Seventeen of these targets were identified across 11 comparisons and included interferon (IFN)-A, IFN A receptors, IL1A and IL12B. Twenty-one additional targets were identified across 10 comparisons and included members of the tumor necrosis factor (TNF) superfamily, CCR4, CCR5, GHR, CXCR4, IL2R, IL4R, IL5, IL5R, IL6R, MPL, and IL20. We also predicted seven targets that were relevant specifically to SARS-CoV-2 including JAK1, FDPS, TLR7, TLR9, PRKCA, TYK2, and VDR.\n\nX: indicates the type of each therapeutic. Drug types against the same target are indicated with commas.\n\nOur analysis predicted twelve existing drugs that are predicted to be useful as repurposed therapeutics against 73.3% of all coronavirus taxa evaluated in this work and 100% of the SARS-CoV-2 comparisons included in our analysis (Table 4). Eight of these twelve drugs are used to treat common autoimmune disorders such as systemic lupus erythematosus (SLE), Crohn’s disease, and multiple sclerosis (MS). Five of the twelve drugs have been associated or used as antiviral measures largely against hepatitis C virus. Another 27 drugs were predicted to have potential therapeutic activity against 66.7% of all coronavirus infections and 30 were predicted as potential therapeutics against 75% of SARS-CoV-2 infections.\n\n**KEY: 1 = Drug predicted to be relevant in comparison; 0 = drug NOT predicted to be relevant in comparison\n\nWe then analyzed the drugs that were identified as having targets in pathways affected by SARS-CoV-2 to determine which were predicted to reverse the effects of the viral infection on the affected pathway. Of the 42 drugs that targeted SARS-CoV-2 related pathways, 27 were predicted to reverse viral effects on these pathways. We then performed a literature search to determine if any of these drugs had been previously used to treat COVID-19 or had been identified as potential therapeutics by other research groups. We found six of the 12 therapeutics that we predicted to be useful against SARS-CoV-2 had already shown positive results in clinical tests including canakinumab, anakinra, tocilizumab, sarilumab, and baricitinib. These results give further support to the validity of our computational workflow.\n\n\nDiscussion\n\nThe computational workflow that we describe in this work predicts human therapeutic targets from signaling pathways and gene expression that are significantly affected during infection. We applied this workflow within the context of a meta-analysis that consisted of multiple public transcriptomic datasets of Betacoronaviruses. We then validated our results by comparing our predictions against recently published studies reporting therapeutics for SARS-CoV-2. Specifically, our downstream analyses enable us to calculate significant signaling pathways from DE genes using the SPIA algorithm as well as to predict potential therapeutics and their respective targets. Our analysis revealed thousands of DE genes, 580 enriched functional terms, as well as 249 significant pathways, including 38 pathways that were specifically affected during infection with SARS-CoV-2. It is important to point out that this workflow focuses on identifying human drug targets for two reasons: 1) to aid in the repurposing of existing drugs against emerging pathogens, and 2) to reduce the likelihood that a pathogen will develop resistance against the therapeutic(s) since they interact with a human protein that is much less likely to mutate than a viral protein.\n\nOur approach differs from prior meta-analyses by focusing on a consistent, robust ARMOR-based RNA-seq preprocessing workflow for all datasets as well as a downstream pathway perturbation analysis. Previous studies have used a variety of approaches to predict possible therapeutics42–46, but none have combined the various aspects that are described in this work. The SPIA algorithm we used in this study has been shown to provide robust statistical results of perturbed pathways while not simply enriching for DE genes34. It also enabled us to identify protein components in signaling pathways that could be reversed to reduce the adverse signs and symptoms that occur during infection, which differs from simply attempting to target DE genes. This approach drastically differs from some attempts to directly target DE genes without accounting for how a treatment may affect the cellular protein-protein interaction network. In this analysis we have compared significant DE genes and pathways identified in multiple different studies that used different MOIs, timepoints, and cell types. We found many DE genes and pathways that were affected across a variety of samples which increases our confidence in our results as those genes and pathways appear to be affected more by the virus itself than by other variables such as cell type, MOI, or timepoint.\n\nAlthough our approach was dependent on identifying DE genes using a consistent preprocessing workflow, the focus of our analysis was to identify relevant functions, pathways, and potential drug targets from the DE genes. These processed data could then be used to better understand the underlying biological mechanisms of pathogenesis, but to better identify host-based therapeutic targets. A subset of the enriched annotations identified by the Camera algorithm have been reported to be relevant during infection with SARS-CoV-2 in clinical studies including “response to chemokine”47, “humoral immune response”48–50, “chronic inflammatory response”51,52, “toll like receptor binding”53,54, “interleukin-6 production”55 and citrate metabolism. A separate study of COVID-19 identified Bradykinin as potentially playing a role in pathogenesis56. Interestingly, the annotations for this gene and its receptor include several of the enriched terms we identified such as arachidonic acid, inflammation, and G-protein coupled receptor activity. We interpret these separate studies to validate the findings of our functional enrichment analysis and anticipate that future studies will shed additional insight into the underlying mechanism(s) of viral pathogenesis.\n\nMany of the signaling pathway components that we identified in this study have also been reported previously. One prior proteomics study reported applying translation inhibitors to Caco-2 cells infected with SARS-CoV-2 reduced virus replication57, which supports our pathway perturbation results. Other studies have reported that the ORF6, ORF8, and nucleocapsid proteins of SARS-CoV-2 are antagonists of type-I interferon and NF-kB in HEK-293 T cells58 or the induction of apoptosis during viral infection59. In contrast, our meta-analysis predicted the type-I interferon pathway to be activated, suggesting either that this response could be dependent on the cell type, or that a potential redundant mechanism in the host cell can still turn on this pathway even if certain components are down-regulated. Our analysis predicted that noncanonical NF-kB signaling was inhibited during MERS and SARS infection, while being activated during SARS-CoV-2 infection in Calu-3 cells. While it is possible that this difference is due to a cell-specific response from the studies included in our meta-analysis, a NF-kB inhibitor applied to Vero E6 cells infected with SARS-CoV-2 has been shown to reduce cytopathic effects and virus plaques60. This result suggests that NF-kB signaling may be active and contribute to the inflammatory signs and symptoms observed during virus infection, which agrees with our results. The Toll-like receptor and JAK-STAT pathways were previously found to be relevant to SARS-CoV-2 infection in A549 cells, which we also identified in infected Calu-3 cells42. Citrate metabolism was also identified as an important pathway by our analysis and has been supported elsewhere61.\n\nAlthough the US FDA has only issued emergency use authorization for therapeutic treatment for severe cases of COVID-19, a multitude of studies have reported results from attempting to treat patients with a variety of existing FDA approved therapeutics62–69. We found that 27 of our 42 predicted therapeutics are predicted to “reverse” the effect on the pathways relevant to the viral infections being compared. Twelve of the 27 drugs that were predicted to be potential therapeutics against SARS-CoV-2 and are used to combat autoimmune or inflammatory diseases such as MS, SLE, and rheumatoid arthritis while others have been used in cancer treatments and against viral infections such as hepatitis C and human immunodeficiency virus. Six of these 12 drugs have been used to treat COVID-19 in patients including canakinumab, anakinra, tocilizumab, sarilumab, baricitinib, and hydroxychloroquine70. Two other drugs, maraviroc and brodalumab, have been identified as potential treatments via cell cultures and computer models71–74. Others on the list such as benralizumab have been identified through anecdotal data as biologics that potentially exert a prophylactic effect for SARS-CoV-2, when they are taken at the time of infection75. Baricitinib is of particular interest as the US FDA has issued emergency use authorization for its use in conjunction with remdesivir in the treatment of COVID-19 patients over the age of two that have been hospitalized and require supplemental oxygen, invasive mechanical ventilation, or extracorporeal membrane oxygenation76. Baricitinib has also been shown to be effective against COVID-19 when combined with corticosteroids77. A small study involving Tocilizumab has also shown it can be useful in improving the outcome of patients with severe COVID-1978.\n\n\nConclusions\n\nIn conclusion, we developed and applied an important bioinformatics workflow, that combines existing tools with custom scripts, to predict potential human therapeutic targets. This workflow was then validated through a meta-analysis of publicly available transcriptomics data. The multiple Betacoronavirus and SARS-CoV-2 datasets revealed significant genes, annotations, signaling pathways, and human proteins that could be targeted by therapeutics during infection with various Betacoronaviruses. It is important to recognize that many of the predictions made by our workflow have been supported by experimental and clinical work on this virus, which suggests that our approach could enable the rapid identification of relevant therapeutics against future emerging pathogens.\n\n\nAbbreviations\n\nSARS-CoV-2: Severe acute respiratory syndrome coronavirus-2\n\nCOVID-19: Coronavirus disease-2019\n\nGO: Gene ontology\n\nSARS / SARS-CoV: Severe acute respiratory syndrome coronavirus\n\nMERS / MERS-CoV: Middle east respiratory syndrome coronavirus\n\nACE2: Angiotensin-converting enzyme 2\n\nFDA: Food and Drug Administration\n\nGEO: Gene expression omnibus\n\nNCBI: National center for biotechnology information\n\nARMOR: Automated Reproducible MOdular Workflow for Preprocessing and Differential Analysis of RNA-seq Data\n\nSPIA: Signaling pathway impact analysis\n\nDE: Differentially expressed\n\nFDR: False-discovery rate\n\n\nData availability\n\nGEO: Transcriptomic analysis of MERS-CoV infected Calu-3 cell with or without AM580 treatment, Accession number GSE122876: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122876\n\nGEO: Transcriptomic analysis of the Novel Middle East Respiratory Syndrome Coronavirus (Human, MRC5 cells, Accession number GSE56192: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56192\n\nGEO: Transcriptional response to SARS-CoV-2 infection, Accession number GSE147507: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147507\n\nGEO: Transcriptomic Analysis Of circRNAs/miRNAs/mRNAs upon Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection, Accession number GSE139516: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE139516\n\nCode for this workflow can be found on GitHub: https://github.com/bpickett/Pathway2Targets.\n\nArchived code as at time of publication: http://doi.org/10.5281/zenodo.470619779.\n\nCode is available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nWe would like to thank the Office of Research Computing at Brigham Young University for their help on this project. We also gratefully acknowledge the original providers of the RNA-seq datasets.\n\n\nReferences\n\nCorman VM, Muth D, Niemeyer D, et al.: Hosts and Sources of Endemic Human Coronaviruses. Adv Virus Res. 2018; 100: 163–88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu A, Peng Y, Huang B, et al.: Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe. 2020; 27(3): 325–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCui J, Li F, Shi ZL: Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2019; 17(3): 181–92. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHelmy YA, Fawzy M, Elaswad A, et al.: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu D, Yang XO: TH17 responses in cytokine storm of COVID-19: An emerging target of JAK2 inhibitor Fedratinib. J Microbiol Immunol Infect. 2020; 53(3): 368–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuang C, Wang Y, Li X, et al.: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; 395(10223): 497–506. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGu J, Han B, Wang J: COVID-19: Gastrointestinal Manifestations and Potential Fecal-Oral Transmission. Gastroenterology. 2020; 158(6): 1518–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDing S, Liang TJ: Is SARS-CoV-2 Also an Enteric Pathogen With Potential Fecal-Oral Transmission? A COVID-19 Virological and Clinical Review. Gastroenterology. 2020; 159(1): 53–61. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nCarvalho-Silva D, Pierleoni A, Pignatelli M, et al.: Open Targets Platform: new developments and updates two years on. Nucleic Acids Res. 2019; 47(D1): D1056–65. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFagone P, Ciurleo R, Lombardo SD, et al.: Transcriptional landscape of SARS-CoV-2 infection dismantles pathogenic pathways activated by the virus, proposes unique sex-specific differences and predicts tailored therapeutic strategies. Autoimmun Rev. 2020; 19(7): 102571. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMagro G: SARS-CoV-2 and COVID-19: Is interleukin-6 (IL-6) the “culprit lesion” of ARDS onset? What is there besides Tocilizumab? SGP130Fc. Cytokine X. 2020; 2(2): 100029. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSallenave JM, Guillot L: Innate Immune Signaling and Proteolytic Pathways in the Resolution or Exacerbation of SARS-CoV-2 in Covid-19: Key Therapeutic Targets? Front Immunol. 2020; 11: 1229. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDrucker DJ: Coronavirus Infections and Type 2 Diabetes-Shared Pathways with Therapeutic Implications. Endocr Rev. 2020; 41(3): bnaa011. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoagland DA, Clarke DJB, Møller R, et al.: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds. 2020 [cited 2020 Sep 17]; 2020.07.12.199687. Publisher Full Text\n\nCoperchini F, Chiovato L, Croce L, et al.: The cytokine storm in COVID-19: An overview of the involvement of the chemokine/chemokine-receptor system. Cytokine Growth Factor Rev. 2020; 53: 25–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Xu J, Jia R, et al.: Protective humoral immunity in SARS-CoV-2 infected pediatric patients. Cell Mol Immunol. 2020; 17(7): 768–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNi L, Ye F, Cheng ML, et al.: Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals. Immunity. 2020; 52(6): 971–7.e3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKellam P, Barclay W: The dynamics of humoral immune responses following SARS-CoV-2 infection and the potential for reinfection. J Gen Virol. 2020; 101(8): 791–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYoung BE, Fong SW, Chan YH, et al.: Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study. Lancet. 2020; 396(10251): 603–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFu Y, Cheng Y, Wu Y: Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools. Virol Sin. 2020; 35(3): 266–71. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBouayad A: Innate immune evasion by SARS-CoV-2: Comparison with SARS-CoV. Rev Med Virol. 2020; 30(6): 1–9. PubMed Abstract | Publisher Full Text\n\nMoreno-Eutimio MA, López-Macías C, Pastelin-Palacios R: Bioinformatic analysis and identification of single-stranded RNA sequences recognized by TLR7/8 in the SARS-CoV-2, SARS-CoV, and MERS-CoV genomes. Microbes Infect. 2020; 22(4–5): 226–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBelhadjer Z, Méot M, Bajolle F, et al.: Acute heart failure in multisystem inflammatory syndrome in children (MIS-C) in the context of global SARS-CoV-2 pandemic. Circulation. 2020; 142(5): 429–436. PubMed Abstract | Publisher Full Text\n\nGarvin MR, Alvarez C, Miller JI, et al.: A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. eLife. 2020; 9: e59177. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBojkova D, Klann K, Koch B, et al.: Proteomics of SARS-CoV-2-infected host cells reveals therapy targets. Nature. 2020; 583(7816): 469–72. PubMed Abstract | Publisher Full Text\n\nLi JY, Liao CH, Wang Q, et al.: The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway. Virus Res. 2020; 286: 198074. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRen Y, Shu T, Wu D, et al.: The ORF3a protein of SARS-CoV-2 induces apoptosis in cells. Cell Mol Immunol. 2020; 17(8): 881–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMa Q, Pan W, Li R, et al.: Liu Shen capsule shows antiviral and anti-inflammatory abilities against novel coronavirus SARS-CoV-2 via suppression of NF-κB signaling pathway. Pharmacol Res. 2020; 158: 104850. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOvermyer KA, Shishkova E, Miller IJ, et al.: Large-scale Multi-omic Analysis of COVID-19 Severity. medRxiv. 2020; 2020.07.17.20156513. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang B, Liu S, Tan T, et al.: Treatment With Convalescent Plasma for Critically Ill Patients With Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Chest. 2020; 158(1): e9–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H, Chen C, Hu F, et al.: Impact of corticosteroid therapy on outcomes of persons with SARS-CoV-2, SARS-CoV, or MERS-CoV infection: a systematic review and meta-analysis. Leukemia. 2020; 34(6): 1503–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYan Y, Shin WI, Pang YX, et al.: The First 75 Days of Novel Coronavirus (SARS-CoV-2) Outbreak: Recent Advances, Prevention, and Treatment. Int J Environ Res Public Health. 2020; 17(7): 2323. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang X, Yu Y, Xu J, et al.: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir Med. 2020; 8(5): 475–81. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMessina F, Piaserico S: SARS-CoV-2 infection in a psoriatic patient treated with IL-23 inhibitor. J Eur Acad Dermatol Venereol. 2020; 34(6): e254–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCaly L, Druce JD, Catton MG, et al.: The FDA-approved drug ivermectin inhibits the replication of SARS-CoV-2 in vitro. Antiviral Res. 2020; 178: 104787. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChoy KT, Wong AYL, Kaewpreedee P, et al.: Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro. Antiviral Res. 2020; 178: 104786. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYao X, Ye F, Zhang M, et al.: In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Clin Infect Dis. 2020; 71(15): 732–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGilzad-Kohan H, Jamali F: Anti-Inflammatory Properties of Drugs Used to Control COVID-19 and their Effects on the Renin-Angiotensin System and Angiotensin-Converting Enzyme-2. J Pharm Pharm Sci. 2020; 23: 259–77. PubMed Abstract | Publisher Full Text\n\nTazikeh-Lemeski E, Moradi S, Raoufi R, et al.: Targeting SARS-COV-2 non-structural protein 16: a virtual drug repurposing study. J Biomol Struct Dyn. 2020; 1–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShamsi A, Mohammad T, Anwar S, et al.: Glecaprevir and Maraviroc are high-affinity inhibitors of SARS-CoV-2 main protease: possible implication in COVID-19 therapy. Biosci Rep. 2020; 40(6): BSR20201256. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBulat V, Situm M, Azdajic MD, et al.: Potential role of IL-17 blocking agents in the treatment of severe COVID-19? Br J Clin Pharmacol. 2020; 87(3): 1578–1581. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRisner KH, Tieu KV, Wang Y, et al.: Maraviroc inhibits SARS-CoV-2 multiplication and s-protein mediated cell fusion in cell culture. bioRxiv. 2020; 2020.08.12.246389. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGarcía-Moguel I, Campos RD, Charterina SA, et al.: COVID-19, severe asthma, and biologics. Ann Allergy Asthma Immunol. 2020; 125(3): 357–9.e1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKalil AC, Patterson TF, Mehta AK, et al.: Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19. N Engl J Med. 2021; 384(9): 795–807. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodriguez-Garcia JL, Sanchez-Nievas G, Arevalo-Serrano J, et al.: Baricitinib improves respiratory function in patients treated with corticosteroids for SARS-CoV-2 pneumonia: an observational cohort study. Rheumatology (Oxford). 2021; 60(1): 399–407. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCala-García JD, Sierra-Bretón JD, Cavelier-Baiz JE, et al.: Recovery of COVID-19 acute respiratory distress syndrome with tocilizumab: successful outcome in two critically ill patients. Immunotherapy. 2020; 12(15): 1127–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPickett BE: Pathway2Targets. Zenodo. 2021. http://www.doi.org/10.5281/zenodo.4706197"
}
|
[
{
"id": "85467",
"date": "02 Jun 2021",
"name": "José Pedro Cerón-Carrasco",
"expertise": [
"Reviewer Expertise Computational Chemistry for Drug Design."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI feel this work touches up an alternative approach to the more classical computational protocol of performing virtual screening by docking methods + molecular dynamics to refine binding energies.\nHerein, the proposed method uses RNA-sequencing data with a focus on defining differentially expressed genes, enriched Gene Ontology (GO) terms, and dysregulated pathways in infected cells.\nOn the brightest side, that theoretical framework allows for a simultaneous search of small molecules, antibody and protein. The authors stated that their predictions yield to a final list of 42 therapeutics. 27 of such drugs have been reported to exhort an effect against the virus. It remains unrevealed if these other 15 are negative positive or pending possible treatments. A more 'experimental' reader might find a next candidate in that list.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "7043",
"date": "26 Aug 2021",
"name": "Brett Pickett",
"role": "Author Response",
"response": "We thank the reviewer for their helpful comment and agree that researchers would could indeed make good use of the complete list of drugs that we predicted to be useful against SARS-CoV-2. To address this comment we will update Table 4 in the next manuscript version to now include not only all of the predicted drugs, but also summaries of how each drug ranks across all analyzed Coronavirus datasets and also across all SARS-CoV-2 datasets. We believe that this change will improve the readability and relevance of our study."
}
]
},
{
"id": "89746",
"date": "02 Aug 2021",
"name": "Babatunde Joseph Oso",
"expertise": [
"Reviewer Expertise Biochemistry"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors presented an original article on the signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases. The authors are commended for the clarity and straight-forward style of the article. However, this manuscript needs to be improved regarding the following aspects:\nIt would be interesting if a bibliographic review on the importance of bioinformatics workflow and meta-analysis vis-à-vis prediction of potential human therapeutics can be included in the introduction section.\n\nThe argument presented in the introduction section should include a clear description of the statement problem.\n\nGenerally, the sentences should be well structured for a better flow and limit the use of possessive pronouns.\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/10-330
|
https://f1000research.com/articles/10-839/v1
|
20 Aug 21
|
{
"type": "Research Article",
"title": "Discovering research trends of urban geology based on a bibliometric analysis",
"authors": [
"Dasapta Erwin Irawan",
"Yuniarti Ulfa",
"Roishe Miyafto Prabowo",
"Benedictus Kombaitan",
"Deny Juanda Puradimaja",
"Yuniarti Ulfa",
"Roishe Miyafto Prabowo",
"Benedictus Kombaitan",
"Deny Juanda Puradimaja"
],
"abstract": "Urbanization contributes to the emerging urban areas across the world. The importance of geology to ensure sustainability, has led to many research publications in the urban geology. This paper aims to discover the research trends through a bibliometric analysis of articles indexed within the Scopus database from 1950 to 2018 on topics related to geology and urban. The analysis found a significant increase in publications during 1999-2016, especially after the 2004 Indian Ocean earthquake and tsunami disaster. The next finding of this study is related to research interest clusters: engineering geological hazard investigation and risk assessment in the urban area (EGR); social geology and urban sustainability (SGS); and urban hydrology and water management (HGW). The EGR studies were mostly in underground engineering geology (geotechnics). In contrast, the least attention was given to the interaction between geology and land-use planning, due to the SGS issues (e.g., urban planning and land use suitability assessment). This study may serve as a platform for scholars to understand the current status and future directions of urban geology.",
"keywords": [
"Bibliometric",
"urban geology",
"environmental geology",
"engineering geology",
"urban planning"
],
"content": "Introduction\n\nThe amount of research publications in the field of geology has reached a significant number. A broad search for articles that included geology as a keyword, was done with the use of the Scopus database, which resulted in at least 120,000 documents in more than 25 subject areas. By some, geology maybe viewed as identical to mining and petroleum, therefore, such topics indeed dominate about 45% of the total searched documents. Ore mining and petroleum industry commonly involved geological application in the less-populated areas. However, the rest of the searched documents (± 55%) showed how geology is applied in the more-populated areas (urban area). This is now known as urban geology (UG), which is less popular among societies, despite it being beneficial for many people.\n\nIn 1950s after World War II, UG began to grow in the United States of America, particularly in California, because of land-use planning, as a result there was tremendous economic growth and urban expansion.1–3 Intense meetings on UG were held in the 1960s till the 1970s,4,5 which was soon followed by the publication of a book called ‘Cities and Geology’.6 As most of the world’s population already live-in urbanized areas (>50%), in developing countries migration to these areas is on the rise.7,8 This can have significant challenges for urban areas since there is an increased pressure on resources, spaces, and services.8,9 For example, the zones that are available for construction are usually the least suitable, however the neglect of its geological setting potentially can lead to severe economic loss, e.g., tsunami destruction or building collapses. Therefore, geology plays a critical part in maintaining sustainable cities.6 At present, since urban areas have been the main attention of regional planning,1 UG has become an essential part of engineering geology. However, the scope of UG is beyond just engineering geology as it connects with various aspects of life.10 Given its importance, UG is not fully appreciated by those in charge of the management and improvement of the world's cities. Perhaps it was because engineering geologists have failed to show the benefits of geological applications in terms of cost and urban environmental improvement.1 In turn, academic research on UG keeps growing, and various articles have been published on this topic. Unfortunately, the existing literature has a broad range which makes it difficult to derive the research trends on UG. Therefore, a better analysis of publications in academic journals would assist researchers and practitioners in exploring the current status and future direction in this area.11 From 1970 till 2000s, organizations such as Association of Environmental and Engineering Geologists (AEG), Economic and Social Commission for Asia and the Pacific (ESCAP), and Geological Association of Canada (GAC), published a few books on UG.6,12–15 Limited articles presented in these books were short case histories on the urban or engineering geology of individual cities.1 In contrast to these books, the present study has analyzed most of the research literature on UG. This study aims to investigate the research trends of UG based on bibliometric analysis. Therefore, the objectives were to assess the annual publication trend of UG-related research from 1950 to 2018. Additionally, this study aims to analyze the research topics of interest in UG from 1950 to 2018, and explain how these topics interact with each other, and investigate the gap in the current research trend.\n\nThe term bibliometric refers to applying a quantitative method to evaluate research within the applied science-related fields.11,16 Bibliometric analysis has become an essential and a frequently used method to detect areas that require further research to strengthen research capacity in the future, without bias.11,17 Bibliometric analysis has been utilised for big data research,18 public-private partnership,19 and stem research.20 This study, however, was among the first to apply bibliometric analysis in the context of UG research.\n\n\nMethods\n\nThe sequence of numerous UG definitions between 1950 till 2018 in various literature is presented in Table 1. Some UG definitions might be similar however they have different terminologies. This fact has led to a group formulation of preferred key concepts for UG that correlate with each other\n\nFrom the definitions in Table 1, it was clear that the terms UG, environmental geology, and engineering geology are interchangeably used.2,21,22 While the term urban was interrelated with the concept of “the city”.23 The city collectively is defined as a concentration of buildings, roads, public and private spaces, people, conflicts, and common efforts that is administratively delimited.21,22 An urban area has always performed with a wide range of city functions.23 It is a settlement with a high population (where most of the population are not primarily engaged in agriculture, or where there is surplus employment), expanded beyond the administrative boundaries, and includes cities, towns even suburbs.23,24\n\nMoreover, the term city is frequently used to describe a metropolitan area, region, and urban agglomeration.25 The Metropolitan area comprises of the urban space as a whole and its primary commuter,26 typically formed around a city with a large concentration of people (i.e., a population of at least 1,000,000). On a larger scale, an urban agglomeration with 10 million or more is called a megacity.27 These definitions suggest that the terms city (cities), urban, metropolitan (area), and megacity are interchangeable, depending on the context used.\n\nThe preferred key concepts (Table 1) also shows how the UG definition was often approached by the concept of urban planning and development.4,25–27,30 Urban planning is the organized planning of the physical environment, where individuals live to create a healthy, reliable, and durable living space by providing safety in line with their social, cultural, and economic needs.32 Earth science factors (e.g., geology) are essential in planning for urban development initiatives. These factors address ground-related problems and other potential constraints on development.33 The use of geology for urban planning and development has been applied to earthquake hazard vulnerability,32 landslide susceptibility and risk zoning,33–35 seismicity,36,37 geotechnical issues such as erosion and expansive soil,38 and flood hazard.39 To emphasise the importance of this matter in 2014 the International Association for Engineering Geology and the Environment (IAEG) XII Congress in Torino, published a series of books as part of its proceedings on environment, processes, issues and approaches, with volume 5 titled “UG, Sustainable Planning and Landscape Exploitation”.31 At present, the need for geology in planning and development in the urban areas are expected to increase due to the rapid population growth.\n\nThe journal articles related to UG from 1950 till 2018 were searched in the Scopus database on July 24, 2018. Scopus was selected because it has the largest single abstract and indexing database.40 Additionally, Scopus is the leading citation source to journal articles, compared to other bibliometric data collection tools.41\n\nThe selection method comprises of three stages. In the first stage, keywords were combined with the use of Boolean operators such as “AND”, “OR”, and “NOT”, in the Scopus search engine. The selection of keywords was taken from the key concepts, that had appeared in various definitions of UG, as explained in the previous section. The first search was “urban geology”, which resulted in 167 documents. The use of quotation marks (“_”) was to search for the exact phrase as it appears in the articles. The second search was environmental AND geology*, which resulted in 14,087 documents. The * symbol was used to search for an alternate word ending, while AND was used to combine the searched phrases without it becoming an exact phrase. It meant that the search results may have been from documents containing the word ‘environmental’, ‘geology’ or both words. The third search was engineering AND geology*, which resulted in 25,303 documents. The fourth search was a combination of geology* AND urban OR city OR cities OR metro* OR megacity* AND planning OR development, that resulted in 4,798 documents. Some key concepts were truncated here as well with the use of the * symbol to obtain various search results (e.g., megacities, megacity for megacity*). OR was used to combine related terms or synonym for urban (i.e., city, cities, metropolitan, megacity). All four searches were thus stored in the search history. Finally, in this stage all four searches were combined as #1 OR #2 OR #3 AND #4. Sets of searches were combined using “OR” and “AND”. This combined stage resulted in 1478 documents. However, these results may include some irrelevant publications that had the searched keywords, that did not relate to UG.\n\nThe second stage involved the exclusion of document types, languages, and subject areas that were not directly related to UG. First, the search for the article type was limited, which resulted in 735 documents. Articles were then filtered for English language, reducing the resulted to 595 articles. The search was further narrowed down with the execution of subject areas such as “medical,” “physics,” “business,” “economy,” “arts,” “decision policy”, “chemical engineering”, “chemistry”, “material”, “mathematics”, “immunology”, “nursing”, “pharmacy”, “psychology”, “energy”, and “computer”. This stage produced 529 documents.\n\nThe third stage involved exclusion of topics that are too broad based on title, abstract, author keywords, and index keywords. Results from the previous step, including information on citation and abstract, author, and index keywords, were included when downloaded as PDF. Hence, to ensure the relevant content, 529 abstracts in the PDF format were scanned to determine further exclusion from the results. At the end, 285 articles were selected (See underlying data42). The summary of the three stages, and their refined results are shown in Table 2.\n\nIn the analytical phase, 285 research articles were analyzed in terms of amount and time of publications, keywords, topics, and sub-topics. The authors used the Scopus feature, such as the metric article module, to statistically analyze the annual publication trend.\n\nHowever, for the observation of the research trends, the authors used the clustering technique provided by the open licence software tool, VOSviewer version 1.6.16.43 VOSviewer clustering was done based on the fractional-counting method on the keywords in relations to the clusters. Visualization was presented in each set by color (i.e., red, blue, or green), which indicated the group in which the cluster was mapped.44 The clusters were further analyzed to answer the research questions.\n\n\nResults and discussion\n\nThe yearly distribution of the UG articles by publication is presented in Figure 1. The search timeline was set from 1950 (the year when the UG topic began to grow) until 2018, however, the years in which publications were found ranged from 1970 to 2018. Figure 1 shows a plateau in the number of publications between 1970 till 1981, with a slow increase in the number of publications from 1982 to 1997. A significant increase was observed during 1999-2016, as the number of research articles increased from 9 to 17. From the 285 articles, one was published in 1998, and 187 articles were published in the 2000s. This could be explained by the fact that global research (including research in UG’s field) declined due to the Asian financial crisis that happened in 1997-1998.45 However, the UG concept emerged in the 2000s, especially after the 2004 Indian Ocean earthquake and tsunami disaster, to address urban resilience against natural disasters.\n\nResearch questions such as, “What was the UG research topic from 1950 to 2018?” and “How did these research topic interests interact with each other?”, were answered with the use of the bibliographic data to construct a co-occurrence map in the VOSviewer software.43 Several examples of similar analyses have been done in the field of general science and technology,46 in geoparks,47 in soil erosion,48 and volcanic geomorphology.49\n\nFor the data selection and thresholds, all keywords were divided into clusters with the minimum number of occurrences set at 15 keywords. Among the 2688 keywords, 42 met the threshold, which were presented as 42 nodes. Eck and Waltman suggested that in constructing the bibliographic coupling networks, “fractional counting” instead of the ordinary “full counting” methodology, can result in all publications to have the same counting portion.50\n\nThe processed bibliographic data resulted in the keywords that were grouped into three clusters as presented by the VOSviewer in Figure 2. The three clusters were represented by three different colors, in which green represents cluster 1, red cluster 2, and blue cluster 3. The nodes in Figure 2 represent a term, and the node's distance reflects the relationship. Close distance between the nodes, reflect an intense relationship and a strong link between the two terms. Larger nodes represent a higher number of occurrences (high weighted). A summary of the clusters and terms are shown in Table 3.\n\nEach term was connected to other terms by a link representing the relationship between the two terms. The stronger the link, the thicker the display line.51 All terms are quantified according to their occurrences and link strength, as shown in Table 4. The link strength indicates the strength of the relationship between the two terms and the total links between the nodes represents the sum of link strength of one node over others.52 As seen in Figure 2, there are several significant nodes on the map which indicate the most common terms. They are “Engineering geology”, “Geology”, “Urban planning”, and “Urban area”. These four terms were covered in cluster one and two.\n\nThe following sub-sectional outline in the three clusters represent the three research topics of interest, such as engineering geological hazard investigation and risk assessment in the urban area (EGR); social geology and urban sustainability (SGS); and urban hydrology and water management (HGW). In general, there are more research on EGR (42%), followed by SGS (33,7%) and HGW (24,3%) topics.\n\nThe green cluster (cluster 1) contains 14 nodes in which the keyword “Engineering geology” has the highest occurrence and total link strength. The node engineering geology showed thick lines connecting with most terms in all clusters, explaining the fact as to why UG research was mostly related to engineering geology. Other prominent terms in this area include “Geotechnical engineering”, “Subsidence”, “Eurasia”, and “Hazard assessment” (Figure 3).\n\nThere were 120 articles in this cluster. The articles were mostly related to hazard investigation and risk assessment on the underground civil planning (geotechnics), karst collapse and subsidence, landslide, seismic evidence for earthquake, and general geological hazard cases. All cases were viewed from the perspective of engineering geology. Almost half of the EGR research articles were focused on underground civil planning (geotechnics) cases in urban areas (56 articles). The most popular topic was tunnelling,53–56 underground spaces,57–59 and geotechnical modelling.60–63 Case studies for these topics were mostly done in developed countries such as the USA (e.g., Los Angeles, New York, San Francisco, Boston), Japan (Tokyo), Canada (e.g., Metro Toronto, Ontario, Saskatchewan), United Kingdom (London), The Netherland, Singapore, etc.\n\nThe next most significant focus of the EGR articles studied were karst collapse and subsidence cases (22 articles), seismic evidence for earthquake cases (16 articles), landslide cases (14 articles), and other types of geohazards cases in general (12 articles). Research on karst collapse and subsidence were mostly done in European countries such as Italy, Spain, and Belgium.63–65 While for landslide, the related topics are land-use and landslide,66,67 landslide vulnerability and risk assessment.68–70 Other issues related to seismic evidence for earthquakes are mostly on earthquake hazard cases, situated in Turkey’s urban area.71–74 Eurasian Plate movement was the most frequently discussed topic in these earthquake hazard cases. In addition, some researchers analyzed the engineering-geological hazard investigation and risk assessment for all possible aspects in the urban area. We found that there were papers that discussed the role of engineering geology for building conservation.75–77\n\nThe oldest publication listed in this cluster was an Indonesian study from 1970, which was on the application of engineering geology for the regional development and UG.78 Previously, the main role of engineering geologists in Indonesia was to give advice to large civil engineering construction projects, in addition to increase the importance of human resources.79 This might suggest that the initial idea of engineering geology as part of UG in Indonesia was not fully researched. However, there were a small number of articles in this cluster that were related to volcanic eruptions,80 flood,81 and building stone decay and preservation82 (Figure 4).\n\nCluster 2 was represented by 14 red colored nodes in which the five highest weight and total link strength keywords were “Urban planning”, “Urban area”, “Land use”, “Urban development”, and “GIS” (Figure 5). However, the close nodes between “Environmental geology” and “Urban planning”, and the very thick line between “Geology” and “Urban planning”, can be used to explain how urban planning and geology were interrelated and what they shared, in the domain of environmental geology.\n\nThere were 96 articles in this cluster with the topic of SGS. The term social geology refers to the discipline of geology that studies the interaction between the geological environment and the social development, especially the influence of geological resources and risks on the territorial and social management of urban zones.83 SGS included geo-environmental appraisal in the developing urban areas. It ranged from UG mapping for land-use planning (54 articles), GIS-based geo-environmental suitability assessment for urban land-use planning (19 articles), environmental monitoring, assessment, and landscape management (13 articles), monitoring, policy, and law for urban planning (10 articles).\n\nThe topic that received the most attention in this SGS cluster was related to UG mapping for land-use planning purposes.84–88 The 54 articles on this topic were mainly published before the 2000s, with a slight decline after this period. This was before GIS (Geographic Information System) studies were well-developed and applied. Since the early 2000s, mapping for urban land-use planning has taken a GIS approach, instead of relying on field geological investigation. GIS-based geo-environmental suitability assessment for urban land-use planning has been the second major topic in this cluster.89–92 Most of GIS approach in the study collaborated with AHP (Analytic Hierarchy Process) method.93,94 Similarly, Ulfa, et al. presented the results of their study with the use of APH in geological research for urban land-use in Indonesia.95 The third topic in this cluster was related to the environmental monitoring and assessment96–98 and monitoring, policy, and law for urban planning99–101 (Figure 6).\n\nThe third cluster was related to HGW. It was consisted of 14 nodes in which almost all terms contain “water” as part of the keyword (Figure 7). The most frequent relevant terms that appeared while linked, were “Storm sewers”, “Runoff”, “Stormwater”, and “Flood”. Stormwater was defined as rainwater that is runoff from land or built-up on surfaces such as roofs, driveways, pavements, footpaths, and road infrastructures, without entering the drainage system.102 The existing issues regarding stormwater are pollution and flood.103,104 One of the best management practices to control stormwater pollution is developing a sewer system called storm sewer, expected to be different from wastewater sewer.105 Moreover, storm sewers can be a solution for reducing floods by minimizing the discharge rate from the urban catchment areas.106 However, this is more relevant to the urban water (hydrology) management, which is a domain of civil or environmental engineering instead of geology.\n\nThere were 69 articles in this cluster (Figure 8), of which 34 articles were focused on stormwater management (including flood assessment and modelling, urban stormwater, and storm sewer). The second focus in the cluster was on articles regarding wastewater treatment, including water quality and geochemistry (21 articles). The third focus was on 14 articles concerning groundwater, which was the only cluster that matched with geology as a scientific topic.99-102 While the first and the second focus emphasized more on water engineering or applied technology aspects.\n\nIn the past 40 years the increasing trend of UG research was in line with urbanization, even though there was a slow trend before the 2000s. Events such as the Indian Ocean earthquake and tsunami in 2004 that led to the killing of thousands of people who lived in urban areas, were triggers that increased the research in UG in the years to come. In 2015 the initiation of Sustainable Development Goal (SDGs) engaged geologists to have a role in helping and ensuring sustainable foundations for future global development.111 Among the agreed geological aspects in SDGs that were in line with this study are engineering geology, geohazard, hydrogeology, and geo-heritage.111 Since then, many UG articles were trying to relate their studies to the sustainable development concept.76,112,113 Therefore, the research and application of UG has been postulated as a promising approach for sustainable development goals, especially for the 11th goal (sustainable cities and communities), since 55% of the world’s population in 2018 was estimated to live in urban areas.114 It is expected that UG research will have increased popularity among researchers in the future.\n\nThe results of this study found that there were more research articles on EGR than on SGS and HGW topics. Most of the current research mainly focused on engineering geology related to hazard investigation and risk assessment for underground geotechnical construction. The main focus of underground geotechnical research was on case studies in developed countries, specifically in the Metropolitan areas, such as New York, San Francisco, Tokyo, Toronto, London, Singapore, etc. It is because the demand for underground infrastructure as solutions for traffic is growing in Metropolitan cities. Recently, those related to natural hazards such as subsidence, landslide, and earthquake in urban areas have also received attention, however they were viewed from an engineering geology perspective. In the future, it would be interesting to explore and examine the influence and challenges of UG in developing countries.\n\nAs shown in Table 4, the term “land use planning” has the lowest link strength within the whole three clusters. Among other terms which have lower link strength was the planning and sustainable development. These results indicate the most significant gap in UG studies was the interaction between geology and the land-use planning studies, which are under the umbrella of SGS. It was also indicated that sustainable cities and the communities have not yet considered geology for measuring a successful goal. Approach methods using GIS and AHP or even SMCE (Spatial Multi-Criteria Evaluation) can be explored in the future studies of geology for urban land-use planning and development.\n\nDiscussions on flood hazard and urban hydrogeology in this article were minimal. Urban water-related articles which are covered in UG topics were mostly discussed in terms of quantitative water management, storm sewer, and stormwater pollution, which does not fit in the scope of geology, even though it is covered in civil engineering. Articles within the scope, published prior to 2000s, were still lacking quantitative analyses. However, they are in need of necessary geological information on the water condition (either groundwater or surface water) presently, in order to answer practical hydrogeologic management and engineering questions. As expected hydrogeologic science is not well suited for quantitative prediction, however, it is best suited for providing theoretical and basic scientific solutions for complex practical problems.115\n\n\nConclusions\n\nAs presented in this article, the bibliometric analysis has offered an effective way to show the trend and gaps in UG research around the world between 1970-2018. The help of clustering software VOSviewer effectively reduced biases in classifying and networking of the topics.\n\nThe term UG has increasingly evolved over the past few decades. UG was first mentioned in an article that was published in 1970,78 as part of the engineering geological assessment for urban planning and development. UG has been further applied beyond the engineering geology and civil engineering. It is emerging as the application of the Earth sciences for any problems arising within the urban areas. UG supports the idea that human impacts the landscape.10 Therefore, the UG topic is always accompanied by keywords such as engineering geology, environmental geology, landscape, urban, city, planning, and development.\n\nA total of 285 urban geology (UG) related articles were analyzed in this study. The three topics of engineering geological hazard investigation and urban risk assessment, social geology and urban sustainability, and urban hydrology and water management have been further categorized into sub-topics. These were underground geotechnics; karst collapse and subsidence; landslide; earthquake; building stones conservation; general engineering geological hazard cases; UG mapping for land-use planning; GIS-based geo-environmental suitability assessment for urban land-use planning; environmental monitoring, assessment, and landscape management; monitoring, policy and law for urban planning; stormwater management; wastewater treatment; and groundwater. The summary of these research interests has provided an overview of the development of UG in the academic field as a platform for scholars to continue the trend, or to explore a new direction in this topic.\n\nThe limitation in this study was the sample size. Ideally, bibliometric analysis should have consisted of data sets collected from Scopus, Web of Science, and Google Scholar, in order to increase the sample size (number of articles),116 and to create a more comprehensive research. Other limitation is that the articles published in the last 3 years were not included, since the manuscript was firstly drafted in mid-2019.\n\n\nAuthor contributions\n\nIrawan, DE: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing; Ulfa, Y: Conceptualization, Writing – Original Draft Preparation, Data Acquisition, Writing – Review & Editing; Prabowo, RM: Data Acquisition, Image Curation; Kombaitan, B: Writing – Review & Editing; Puradimaja, DJ: Writing – Review & Editing\n\n\nData Availability statement\n\nFigshare: Discovering research trends of urban geology based on a bibliometric analysis\n\nDOI: https://doi.org/10.6084/m9.figshare.14864895.v7.42\n\nThe project contains the following underlying data:\n\n- Scopus_285_urbangeology.csv (raw dataset containing corpus downloaded from Scopus)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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Eng Geol. 2003.\n\nMoss PJ: Influence of Earthquake fault-lines on town planning. Bull New Zeal Natl Soc Earthq Eng. 1987. Publisher Full Text\n\nLuberti GM, Prestininzi A, Esposito C: Development of a geological model useful for the study of the natural hazards in urban environments: An example from the eastern sector of Rome (Italy). Ital J Eng Geol Environ. 2015. Publisher Full Text\n\nAcharjee S: Urban land use and geohazards in Itanagar, Arunachal Pradesh, India: The need for geotechnical intervention and geoethical policies in urban disaster resilience programmes in a changing climate. Geol Soc Spec Publ. 2015. Publisher Full Text\n\nKlein J, Jarva J, Frank-Kamenetsky D, et al.: Integrated geological risk mapping: A qualitative methodology applied in St. Petersburg, Russia. Environ Earth Sci. 2013. Publisher Full Text\n\nPurbo-Hadiwidjojo MM: The Status of Engineering Ge-Hadiwidjojoology in Indonesia: 1970. Bull Int Assoc Eng Geol. 1970; 4(1): 33–41.\n\nUlfa Y, Irawan DE, Furqan A, et al.: Urban geology in Indonesia: An overview. In: Yogyakarta Joint Convention. Yogyakarta: HAGI-IAGI-IAFMI-IATMI. 2019.\n\nKereszturi G, Bebbington M, Németh K: Forecasting transitions in monogenetic eruptions using the geologic record. Geology. 2017. Publisher Full Text\n\nTehrany MS, Lee MJ, Pradhan B, et al.: Flood susceptibility mapping using integrated bivariate and multivariate statistical models. Environ Earth Sci. 2014.\n\nPerez-Monserrat EM, de Buergo MA, Gomez-Heras M, et al.: An urban geomonumental route focusing on the petrological and decay features of traditional building stones used in Madrid, Spain. Environ Earth Sci. 2013. Publisher Full Text\n\nMata-Perelló JM, Mata-Lleonart R, Vintró-Sánchez C, et al.: Social geology: a new perspective on geology. DYNA. 2012; 79(171): 158–66.\n\nHaworth RJ: The shaping of Sydney by its urban geology. Quat Int. 2003; 103(1): 41–55. Publisher Full Text\n\nSuhari S, Siebenhüner M: Environmental geology for land use and regional planning in the Bandung Basin, West Java, Indonesia. J Southeast Asian Earth Sci. 1993; 8(1–4): 557–66. Publisher Full Text\n\nBrowne MAE, Forsyth IH, McMillan AA: Glasgow, a case study in urban geology (UK). J - Geol Soc. 1986; 143(3): 509–20. Publisher Full Text\n\nHofmann G: Mapping for urban land-use planning in Southeast Queensland - a first approach. Bull Int Assoc Eng Geol. 1976; 14(1): 113–7. Publisher Full Text\n\nBaker VR: Urban geology of boulder, colorado: A progress report. Environ Geol. 1975; 1(2): 75–88. Publisher Full Text\n\nArca D, Citiroglu HK, Kutoglu HS, et al.: Assessment of geo-environmental properties depressing urban development with GIS: a case study of Kozlu settlement, Turkey.Nat Hazards; 2017.\n\nYilmaz I: GIS based susceptibility mapping of karst depression in gypsum: A case study from Sivas basin (Turkey). Eng Geol. 2007. 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Bandung: Program Studi Fisika - FMIPA ITB; 2019. p. 97–108. Reference Source\n\nZuquette LV, Pejon OJ, Dantas-Ferreira M, et al.: Environmental degradation related to mining, urbanization and pollutant sources: Poços de Caldas, Brazil. Bull Eng Geol Environ. 2009. Publisher Full Text\n\nDe Waele J, Di Gregorio F, El Wartiti M, et al.: Geo-environmental risk in the upper valley of the Oued Sebou (Fès, Central Morocco): A preliminary approach. J African Earth Sci. 2004; 39(3–5): 491–500. Publisher Full Text\n\nKellaway GA: Environmental geology of Bath. England. 1995; 26(March): 189–91. Publisher Full Text\n\nSumatokhina I, Duk N: Risk of dangerous exogeodynamical processes development on the territory of large cities. Polish Geol Inst Spec Pap. 2004.\n\nNarvi S, Vihavainen U, Korpi J, et al.: Legal, administrative and planning issues for subsurface development in Helsinki. Tunn Undergr Sp Technol Inc Trenchless. 1994. Publisher Full Text\n\nRussell M: Integrated environmental management. J Air Pollut Control Assoc. 1986; 36(4): 361–3. Publisher Full Text\n\nJusic S, Hadzic E, Milisic H: Urban Stormwater Management – New Technologies. In: Springer Nature Switzerland. Sarajevo; 2019. p. 736–45. Reference Source\n\nJiang Y, Zevenbergen C, Ma Y: Urban pluvial flooding and stormwater management: A contemporary review of China’s challenges and “sponge cities” strategy. Environmental Science and Policy. 2018; Vol. 80. Publisher Full Text\n\nNurhikmah D, Nursetiawan, Akmalah E: Pemilihan Metode Sistem Drainase Berkelanjutan Dalam Rangka Mitigasi Bencana Banjir Di Kota Bandung. J Reka Racana. 20161; 2(3). Publisher Full Text\n\nYufen R, Xiaoke W, Zhiyun O, et al.: Stormwater Runoff Quality from Different Surfaces in an Urban Catchment in Beijing, China. Water Environ Res. 2008; 80(8): 719–24. PubMed Abstract | Publisher Full Text\n\nChocat B, Krebs P, Marsalek J, et al.: Urban drainage redefined: From stormwater removal to integrated management. Water Sci Technol. 2001; 43(5): 61–8. Publisher Full Text\n\nRamalho EC, Fernandes J, Daudi E, et al.: Input of geophysics to understand hydrogeology towards the assessment of geoenvironmental conditions in Beira city, Mozambique. Environ Earth Sci. 2018. Publisher Full Text\n\nSharma BR, Ambili GK: Hydro-geology and water resources of indus-gangehc basin: Comparative analysis of issues and opportunities. Ann Arid Zone. 2009.\n\nIbe KM, Nwankwor GI, Onyekuru SO: Assessment of ground water vulnerability and its application to the development of protection strategy for the water supply aquifer in Owerri, Southeastern Nigeria. Environ Monit Assess. 2001. PubMed Abstract | Publisher Full Text\n\nClark TP: Survey of Ground-Water Protection Methods for Illinois Landfills. Groundwater. 1975; 13(4): 321–31.\n\nGill JC: Geology and the Sustainable Development Goals. Episodes. 2017; 40(1): 70–6. Publisher Full Text\n\nLi XZ, Li C, Parriaux A, et al.: Multiple resources and their sustainable development in Urban Underground Space. Tunn Undergr Sp Technol. 2016. Publisher Full Text\n\nMiguez MG, Rezende OM, Veról AP: City growth and urban drainage alternatives: Sustainability challenge. J Urban Plan Dev. 2015. Publisher Full Text\n\nRitchie H, Roser M, Hannah R: OurWorldInData.org. 2018;(Online Resources). Reference Source\n\nVoss CI: The future of hydrogeology. Hydrogeol J. 2005. Publisher Full Text\n\nDynako J, Owens GW, Loder RT, et al.: Bibliometric and authorship trends over a 30 year publication history in two representative US sports medicine journals. Heliyon. 2020; 6(3). PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "94303",
"date": "11 Oct 2021",
"name": "Floris F. van Ogtrop",
"expertise": [
"Reviewer Expertise Hydrology",
"environmental science",
"data science"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript performs a bibliometric analysis with focus on “urban geology” (UG). The analysis identifies 3 main clusters within the literature pointing to risk, water and society. The analysis appears sound and is overall well-presented and summarises past, current and future trends in research quite well. However, the is considerable room for improving the manuscript, particularly in formulating clearer aims and requires careful editing to ensure the outcomes are clear.\nThe abstract is okay, needs a bit of editing to make it clearer, and importantly to sell the findings. Why, for example, is the discovery of the 3 clusters important and useful for UG? You state it might inform researchers of where the research is at and inform future research. Perhaps you can provide supportive examples that show the way forward. To give a fictitious example, “very few articles address links between geology and human health in built up areas”.\nIn my opinion, the article seems to adopt an 'analyse and see approach' as opposed to starting with testable questions. This is in principle okay, but you still need to clearly explain early on why you are doing this study. For example, why is doing this exercise important for the study of Urban Geology? For example, after reading and introduction, I did not really understand why this research is important or in fact why “urban geology” is important. It would be great if you can start by defining the science and why it is important. Perhaps provide a bit of history and context of UG. For example, I recommend starting the introduction with “Urban geology is the science behind understanding and managing the subsurface in urban areas. This includes, research areas such as hydrogeology, geoheritage, geoengineers,… “. You could move the second introductory paragraph to the first, the first paragraph may be better in the abstract as it is results. Furthermore, in my opinion, bibliometrics hardly needs a mention in the introduction as this is the method you will use to get a better understanding of the directions UG is taking and whether there are clear gaps in the research. Where you do mention bibliometric analysis, you might consider providing evidence as to other research areas have benefitted from this type of analysis to convince that it is the right analysis for the job.\nThe methods are okay, bibliometric analysis is fairly well described. However, I was wondering why you have not considered a citation analysis as part of your analysis as this can elucidate some weight or influence in different research areas identified (quantity and quality)? Other metrics to include that indicate quality might be journal rankings in field or similar.\nIn my opinion there are quite a few statements with little or no support. For example, the following statement claims that UG will increase in popularity because 1) the SDGs and 2) increasing urban population. But it is not clear whether growth in 1) & 2) implies growth in UG (causality): “Therefore, the research and application of UG has been postulated as a promising approach for sustainable development goals, especially for the 11th goal (sustainable cities and communities), since 55% of the world’s population in 2018 was estimated to live in urban areas. It is expected that UG research will have increased popularity among researchers in the future”. - Evidence for causality would be, for example, that many of the recent publications in UG mention the specific SDG.\nSimilarly, it is stated that “It was also indicated that sustainable cities and the communities have not yet considered geology for measuring a successful goal.” This needs more explanation. How might a city consider geology in measuring success? This and the previous example are just a few examples of where the article would benefit from articulating what the key findings are of the bibliometric analysis and why they are important.\nA final example is, “There were 69 articles in this cluster (Figure 8), of which 34 articles were focused on stormwater management (including flood assessment and modelling, urban stormwater, and storm sewer). The second focus in the cluster was on articles regarding wastewater treatment, including water quality and geochemistry (21 articles). The third focus was on 14 articles concerning groundwater, which was the only cluster that matched with geology as a scientific topic.99-102 While the first and the second focus emphasized more on water engineering or applied technology aspects”. - Given this is part of the discussion, would it not be a good space to relate this back to why this is relevant to UG. Currently this reads exclusively as results and so the importance in the context of the paper is lost.\nIn addition to the above, the manuscript also uses examples specific to Indonesia, I am wondering whether this may be more useful as a case study to show how UG is developing in Indonesia (trends). However, this will very much regionalise the paper so it should be part of a broader comparison or together with case studies in other regions i.e. you mention New York and other cities.\nMaybe it was buried within the article, but the world health was only mentioned once – understanding linkage between UG and health within a “one health” framework or similar would appear to be a big gap in the current research.\nIn summary, while I think the analysis is a good start and there are some potentially interesting findings, these are still very much presented as statements of the results. While there are glimpses of potential, I believe that the paper needs to better discuss the findings in the context of historic development of UG and show the way forward in UG. Essentially, you have some evidence that it is a growing science, but you want to convince that it is a critical field of research to ensure the sustainability of modern cities now and into the future.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "7304",
"date": "13 Oct 2021",
"name": "Yuniarti Ulfa",
"role": "Author Response",
"response": "Dear reviewer, Thank you for the detailed review and some insights given. We will do revisions as suggested."
}
]
},
{
"id": "142502",
"date": "04 Jul 2022",
"name": "Károly Németh",
"expertise": [
"Reviewer Expertise geology",
"sedimentology",
"volcanology",
"geoheritage",
"geodiversity",
"geoconservation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting and eye-opening manuscript that could be developed to be a good research publication. As I answered \"partly\" to each of the Journal Review Report questions, it reflects my feeling that the manuscript left many questions open or not fully developed to provide a reasonable answers. I have this impression in every part of the manuscript.\nHere I provide a short summary to support my report:\nThe manuscript is well designed and offers an easy to follow structure with clear references to figures and other external data/information. While this is very promising, nearly every section contains paragraphs that contain isolated statements without deeper explorations of the reason behind those findings. I was expecting that in the discussion I would read a more in depth analysis of the results (e.g. as a comparative study), but the text offered very little in that direction.\n\nThe Abstract is okay, but somehow it lacks a real punchline. The key essence of the research outcome should have been the main part of the abstract instead of the too general statements as the Abstract is currently designed.\n\nThe Introduction provides a good summary, but completely lack of some sort of \"aim - objective\" section where the reader directly pointed to the Authors null hypothesis, the aim to conduct such research and what potential benefit we can have if we do something like this. I think this is probably one of the major flaw of the manuscript. While I am involved in similar research the manuscript provided limited reason why I should read this work. These days similar literature reviews are common and the reader really needs to know why a work like this important.\n\nFollowing the previous point, similar works commonly referred to as \"systematic literature review\" or \"systematic mapping of xyz\" and such researches has an extensive literature mostly within social sciences. Some citation to those key works would have been good here. Check those few listed after the report.\n\nFrom a methodological point of view, more detail is needed to justify why Scopus is the best for this research. In a very short section this is mentioned but not fully elaborated. Technically, Scopus indeed the most practical database to handle, but obviously the results will be limited. Some sort of evaluation, at least a very simple one about what to expect if we have Web of Science, Science Direct, Google Scholar or JSTOR for instance in the analysis. I think such critical expression over the expected trends would be a very good addition to the work.\n\nSomehow it is \"overrated\" that over time an explosion of publications within geology can be seen. This is however not only true for geology but any other subjects and controlled by a multitude of factors. It would have been really great to read some lines how this global trend filtered out.\n\nThe data presenting section is fine but always stops before actually some interesting conclusion reached.\n\nSame as the point above, the discussion has a lot of room to develop. For the results, it would be good to have a contrast in a regional base, or country, if possible. While as a reader, the manuscript helped me develop some sort of conclusion on how to interpret the results presented here, to elevate the scientific value of the manuscript, the authors need to offer this. For instance, the research results indicate some urgent policy developments through some fields, or the results reflects some sort of limited directions everyone focuses but for manage urban sustainability other research directions need to be identified, ... then how ...? A little bit of philosophical critical evaluation of the research result would be a very interesting part of the manuscript.\nOverall I think this manuscript can be a valuable work if the authors find the focus and big picture aim to present their results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-839
|
https://f1000research.com/articles/10-832/v1
|
19 Aug 21
|
{
"type": "Research Article",
"title": "Unbiased K-L estimator for the linear regression model",
"authors": [
"Benedicta Aladeitan",
"Adewale F Lukman",
"Esther Davids",
"Ebele H Oranye",
"Golam B M Kibria",
"Adewale F Lukman",
"Esther Davids",
"Ebele H Oranye",
"Golam B M Kibria"
],
"abstract": "Background: In the linear regression model, the ordinary least square (OLS) estimator performance drops when multicollinearity is present. According to the Gauss-Markov theorem, the estimator remains unbiased when there is multicollinearity, but the variance of its regression estimates become inflated. Estimators such as the ridge regression estimator and the K-L estimators were adopted as substitutes to the OLS estimator to overcome the problem of multicollinearity in the linear regression model. However, the estimators are biased, though they possess a smaller mean squared error when compared to the OLS estimator. Methods: In this study, we developed a new unbiased estimator using the K-L estimator and compared its performance with some existing estimators theoretically, simulation wise and by adopting real-life data. Results: Theoretically, the estimator even though unbiased also possesses a minimum variance when compared with other estimators. Results from simulation and real-life study showed that the new estimator produced smaller mean square error (MSE) and had the smallest mean square prediction error (MSPE). This further strengthened the findings of the theoretical comparison using both the MSE and the MSPE as criterion. Conclusions: By simulation and using a real-life application that focuses on modelling, the high heating values of proximate analysis was conducted to support the theoretical findings. This new method of estimation is recommended for parameter estimation with and without multicollinearity in a linear regression model.",
"keywords": [
"Linear regression model",
"Ordinary Least Square estimator",
"Ridge regression",
"K-L estimator",
"High Heating values",
"Proximate analysis."
],
"content": "Introduction\n\nConsidering the general linear regression model\n\nsuch that εi is normally distributed with mean 0 and variance σ2I where I is the identity matrix. y is an n × 1 vector of dependent variable, X is an n × p matrix of the independent variables, β is a p × 1 vector of unknown regression parameters of interest. The method of ordinary least square (OLS) is well known and generally accepted for estimating the parameters (β’s) in the linear regression model. The model is defined as:\n\nWhere H = X′X and β^OLS is normally distributed that is β^OLS ~ N(β, σ2H–1). However, when the OLS estimator is applied to a model where there is correlation between the independent variables, then the variance of the regression estimates becomes inflated1,2. This relationship between the independent variables is referred to as multicollinearity3,4.\n\nIn addressing the problem of multicollinearity, various biased estimators with mean square error smaller than the OLS have been developed by different authors2–15. The limitations of these estimators is that they are biased , however the unbiased versions of some of them have been developed. The advantage of these estimators is that they produced estimates that were similar to the OLS estimator with better mean squared error. Crouse et al.16,17 developed the unbiased ridge and the Liu estimators. Wu18 developed the unbiased version of the two-parameter estimator by Ozkale and Kaciranlar9. Lukman et al.19 developed the unbiased modified ridge-type estimator. Recently, the K-L estimator was proposed to circumvent the problem of multicollinearity in the linear regression model13. The K-L estimator is classified as a biased estimator with a single biasing parameter13.\n\nIn this study, a new unbiased technique is developed based on the K-L estimator and its properties are derived. We compared the unbiased K-L estimator with some existing techniques using the mean square error (MSE) criterion.\n\n\nMethods\n\nHoerl and Kennard5 developed the ridge estimator to mitigate multicollinearity in the linear regression model. The ridge estimator of β with the biasing parameter k is:\n\nThe modified ridge technique was proposed with the addition of the prior information6. This is expressed as follows:\n\nAccording to 16, the unbiased ridge estimator with the introduction of prior information J is given as\n\nwhere J and β^OLS are uncorrelated and J ̴ N(β, D) such that D=(σ2k)Ip and Ip is p × p identity matrix. J is estimated by J=∑i=1pβ^ip.\n\nModified ridge-type method proposed by 3 is given as follows:\n\nwhere Akd = [S+k(1+d)]–1S.\n\nThe unbiased modified ridge type estimator19 was developed and defined as follows:\n\nwhere Akd = [H+k(1+d)]–1 H such that D=σ2k(1+d). Consequently, J~N(β,σ2k(1+d)) for\n\nk ˃ 0, 0<d<1.\n\nRecently13, proposed the K-L estimator and found that this estimator generally outperform the ridge regression estimator. The K-L estimator of β is defined as:\n\nwhere Ak = (H + kI)-1 (H – kI)\n\nThis research proposes an unbiased K-L estimator following the convex method. The convex method is defined as:\n\nwhere G is a p×p matrix and I is an identity matrix of p×p dimensions. Thus, the MSE of β^ (G, J) is\n\nSuch that,\n\nThe value of G from (11) is G = D(σ2H–1 + D)–1. Accordingly, D = σ2(I – G)-1GH-1). We observed that the convex estimator β(G, J) is an unbiased estimator of β and possesses minimum MSE for optimal value of G. Consequently, the new unbiased estimator is defined as\n\nwhere Ak = (H + kI)–1(H – kI) and the value of V=σ2(S−kI)S−12k. Therefore, J~N(β,σ2(S−kI)S−12k) for k ˃ 0.\n\nIt can be expressed conveniently that β^UKL(k,J) is unbiased for β The new estimator has properties defined as follows:\n\nIt follows from Equation (13) that the proposed estimator is unbiased. This classified the new estimator into the same class with the OLS estimator. The biasedness of the estimator is also zero. This is proved as follows:\n\nGiven that there exists an orthogonal matrix Q, such that Q′X′XQ = Ε = diag (e1,e2,...,ep) where ei is the ith eigenvalue of X′X, E and Q are the matrices of eigenvalues and eigenvectors of X′X respectively. Equation (1) can be expressed canonically as:\n\nwhere Z = XQ, α=Q′β and Z′Z=E = Ε. For Equation (15), we get the following representations:\n\nLemma 1.1 Let N be an n×n positive definite matrix and α be some vector, then N−αα′≥0 if and only if α′N−1α≤120.\n\nLemma 1.2 Let α^i = Ciy i = 1, 2 be two linear estimators of α. Suppose that D = Cov(α^1) – Cov(α^2) > 0, where Cov(α^i), i = 1, 2 denotes the covariance matrix of α^i and bias(α^i) = b = (CiX – I)α, i = 1, 2. Consequently,\n\nif and only if b2′[σ2D+b1b1′]−1b2<1 where MSEM(α^i)=Cov(α^i)+bibi′21.\n\nα^OLS and α^UKL(k,J)\n\nTheorem 1.1. α^UKL(k,J) is preferred to α^OLS by using the matrix mean square error as criteria for k > 0.\n\nProof\n\nRecall that,\n\nThe difference between (23) and (24) is as follows:\n\nSimplifying (25) further, we observed that E–1 – (E + k)–1 (E – k)Λ–1 will be positive definite since 2k > 0 for k > 0.\n\nα^RR(k) and α^UKL(k,J)\n\nTheorem 3.2. α^UKL(k,J) is preferred to α^RR(k) by using the matrix mean square error as criteria for k > 0.\n\nProof\n\nwhere Bk = (E + kI)–1\n\nThe difference of Equation (24) and (26) is as follows:\n\nSimplifying (27) further, we observed that E(E + k)–2 – (E + k)–1 (E – k)E–1 will be positive definite since k2 > 0.\n\nα^URR(k) and α^UKL(k,J)\n\nTheorem 3.3. α^UKL(k,J) is preferred to α^URR(k) by using the matrix mean square error as criteria for k > 0.\n\nProof\n\nWe observed that σ2(E + k)–1 – σ2(E + k)–1(E – k)E–1 will be positive definite since k > 0.\n\nα^KL(k) and α^UKL(k,J)\n\nTheorem 3.4. α^UKL(k,J) is preferred to α^KL(k) by using the matrix mean square error as criteria for k > 0.\n\nProof\n\nwhere Ek = (E + k)–1. Consequently,\n\nWe observed that σ2(E – k)2E–1(E + k)–2 – σ2(E – k)E–1(E + k)–1 will be positive definite if k > 2Λ for k > 0.\n\nIn this study, we adopt the following biasing parameter for the ridge and the unbiased ridge estimators:\n\nFor the K-L estimator, we adopted:\n\nFor the proposed estimator, the following biasing parameters were examined:\n\n\nResults\n\nR Studio was used for both the simulation and real-life analysis. The independent variables were generated by following the study of McDonald and Galarneau22 given as:\n\nwhere Zij are independent standard normal pseudorandom numbers, r2 is the relationship between any two independent variables and p is the number of independent variables taken as three and seven in this study. The values of r2 varies between 0.8, 0.9, 0.99 and 0.999 respectively. For p=3, the response variable is defined as:\n\nwhere ei is normally distributed with mean 0 and variance σ2. β is chosen such that β′β= 123. Samples of size 30, 50, and 100 were used. Values of σ are 1 and 5. The mean square error is calculated as:\n\nwhere β^ij is the estimate of the ith parameter in jth replication and βi are the true parameter values. The MSE results are presented in Table 1 and Table 2. We observed the following:\n\n1. All other alternative techniques studied in this work outperforms the OLS estimator at all the levels of multicollinearity.\n\n2. The ridge estimator outperforms its unbiased version when the MSE is used as a criterion.\n\n3. The proposed unbiased estimator (UKL) in this study outperform its K-L estimator counterpart.\n\n4. There was a general better performance of the proposed estimator over all the estimators considered in this work though its performance is a function of the choice of biasing parameters.\n\nIn this study, the following trends about the mean square error and the factors in the simulation were observed:\n\n1. There is a decrease in the MSE when there is an increase in the sample size at a particular level of multicollinearity.\n\n2. Increase in the value of σ leads to a corresponding increase in the mean square errors of each of the estimators when other variables are kept constant.\n\n3. An increase in the number of explanatory variables leads to a corresponding increase in the MSE of all estimators at varying level of multicollinearity and σ.\n\nThe poultry waste data adopted in this study was found and analyzed in Qian et al.24,25 and was also recently employed by Lukman et al.19. The study was aimed at modelling the high heating values of proximate-based model. The response variable is High Heating Values (HHV), while the independent variables are Fixed Carbon (FC), Volatile Matter (VM), and Ash (A). The linear regression model is:\n\nwhere ε is the normally distributed random error term. In this study, the Jarque-Bera (JB) test was employed to know the distribution of the residual. The test statistic and its p-value are 0.6409 and 0.7258, respectively. The result shows that the residual in the model is normally distributed. We diagnosed if the model has the problem of multicollinearity. According to Lukman et al.14, the model suffered from the problem of multicollinearity because the variance inflation factors (VIFFC =997.819, VIFVM =2163.504, VIFASH =1533.782) are greater than ten (10). Also, there is evidence of multicollinearity with the use of the condition number (CN).\n\nFollowing Lukman et al.3,4, moderate level of multicollinearity is observed if the CN ranges are between 100 and 1000 but severe multicollinearity is encountered if CN is greater than 1000. For effective modelling, we considered some alternative estimators to the ordinary least squared estimator in this study. These include the ridge estimator, unbiased ridge estimator, K-L estimator and the unbiased K-L estimator. The estimators’ performance was examined using the mean square error. We also adopt the leave-one-out cross-validation to validate how well the estimators perform14. The performance of the estimator is assessed through the mean squared prediction error (MSPE). The estimator with the least MSE and MSPE is considered as the best. The result is available in Table 3.\n\nFrom Table 3, the regression estimates of the following methods are the same: URR, UKL, and OLS as expected. They also possess a smaller mean squared error when compared with the OLSE. The estimators all exhibit the same regression coefficient signs. The proposed estimator UKL demonstrated the best performance in terms of the MSE and the MSPE. Although its performance is a function of the biasing parameter k.\n\n\nConclusion\n\nThere is high inconsistency in the performance of the OLS estimator for parameter estimation in the linear regression model with multicollinearity problem. The estimator is unbiased but no longer has minimum variance. Due to this setback, in this study, the unbiased K-L estimator was developed and the properties of this new estimator was derived and established. It was found that the estimator is in the class of the unbiased estimator. An added advantage of this estimator over the OLS estimator is that it possesses minimum variance when multicollinearity is present. The superiority of the proposed estimator over the existing methods was theoretically established. The estimator is preferred to other estimators considered in this study.\n\nFurthermore, the simulation and real-life results strengthened the findings of the theoretical comparison in terms of the mean squared error and the mean square prediction error. We recommend this new estimator for parameter estimation in a linear regression model with and without multicollinearity. In further studies, we will extend the new unbiased estimator to other generalized linear models such as the logistic regression model, Beta regression model, Gamma regression model etc.\n\n\nData availability\n\nZenodo: Regression Model to Predict the Higher Heating Value of Poultry Waste from Proximate Analysis. http://doi.org/10.5281/zenodo.507897725.\n\nThis project contains the following underlying data:\n\nhhv data.txt\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nLukman AF, Ayinde K: Review and classifications of the ridge parameter estimation techniques. Hacet J Math Stat. 2017; 46(5): 953–967. Publisher Full Text\n\nAhmad S, Aslam M: Another proposal about the new two-parameter estimator for linear regression model with correlated regressors. Commun Stat Simul Comput. 2020. Publisher Full Text\n\nLukman AF, Ayinde K, Binuomote S, et al.: Modified ridge-type estimator to combat multicollinearity: Application to chemical data. J Chemom. 2019a; 33(5): e3125. Publisher Full Text\n\nLukman AF, Adewuyi E, Oladejo N, et al.: Modified Almost Unbiased Two-Parameter Estimator in linear regression model. IOP Conf Ser Mater Sci Eng. 2019b; 640: 012119. Publisher Full Text\n\nHoerl AE, Kennard RW: Ridge Regression: Applications to Nonorthogonal Problems. Technometrics. 1970; 12(1): 69–82. Publisher Full Text\n\nSwindel BF: Good ridge estimators based on prior information. Commun Stat Theory Methods. 1976; 5(11): 1065–1075. Publisher Full Text\n\nKejian L: A new class of blased estimate in linear regression. Commun Stat Theory Methods. 1993; 22(2): 393–402. Publisher Full Text\n\nYang H, Chang X: A new two-parameter estimator in linear regression. Commun Stat Theory Methods. 2010; 39(6): 923–934. Publisher Full Text\n\nÖzkale MR, Kaçiranlar S: The restricted and unrestricted two-parameter estimators. Commun Stat Theory Methods. 2007; 36(15): 2707–2725. Publisher Full Text\n\nSakallioǧlu S, Kaçiranlar S: A new biased estimator based on ridge estimation. Stat Papers. 2008; 49(4): 669–689. Publisher Full Text\n\nDorugade AV: A Modified Two-Parameter Estimator in Linear Regression. Statistics in Transition New Series. 2014; 15(1): 23–36. Reference Source\n\nAyinde K, Lukman AF, Olarenwaju SO, et al.: Some new adjusted ridge estimators of linear regression model. Int J Civ Eng Technol. 2018; 9(11): 2838–2852. Reference Source\n\nKibria BMG, Lukman AF: A new ridge-type estimator for the linear regression model: Simulations and applications. Scientifica (Cairo). 2020; 2020: 9758378. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLukman AF, Kibria GBM, Ayinde K, et al.: Modified One-Parameter Liu Estimator for the Linear Regression Model. Model Simul Eng. 2020b; 2020: 1–17. Publisher Full Text\n\nAslam M, Ahmad S: The modified Liu-ridge-type estimator : a new class of biased estimators to address multicollinearity. Commun Stat Simul Comput. 2020. Publisher Full Text\n\nCrouse RH, Jin C, Hanumara RC: Unbiased ridge estimation with prior information and ridge trace. Commun Stat Theory Methods. 1995; 24: 2341–2354. Publisher Full Text\n\nSakallioglu S, Akdeniz F: Unbiased Liu estimation with prior information. Int J Math Sci. 2003; 2(1): 205–217. Reference Source\n\nWu J: An unbiased two-parameter estimation with prior information in linear regression model. ScientificWorldJournal. 2014; 2014: 206943. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLukman AF, Ayinde K, Aladeitan B, et al.: An unbiased estimator with prior information. Arab J Basic Appl Sci. 2020a; 27(1): 45–55. Publisher Full Text\n\nFarebrother RW: Further results on the mean square error of ridge regression. J R Stat Soc Ser B Methodol. 1976; 38(3): 248–250. Publisher Full Text\n\nTrenkler G, Toutenburg H: Mean squared error matrix comparisons between biased estimators an overview of recent results. Stat Pap. 1990; 31(1): 165–179. Publisher Full Text\n\nMcDonald G, Galarneau DI: A Monte Carlo evaluation of some ridge-type estimators. J Am Stat Assoc. 1975; 70(350): 407–416. Publisher Full Text\n\nNewhouse JP, Oman SD: An evaluation of ridge estimators. A report prepared for United States Air Force project RAND. 1971. Reference Source\n\nQian X, Lee S, Soto A, et al.: Regression model to predict the higher heating value of poultry waste from proximate analysis. Resources. 2018; 7: 39. Publisher Full Text\n\nXuejun Q, Seong L, Ana-maria S, et al.: Regression Model to Predict the Higher Heating Value of Poultry Waste from Proximate Analysis. [Data set]. Zenodo. 2018. http://www.doi.org/10.5281/zenodo.5078977"
}
|
[
{
"id": "92414",
"date": "03 Sep 2021",
"name": "Oluwayemisi Oyeronke Alaba",
"expertise": [
"Reviewer Expertise Statistical Modelling",
"Econometrics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the abstract, inefficiency is better used than performance drops when multicollinearity is present. The new unbiased estimator should be clearly stated and the reason why there is a need to modify it, which was clearly stated in the body of the work.\nWhy did you choose the biasing parameter - did you check the unbiasedness of KL estimator, what were the limitations in previous studies before the need to modify it? You only stated that you classified it as a biased estimator with a single biasing parameter. The results of the simulation did not display well, but it will be better if few figures could be picked to discuss 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": "92412",
"date": "13 Sep 2021",
"name": "Muhammad Amin",
"expertise": [
"Reviewer Expertise Linear and generalized linear models",
"Biased Estimation Methods",
"Outlier 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\nReport on manuscript “Unbiased K-L estimator for the linear regression model''\nIn this paper, the authors introduced a new unbiased KL estimator for the linear regression model to overcome the effect of multicollinearity. The paper is original and deals with a topic of interest. This paper can be indexed after incorporating the following points:\nPage 1, paragraph 1, line 3, the estimator should be the OLS estimator\n\nIn the abstract, the conclusion is not appropriate, I request the authors to rewrite the conclusion\n\nPage 3, above equation 2, \"the model is defined as\" should be \"the OLS estimator is defined as\"\n\nPage 3, change “of the two-parameter estimator by Ozkale and Kaciranlar9.” to “of the two-parameter estimator based on the work of Ozkale and Kaciranlar9.\"\n\nPage 3, introduction the last paragraph, change “a new unbiased technique is developed based on the K-L estimator” to “a new unbiased K-L estimator is developed for the linear regression model\"\n\nBelow equation 4, \"According to 16, the unbiased ridge estimator with the introduction\", the authors should be clear is 16 an equation or a reference number?\n\nAbove equation 6, “Modified ridge-type method proposed by 3 is given as follows”, here, indicate the author's name with reference number\n\nWrite the reason for your proposed estimator over other estimators in the last paragraph of the introduction section\n\nThe expression below equation 7, change 1 to I\n\nAbove equation 8, “Recently13, proposed the K-L estimator”, indicate here the author's names and reference numbers\n\nIn the results section line 1, change “The independent variables were generated” to “ The correlated explanatory variables were generated”\n\nEquation 19 is not correct, authors should correct this equation\n\nAll simulation results behaviour is not indicated which should be indicated - when and which estimator over the other gives better performance?\n\nThere are some grammatical issues that should be corrected\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "92410",
"date": "16 Sep 2021",
"name": "Mohammad Arashi",
"expertise": [
"Reviewer Expertise Shrinkage estimation",
"High-dimensional analysis",
"Penalized regression"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReport on the paper “Unbiased K-L estimator for the linear regression model”\nIn this study, an unbiased estimator is developed for multicollinear situations. Analytical comparisons are carried out to demonstrate the superiority of the proposed estimator over some existing ones in the literature using the MSE of estimation and MSE of prediction. Numerical analyses, including Monte Carlo simulation and read data, are conducted to support the findings. The mathematical results sound correct, and the topic is eye-catching. Advancing estimation strategies to combat multicollinearity is improving; however, they are mostly biased. In this study, an unbiased version is proposed. I recommend making a minor revision addressing the following comments before acceptance.\nEverywhere applies, change “ordinary least square” to “ordinary least squares”.\n\nWhat is K-L in the Abstract? Whenever you use an abbreviation for the first time, define it completely.\n\nThe authors claim, “However, the estimators are biased, though they possess a smaller mean squared error when compared to the OLS estimator” in the Abstract, which is not correct.\n\nEquation (2) exists if is invertible.\n\nTo improve the literature and cover some existing results, the authors may refer to a couple of related studies such as Arashi et al. (2021a, 2021b), Norouzirad, and Arashi (2019), and Saleh et al. (2019). Since the core of this research is oriented on the multicollinearity problem and its defects in estimation, knowing remedies and strategies to combat multicollinearity comes to be important. The ridge regression (RR) estimation and other estimation strategies built upon it such as shrinkage ridge or scaled lasso thus are important strategies to be used in this context.\n\nProvide more details for obtaining in Eq. (11).\n\nAfter Eq. (16), what is ?\n\nFor selecting ridge parameter in Eqs (32)-(37), provide a reference.\n\nIn Eq. (37), should read .\n\nIn Eq. (38), the pseudo normal variables are denoted by small ; however, capital has defined the line after.\n\nIt is helpful to provide a table for the real data used in the Application, although a data availability statement is added.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-832
|
https://f1000research.com/articles/10-827/v1
|
18 Aug 21
|
{
"type": "Policy Brief",
"title": "Global resilience through knowledge-based cooperation: a new Protocol for Science Diplomacy",
"authors": [
"Ewert Aukes",
"James Wilsdon",
"Gonzalo Ordóñez-Matamoros",
"Stefan Kuhlmann",
"James Wilsdon",
"Gonzalo Ordóñez-Matamoros",
"Stefan Kuhlmann"
],
"abstract": "The world is currently dealing with one of the most severe health, economic and social crises in recent memory, through coronavirus disease 2019 (COVID-19). Scholars are converging on the perspective that traditional means of addressing these crises have served their time. On the additional backdrop of a global political landscape in transition, realising a post-pandemic recovery will require new modes of international collaboration with scientific knowledge and expertise figuring more prominently. A smart approach to science diplomacy—to global resilience through knowledge-based cooperation—does not prescribe the content, but rather focuses on the process of science-based international exchange. The new Protocol for Science Diplomacy presented in this policy brief inspires the alignment of shared, cosmopolitan interests and their application to cross-border societal challenges. It comprises a set of 12 procedural and infrastructural principles with which actors can create a space for constructive and productive science diplomacy interactions. These principles are: sensitivity; inclusiveness; transparency; deliberation; reciprocity; complementarity & manoeuvrability; legitimacy; alignment; evaluation; capacities; capabilities; trust. Our Protocol for Science Diplomacy identifies ground rules for international scientific and policy collaboration that enable us, inter alia, to make meaningful steps towards tackling the United Nations’ (UN) Sustainable Development Goals (SDGs) by their 2030 deadline. As such, it offers a roadmap for science diplomacy in the next decade and beyond.",
"keywords": [
"science diplomacy",
"cosmopolitan realism",
"knowledge-based cooperation",
"protocol"
],
"content": "Introduction\n\nAs 2021 gets underway, large parts of the world are grappling with one of the most severe health, economic and social crises of our lifetimes. Coronavirus disease 2019 (COVID-19) is laying bare the interdependence, complexity and fragility of our societies (Young, 2020). As the President of the European Commission has argued, the crisis also reminds us that “never before has [the] enduring promise of protection, stability and opportunity been more important than it is today” (von der Leyen, 2020). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus, but it has thrown into sharp relief a series of longstanding global challenges, well-articulated by the United Nations’ (UN) 2030 Sustainable Development Goals (SDGs), that are increasingly difficult to address by traditional means (Beck, 2009; Haas, 2016; Kuhlmann & Rip, 2018). Vaccine nationalism; recent assaults on democracy in Washington DC; the departure of the United Kingdom (UK) from the European Union; geopolitical and security tensions with Russia and China; policy failures over climate change—all reflect a fragmentation of national interests, instead of a cooperative pooling of expertise and capacity. Faced with competing claims to knowledge and truth, realising the European Union’s ambitious post-pandemic recovery plan—NextGenerationEU— will require new modes and methods of (funding) international collaboration, in which the role of scientific knowledge and expertise in tackling these challenges is more prominent (European Commission, 2020). A smart approach to science diplomacy – to global resilience through knowledge-based cooperation – does not prescribe the content of science-based international exchanges and related processes, e.g. funding instruments. Rather, it outlines the characteristics of the process by which science diplomacy actors decide on what mechanism is best applied in their specific situation. As we have explored elsewhere (Aukes et al., 2020):\n\na. Grand societal challenges require diplomatic efforts and science-based knowledge,\n\nb. Science-based knowledge production is diverse and evolving,\n\nc. Diplomacy means reconciling a variety of interests, and\n\nd. Science diplomacy requires both science literacy and diplomacy literacy.\n\nBuilding on these points, the Madrid Declaration on Science Diplomacy, and other recent contributions (Flink, 2021; Melchor et al., 2020; S4D4C, 2019), we now present a new Protocol for Science Diplomacy, designed to inform a new procedural turn in scientific-diplomatic interactions. The Protocol envisages science diplomacy as less about soft power being deployed in pursuit of national interests, and more about shared, cosmopolitan interests being aligned and applied to cross-border societal challenges (Beck, 2009). The Protocol should be deployed as a set of practical guidelines, primarily aimed at science diplomatic exchanges involving the European Union (including Member States and strategic partners), intergovernmental organizations, science and knowledge institutions, and civil society and philanthropic organizations.\n\n\nPrinciples of the new Protocol for Science Diplomacy\n\nScience diplomacy occurs at the intersection of foreign policy, problem articulation (e.g. the UN SDGs), scientific knowledge, technology and innovation, and is characterised by fluidity. Its definition, stakeholders and job descriptions are not fixed. This new Protocol for Science Diplomacy should be applied in collaborative situations based on shared interests. This will help to create a constructive and productive interaction space. The protocol proposes principles of agency and governance that are applicable to various configurations of stakeholders and topics pertaining to the challenges societies face today. The new Protocol for Science Diplomacy outlines a set of 12 procedural and infrastructural principles that need to be considered in the design and delivery of transformative science diplomacy interactions. Not all are applicable to every situation, but it will be useful to consider several of the principles in most situations. Depending on the specific situation, it is possible that several of the principles need to be balanced against each other and some trade-offs between them are inevitable. The choice of which principles to combine in tackling a specific societal challenge highlights the importance of ensuring such interactions remain flexible and contextually sensitive.\n\nNote: each principle is explained by means of a definition and key questions, as well as illustrated with a fictive case. Each fictive case is an excerpt of a full example on the S4D4C website. Each principle presented here is provided with a link that leads to the full principle description.\n\n\nProcedural principles\n\nScience diplomatic activities should respect the specific political, socio-economic and environmental context they are designed for and be able to adapt to changes in them.\n\nThis principle would be demonstrated, for example, in a case in which country A has a rather elaborate science diplomacy scheme running that supports brain circulation and capacity building with a focus on biomedical and health sciences. Country B is a participant in the scheme but takes a turn for the worse regarding democratic values and misuse of resources gained through the scheme. Based on a contextual risk assessment, programme mechanisms for speaking up against infringements are reinforced and frequently used by the programme management.\n\nScience diplomatic activities should be aware of different degrees of inclusiveness vs. exclusiveness as well as that inclusion is a political, strategic choice and a component of the diplomatic game, too. Where useful, one should involve a broadly representative portion of the relevant scientific, political and diplomatic communities.\n\nThis principle would be demonstrated, for example, in a case in which the review committee of an international joint research laboratory discusses the statistics of accepted proposals in their yearly meeting. Significant differences between acceptance rates of research proposals from the various participating countries are discussed. Due to the collaborative nature of the laboratory’s mission, the committee agrees to implement anti-discrimination rules into the proposal review process to pre-empt potential issues.\n\nScience diplomatic activities should be appropriately visible to enable monitoring and accountability activities by observing communities, thereby increasing the legitimacy of the activity.\n\nThis principle would be demonstrated, for example, in a case in which relations between countries are asymmetrical in terms of socio-economic and governance performance, constructing a stable, accountable quality management system for jointly setting up, evaluating and managing international research projects, takes great efforts in terms of science diplomacy. Transparent, permanent and thorough documentation can not only help alleviate potential conflicts over decisions due to those asymmetries, but also ensure sustainability of programs through political upheavals and management changes.\n\nScience diplomatic activities should encourage mutual understanding of actors’ perspectives, needs and objectives, as well as of problem definitions and associated solutions, the disciplinary and interdisciplinary knowledge required (incl. probing for other relevant scientific disciplines) and common narratives for the support of science diplomacy processes.\n\nThis principle would be demonstrated, for example, in a case in which several representatives of international institutions (policymakers, non-governmental organizations [NGOs], experts) discuss how to tackle water-related challenges on the global level during a sequence of international negotiations. Having shared and discussed each others’ divergent viewpoints, two framings or definitions of the water-related issues dominate debate: water quality and water security. Often a problem framing is complex, which makes agreeing on a problem definition hard to achieve, however, by including mediation experts conflicting parties can find common ground.\n\nScience diplomatic activities should foster an attitude of understanding and cooperation leading stakeholders to trust that each actor is contributing to addressing grand challenges in roughly equivalent ways according to their relative abilities, through knowledge or other resources.\n\nThis principle would be demonstrated, for example, in a case in which the topic of research cooperation with a country in the global south arises in an inter-ministerial government meeting. Two representatives from the science ministry and foreign ministry quarrel about how to view the research cooperation funds invested in another country. While the latter proposes to use it as leverage to push this country on controversial policy issues, the science ministry officer maintains that the status quo of open communication channels would be threatened with such reinterpretation of the investments. She proposes to focus on improving the capacity building and the conditions for enhanced scientific reciprocity so that these countries can be better partners in their efforts on global challenges. Maybe promoting more research cooperation on the controversial topics could also be a way to draw more attention to them.\n\nScience diplomatic activities should build on stakeholders’ strengths to balance out others’ weaknesses and embed them in governance arrangements that leave enough room to manoeuvre for these strengths to flourish.\n\nThis principle would be demonstrated, for example, in a case in which science policymakers, managers and academics of two states aim at setting up a bilateral funding mechanism based on a common pot system (each party paying a share), joint calls for proposals for bi-national consortia and a joint evaluation procedure under an international joint programming initiative. The joint programming setting is asymmetrical concerning the question how many and which resources each country should contribute. While country A has more financial resources and more advanced management systems to provide, country B also contributes its considerable regional expertise. The art of science diplomacy in such an initiative is to create an atmosphere allowing each country’s actors to play to their strengths and pursue their interests without either side feeling less respected or unqualified.\n\nScience diplomatic activities should strive for the mutual acceptance of shared “rules of the game” in the interaction space, respecting the expertise and framings of participating stakeholders. Science diplomacy activities should enable ‘democratic quality’ of proposed and implemented mechanisms, processes and solutions.\n\nThis principle would be demonstrated, for example, in a case in which a new and contagious virus breaks out in country A and spreads quickly. Country A realizes soon that it needs to put the fight against the virus on the international agenda of the upcoming G20 summit to secure support for substantial funds and multinational research efforts from partner countries. Country A’s academy of sciences works with its prime minister’s office to prepare thoroughly in advance of the G20 Sherpa meetings and the summit. It turns out to be a success: all G20 countries commit to the new global health agenda and a fund for international and multidisciplinary research on the virus is set up.\n\nScience diplomatic activities should address problems on the lowest, i.e. most local and concrete, appropriate policy/instrumental level while coordinating all involved scales (temporal, spatial and administrative), governance dimensions (horizontal and vertical) and communities.\n\nThis principle would be demonstrated, for example, in a case in which country A identifies the need to conduct more research on rising sea levels and adaptation strategies. Although a partner country is found in country B, the political and research systems of both countries are drastically different, which complicates the work of negotiators. The negotiating funding agency has several instruments available, including a set of expert guidelines on how country B’s systems work and how to negotiate with its representatives, from which negotiators benefit greatly. The funding agency is also in constant communication with the foreign affairs office and works closely with the science attaché posted in country B. Both countries eventually agree to a mutually beneficial scheme to fund research on rising sea levels.\n\nScience diplomatic activities should be reflective and facilitate learning throughout the process. As is common practice in other policymaking, evaluating the activities undertaken also needs to become a routine part of science diplomacy. This process should include, among others, not only reflecting on the frames, ambitions, interests, outcomes of the involved countries and other actors, but also comparing various similar science diplomacy activities to gauge the efficacy of the one in question.\n\nThis principle would be demonstrated, for example, in a case in which for a long time, a world leading research institution has searched for ways to cope with the Zika virus which affects thousands of pregnant women in tropical countries in the Americas, causing certain birth defects. An evaluation process brought to light that the research process would become more efficient if performed by a broader international collaboration program that also involved scientists located in the global south. The integrated research group of natural scientists, health scientists and social scientists both from the global north and from several of the targeted countries in the global south succeeded in bringing the Zika virus under relative control in tropical countries such as Colombia.\n\n\nInfrastructural principles\n\nScience diplomatic activities should create, reinforce and/or draw on suitable and sufficient institutional, organizational, and management resources (e.g. budgets, staff etc.), political will, reliable and inclusive knowledge resources, and gatekeeping proficiency.\n\nThis principle would be demonstrated, for example, in a case in which a joint scientific infrastructure was established to bring together scientists from countries traditionally in conflict. As a next step to achieving its goals of intercultural cooperation and knowledge-sharing, the joint scientific infrastructure board launched new interaction mechanisms such as international teams, deliberation and dialogue structures based on sharing distinct perspectives of relevant actors. Eventually, these mechanisms improved inter-group cooperation and communication leading to a more constructive attitude within the whole institution.\n\nScience diplomatic activities should empower individuals to become trained ‘translators’, ‘multilingual’ in the sense of speaking the languages of science and diplomacy and able to opportunistically or incidentally interact with communities beyond their daily circles both in the domain of science and/or diplomacy.\n\nThis principle would be demonstrated, for example, in a case in which a nuclear disaster occurs in country A. Country B with considerable expertise in nuclear sciences, nuclear crisis management, and an international cooperation mission, offers its support including the involvement of her chief scientific adviser. A scientific task force set up for the purpose is the platform for the chief scientific adviser to engage with other scientific experts and chief scientific advisers from country A throughout the crisis management period. The chief scientific adviser acts as a linchpin between peers in country A, diplomats and policy makers, adapting the communication style and taking into account cultural differences.\n\nScience diplomatic activities should produce mutual recognition and credibility on an individual level as well as clear ‘rules of the game’ on the process level, thereby stabilizing the process and contributing to the legitimacy of the process and involved individuals alike.\n\nThis principle would be demonstrated, for example, in a case in which a science attaché from country A deployed to her embassy in country B, and a science attaché from country B deployed to her embassy in country A, interact with each other for the first time during a coffee break of a scientific conference in country B. They develop a good mutual feeling out of which a long-standing diplomatic collaboration between their home countries develops.\n\n\nImplications\n\nThese principles are meant as a guideline to organise science diplomacy activities. It is by no means necessary to apply all of them all the time. Rather, a conscious reflection at the onset of a potential cooperation on the intersection between science and foreign policy should lead to a conscious choice of an appropriate, implementable subset. In turn, these should then guide stakeholders to a collaborative science diplomacy arrangement addressing global resilience based on the ‘worldview’ sketched above.\n\n\nActionable recommendations\n\nThe new science diplomacy protocol is not directed at specific actors but at the system as a whole. It is paramount to build science diplomacy literacy, i.e. for individuals or organisations to be well acquainted with both the world of science (and its diversity) and the world of foreign policy/diplomacy (and its complexity). To this end, there are training opportunities (also available through S4D4C) and emerging networks (e.g. the European Science Diplomacy Alliance). Some governments and scientific bodies have also appointed dedicated science diplomacy attachés or others with experience of mediating between these worlds.\n\n\nConclusion: 2030, SDGs and a new wave in Science Diplomacy\n\nAs the COVID-19 crisis has revealed, international efforts to produce and disseminate scientific knowledge can achieve exceptional results at remarkable speed. The development of various functional vaccines against the SARS-CoV-2 virus in less than a year, the open availability of around 200,000 scientific publications investigating the virus and its effects, and the pivotal involvement of scientific advisors in the management of the crisis prove the possibility of fruitful collaboration between scientists and policymakers in both national and international realms.\n\nYet there are many other ongoing societal challenges which have lingered, and not been tackled with anything like the urgency of this crisis mode. Here, the ground rules of international scientific and policy collaboration need to change if we are to make meaningful steps towards tackling the UN SDGs by their 2030 deadline. The complexities that come with knowledge-based cooperation can be daunting, but they also offer opportunities –particularly for a European Union looking to renew and reassert its progressive, values-based role in the world.\n\nReflecting on the lessons of the pandemic in her December 2020 State of the Union Address, EU President von der Leyen said, “When we felt fragility around us, we seized the moment to breathe new vitality into our Union. When we had a choice to go it alone like we have done in the past, we used the combined strength of the 27 to give all 27 a chance for the future. We showed that we are in this together and we will get out of this together” (von der Leyen, 2020). Getting out of COVID-19 together has depended upon – and will continue to demand – knowledge-based cooperation between science, innovation, policy and diplomacy at multiple levels of national, regional and global governance. As vaccination programmes accelerate worldwide, we need to look beyond the present crisis towards the multiple, interdependent challenges of the SDGs, and the wider imperatives of resilience and preparedness that this past year has reminded us of. As a contribution to this task, the new Protocol offers a roadmap for science diplomacy in the next decade and beyond.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nAn earlier version of this article can be found on research.utwente.nl, s4d4c.eu, and eprints.whiterose.ac.uk.\n\n\nReferences\n\nAukes E, Honarmand Ebrahimi S, Ordóñez-Matamoros G, et al.: Towards effective science diplomacy practice. S4D4C Policy Brief #2. Vienna: S4D4C. 2020. Reference Source\n\nBeck U: Macht und Gegenmacht im globalen Zeitalter: Neue weltpolitische Ökonomie. Frankfurt am Main: Suhrkamp. 2009.\n\nEuropean Commission: Recovery Plan for Europe. Online summary. 2020. Reference Source\n\nFlink T: Evaluating Science Diplomacy – discerning talk and action. S4D4C POLICY BRIEF. 2021; forthcoming.\n\nHaas PM: Social Constructivism and the Evolution of Multilateral Environmental Governance. In P.M. Haas (Ed.), Epistemic Communities, Constructivism, and International Environmental Politics. London: Routledge. 2016; 121–149. Reference Source\n\nKuhlmann S, Rip A: Next-Generation Innovation Policy and Grand Challenges. Sci Public Policy. 2018; 45(4): 448–454. Publisher Full Text\n\nMelchor L, Elorza A, Lacunza I: Calling for a Systemic Change: Towards a European Union Science Diplomacy for Addressing Global Challenges. V 1.0. S4D4C Policy Report, Madrid: S4D4C. 2020. Reference Source\n\nS4D4C: The Madrid Declaration on Science Diplomacy. Madrid: S4D4C. 2019. Reference Source\n\nvon der Leyen U: State of the Union Address 2020 by Ursula von der Leyen, President of the European Commission. 2020. Reference Source\n\nYoung M: Building Better Science Diplomacy for Global Challenges: insights from the COVID-19 crisis. S4D4C POLICY BRIEF, Vienna: S4D4C. 2020. Reference Source"
}
|
[
{
"id": "92191",
"date": "08 Nov 2021",
"name": "Nicolas Rüffin",
"expertise": [
"Reviewer Expertise science diplomacy",
"scientific infrastructures",
"international science policymaking",
"politics of big 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\nThank you for the opportunity to read the policy brief with the title \"Global resilience through knowledge-based cooperation: a new Protocol for Science Diplomacy\". I very much enjoyed reading it.\n\nAs the title indicates, the policy brief presents a set of principles that all kinds of actors in science diplomacy (SD) should take into consideration when planning new initiatives. In the following, after a short recap of the content, I will address the questions spelled out in the reviewing guidelines of F1000.\nThe authors begin by observing that many of the contemporary societal problems can only be solved with the help of international cooperation and scientific knowledge, the ongoing COVID-19 pandemic being a case in point. For policies and initiatives at this nexus of science and foreign policy, Aukes et al. distilled 12 overarching principles that aim to \"help to create a constructive and productive interaction space.\" They distinguish procedural from infrastructural principles. The former are meant to be considered in the design of actual SD-projects; the latter address prerequisites of successful SD-policies. Yet the authors do not provide the reader with a toolbox of ready-made solutions but rather a framework of ideas that should guide the design of (any) SD-initiative. Nevertheless, the principles are not theoretically deduced guidelines. On the contrary, each point is supported by, and rooted in, empirical findings from a Horizon 2020 research project.\nThe policy brief is well-structured and well-written. The argument is clear and comprehensible. The introductory remarks on COVID-19 strikingly illustrate current global challenges and their possible solutions via international scientific collaboration.\n\nI have just a minor remark here: What I missed in the introduction was an explicit statement on power imbalances in the relations between the Global North and the Global South that impact science-related interactions. This topic is addressed subsequently in several of the procedural principles. Yet I wonder if it should be elevated from the beginning to the same level as the challenges already mentioned in the brief which almost all unfold in the north (EU-UK tensions, crises of democracy in the US, conflicts between the EU and Russia/China, etc.).\nThe text is written for a community that is already involved or interested in the pursuit of SD. In consequence, a certain familiarity with the discourse is helpful for the reader to understand the compact policy brief. For a broader audience, the text can act as a gateway to extended information on the discourse through the cited case studies. The authors manage the balancing act of combining general principles and specific case studies without overemphasizing any side. In this way, they avoid the danger of drawing hasty conclusions from individual anecdotes, as is sometimes the case in the general science diplomacy discourse. They point out that not all principles will always be relevant or effective at the same time.\nRelating to this statement I noticed that the implications of the set of principles remain (and maybe: have to remain) on a rather general level. Given the restrictions of a policy brief, this is understandable. Yet I would like to comment on the absence of a more nuanced structure of the principles. For instance, many of the principles presented contain a tendency towards increasing bureaucratic procedures, for instance, adding \"programme mechanisms\", implementing \"anti-discrimination rules\", providing \"Transparent, permanent and thorough documentation\", or increasing the amount of evaluations. In contrast, other principles stress the importance of personal interactions. Good working relations on the \"individual level\" shine through, for example, in the principles of Evaluation, Capacities, and Trust. The tension between both personal flexibility and administrative procedures is one example of principles that might be at odds with each other. The authors are aware that \"it is possible that several of the principles need to be balanced against each other and some trade-offs between them are inevitable\". Yet they do not spell out these trade-offs. I wonder whether some examples might be helpful here to illustrate potentially conflicting principles. Maybe it is possible to build on the cases the authors cite to illustrate commonly experienced trade-offs.\nThe policy brief makes use of pertinent literature and cites relevant sources. However, I noticed that the authors decided to exclusively focus on the collaborative side of SD. This focus is well justified yet it (deliberately) excludes the other side of the coin, i.e. competitive SD in the national interest. This strand of SD is discussed frequently as well (e.g. Flink & Schreiterer, 20101; Gluckman et al., 20172; Ruffini, 2020a3, 2020b4) but is absent from the policy brief. This made me wonder whether a short reflection is needed dealing with the relation between both types of SD. For instance, does the protocol really exclude/prevent national or particularist agendas of involved actors? Are national interests and common goals orthogonal to each other? Or can they align and co-exist in some cases? Is a \"shared worldview\" really necessary to design collaborative SD-projects or can self-interested parties also build on the principles in their conduct of SD? I am aware that a policy brief is not the right place to answer these questions in detail but given that the text addresses \"the system as a whole\", I think it should briefly reflect on this duality.\nApart from these general comments and questions, the policy brief –in my view–already presents a helpful tool of orientation for designing initiatives, policies, and programs relating to SD.",
"responses": []
},
{
"id": "100969",
"date": "09 Dec 2021",
"name": "Meredith Gore",
"expertise": [
"Reviewer Expertise conservation social science",
"science diplomacy",
"coupled human and natural systems",
"human dimensions of global environmental change."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article offers an array of best practices for science diplomacy framed around the notion of a post-covid society or a society facing changes in contemporary science diplomacy because of covid. There are many opportunities to elaborate on some key ideas to enhance reader clarity and impact of ideas. Please see the attached document for my comments.",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-827
|
https://f1000research.com/articles/10-826/v1
|
18 Aug 21
|
{
"type": "Data Note",
"title": "Genome of Serratia plymuthica UBCF_13, Insight into diverse unique traits",
"authors": [
"Raudhatul Fatiah",
"Irfan Suliansyah",
"Djong Hon Tjong",
"Lily Syukriani",
"Roza Yunita",
"Robi Trivano",
"Nurefni Azizah",
"Jamsari Jamsari",
"Raudhatul Fatiah",
"Irfan Suliansyah",
"Djong Hon Tjong",
"Lily Syukriani",
"Roza Yunita",
"Robi Trivano",
"Nurefni Azizah"
],
"abstract": "Background: Whole genome sequencing is become an essential tool to explore potential of microorganism and evolutionary study. The Serratia plymuthica UBCF_13 is one of phylloplane associated plant bacteria showing antifungal activity. For that reason, its complete genome information is necessary to enhance its potential as biocontrol against plant pathogenic fungal. Here, we report the genome sequence of Serratia plymuthica UBCF_13 to understand the molecular mechanism regarding its biocontrol ability. Methods: Continuous short reads were attained from Illumina sequencing runs and reads 150 bp were merged into a single dataset. Pan-genome based method was used to identify core-genome of S. plymuthica species and unique gene in UBCF_13. Results: Assambled Illumina reads of S. plymuthica strain UBCF_13 genome was produced a 5.46 Mb circular genome sequence. It was found 3321 genes belong to the core-genome sheared by the 18 strains evaluated. The UBCF_13 genome harbor 485 unique genes, where 300 of them only can be found in this strain Conclusions: The sequence of UBCF_13 genome sequence data will contribute for further exploration of the potential of S. plymuthica UBCF_13 as bacteria producing antibiotic.",
"keywords": [
"Pan-genomic",
"core-genome",
"unique gene",
"Serratia plymuthica",
"genome sequencing",
"comparative genomic"
],
"content": "Introduction\n\nSerratia plymuthica bacteria have been isolated from many environmental sources and are found associated with diverse plants1–5. Many strains of this species have been reported to have the ability to inhibit the growth of plant-pathogenic fungi and stimulate plant growth6–9. UBCF_13 is one strain of this species. It has ability to inhibit Colletotrichum gloeosporioides, a species of post-harvest pathogenic fungi that causes anthracnose disease in various plants10.\n\nHere, we report the complete genome sequence of this bacterium, constructed using Illumina sequencing technology. Our dataset may be useful as a comparative genome for evolutionary and speciation studies, as well as for the analysis of protein-coding RNA, biosynthetic gene clusters and may also useful for further study such as the regulation of gene expression in relation to the antifungal activity of this bacterium.\n\n\nMethods\n\nS. plymuthica strain UBCF_13 was isolated from phylloplane of Brassica juncea L. in 2012 from District of Solok, Province of West Sumatera, Indonesia10. The bacterium was cultivated in Luria–Bertani (LB) broth at 27°C for 16 hours with 150 rpm. The genomic DNA was extracted using the method of Chen and Kuo (1993)11, followed by degrading residual RNA by RNAse. Library preparation and sequencing was done by Novogen (Hong Kong). Sequencing was performed using Illumina NovaSeq 6000 (Illumina NovaSeq 6000 Sequencing System, RRID:SCR_016387).\n\nContinuous short reads of 150 bp were merged into a single dataset. The dataset was obtained by using combination of map-based gene references and de novo assembly that was performed in Geneious software (Geneious, RRID:SCR_010519)12. The annotation in genome submission was carried out using NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAP)13. The annotated genome sequence of UBCF_13 has been deposited in the NCBI GenBank under accession number CP068771.\n\nComparative genomics analysis was carried out using genome sequences of UBCF_13 from this research and 17 whole sequenced genomes of other Serratia plymuthica strains retrieved from NCBI’s GenBank. The genomes were reannotated using the Prokka software tool (Prokka, Galaxy Version 1.14.6+galaxy0) (Prokka, RRID:SCR_014732)14,15 that is available from the NCBI. Identification of genes shared between the strains, and ‘presence-absence gene set’ was carried out using Roary; Galaxy Version 3.13.0+galaxy1, (Roary, RRID:SCR_018172)16 with a threshold similarity of 70%.\n\nGenes that exist in all the strains are the core-genome. Phylogenetic trees were constructed using Maximum Likelihood based inference of large phylogenetic trees-RAxML, Galaxy Version 8.2.4+galaxy2 (RAxML, RRID:SCR_006086)17 based on multialignment of concatenate core-genome. Phandango (Phandango, RRID:SCR_015243)18 was used to view the resulted output graphs.\n\nThe translated protein coding genes of UBCF_13 was used for identification of cluster of orthologous groups (COG). This was obtained from NCBI BLAST+rpsblast (Galaxy Version 2.10.1+galaxy0)19 and eggNOG Mapper (Galaxy Version 2.0.1+galaxy1) (eggNOG, RRID:SCR_002456)20. The result of COG identification was classified based on the categories in COG database NCBI21.\n\n\nResult and discussion\n\nThe whole genome sequencing reads of Serratia plymuthica UBCF_13 were assembled into a single circular 5.46 Mb chromosome with overall GC content of 56.2% (Table 1). S. plymuthica has a genome size in the range 5.40–5.70 Mb. The GC content percentage is 55.70–56.60. Based on genome reannotation by Prokka, it was found different number of CDS in each genome S. plymuthica (Table 1). All of the compared S. plymuthica genomes shared a highly conserved genomic architecture as inferred from synteny of protein coding orthologs.\n\nFigure 1A shows the phylogenetic tree of 18 strains S. plymuthica. The phylogenetic tree shows that S. plymuthica UBCF_13 is in same cluster with strain AS9, PRI-2C, NCTC8015, and NCTC8900. The strain PRI-2C is reclassified and transferred to the species S. inhibens22. The pangenome was performed together with other strains in order to obtain further insight into specific features in the UBCF_13. It was found 3315 belong to the core-genome shared by the 18 strains evaluated. The genome of the UBCF_13 harbors 488 unique genes, of which 300 genes are only contained by this strain. The presence-absence gene set was shown in file supplementary data 1\n\n(a) Phylogenetic of 18 strains S. plymuthica based on concatenate core-genome multialignment; and (b) visualization of presence (blue bar)-absence (white bar) gene in each of the strains.\n\nFunctional categories of the CDS in S. plymuthica UBCF_13 based on the Cluster of Orthologous Groups (COG) categories are shown in Table 2. The list of UBCF_13 COG and its function classification based on COG database was shown in extended dataset 223.\n\n\nData availability\n\nData from Serratia plymuthica UBCF_13 is available at NCBI under Bio-Project PRJNA692765, including the complete genome with annotation at GenBank accession CP068771, and the read data in the Sequence Read Archive (SRA) database under the accession number SRR15012717.\n\nDataset 1:\n\nDryad: Gene presence absence in Serratia plymuthica strains. https://doi.org/10.5061/dryad.1zcrjdfsj24\n\nThis project contains the following extended data;\n\nGene_presence_absence_in_Serratia_plymuthica_strains.csv (This data shows gene presence or absence across strain Serratia plymuthica species. It contains a list of coding protein gene (CDS) name and region where the gene exist in each genome (locus_tag). The region/locus where the CDS are existing has a specific tag for each genome, whereas the number after locus names represents the order of CDS in each genome. This data could be used to identify conserved and unique genes in Serratia plymuthica.)\n\nReadme_Gene_presence_absence_in_Serratia_plymuthica_strains.txt (This text file provides information about the above data)\n\nDataset 2:\n\nDryad: Classification of the UBCF_13 COG based on COG database in NCBI https://doi.org/10.5061/dryad.sn02v6x4g23\n\nThis project contains the following extended data;\n\nClassification_of_the_UBCF_13_COG_based_on_COG_database_in_NCBI.csv (This data contains information about the assignment of Clusters of Orthologous Gene (COG) for each coding protein gene in Serratia plymuthica UBCF_13 and their functional classification based on COG database in NCBI)\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\nNeupane S, Högberg N, Alström S, et al.: Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9. Stand Genomic Sci. 2012; 6(1): 54–62. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdam E, Müller H, Erlacher A, et al.: Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities. Stand Genomic Sci. 2016; 11(1): 61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCleto S, van der Auwera G, Almeida C, et al.: Genome Sequence of Serratia plymuthica V4. Genome Announc. 2014; 2(3): e00340–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNeupane S, Finlay RD, Kyrpides NC, et al.: Complete genome sequence of the plant-associated Serratia plymuthica strain AS13. Stand Genomic Sci. 2012; 7(1): 22–30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Vleesschauwer D, Chernin L, Höfte MM: Differential effectiveness of Serratia plymuthica IC1270-induced systemic resistance against hemibiotrophic and necrotrophic leaf pathogens in rice. BMC Plant Biol. 2009; 9(1): 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMüller H, Fürnkranz M, Grube M, et al.: Genome Sequence of Serratia plymuthica Strain S13, an Endophyte with Germination- and Plant-Growth-Promoting Activity from the Flower of Styrian Oil Pumpkin. Genome Announc. 2013; 1(4): e00594–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKurze S, Bahl H, Dahl R, et al.: Biological Control of Fungal Strawberry Diseases by Serratia plymuthica HRO-C48. Plant Dis. 2001; 85(5): 529–534. PubMed Abstract | Publisher Full Text\n\nVleesschauwer D: Using Serratia plymuthica to control fungal pathogens of plants. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour. 2007; 2(046): 1–9. Publisher Full Text\n\nCampos D, Cottet L, Castillo A: Antifungal activity of Serratia plymuthica CCGG2742 against a new wild isolate of the phytopathogenic fungus Alternaria tenuissima. Plant Dis. 2018; PDIS-05-17-0709-RE. Reference Source\n\nAisyah SN, Sulastri S, Retmi R, et al.: Suppression of Colletotrichum gloeosporioides by Indigenous Phyllobacterium and its Compatibility with Rhizobacteria. Asian J Plant Pathol. 2017; 11(3): 139–147. Publisher Full Text\n\nChen WP, Kuo TT: A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res. 1993; 21(9): 2260. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKearse M, Moir R, Wilson A, et al.: Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12): 1647–1649. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi W, O'Neill KR, Haft DH, et al.: RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2021; 49(D1): D1020–D1028. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCuccuru G, Orsini M, Pinna A, et al.: Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics. 2014; 30(13): 1928–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeemann T: Prokka: Rapid prokaryotic genome annotation. Bioinformatics. 2014; 30(14): 2068–9. PubMed Abstract | Publisher Full Text\n\nPage AJ, Cummins CA, Hunt M, et al.: Roary: Rapid large-scale prokaryote pan genome analysis. bioRxiv. 2015; 019315. Publisher Full Text\n\nStamatakis A: RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9): 1312–1313. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHadfield J, Croucher NJ, Goater RJ, et al.: Phandango: An interactive viewer for bacterial population genomics. Bioinformatics. 2018; 34(2): 292–293. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCock PJA, Chilton JM, Grüning B, et al.: NCBI BLAST+ integrated into Galaxy. Gigascience. 2015; 4(1): 39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuerta-Cepas J, Forslund K, Coelho LP, et al.: Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Mol Biol Evol. 2017; 34(8): 2115–2122. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGalperin MY, Wolf YI, Makarova KS, et al.: COG database update: focus on microbial diversity, model organisms, and widespread pathogens. Nucleic Acids Res. 2021; 49(D1): D274–D281. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHennessy RC, Dichmann SI, Martens HJ, et al.: Serratia inhibens sp. nov., a new antifungal species isolated from potato (Solanum tuberosum). Int J Syst Evol Microbiol. 2020; 70(7): 4204–4211. PubMed Abstract | Publisher Full Text\n\nRaudhatul F, Irfan S, Djong HT, et al.: Classification of the UBCF_ 13 COG based on COG database in NCBI, Dryad. Dataset. 2021. http://www.doi.org/10.5061/dryad.sn02v6x4g\n\nRaudhatul F, Irfan S, Djong HT, et al.: Gene presence absence in Serratia plymuthica strains, Dryad. Dataset. 2021. http://www.doi.org/10.5061/dryad.1zcrjdfsj"
}
|
[
{
"id": "100842",
"date": "06 Dec 2021",
"name": "Zulema Udaondo",
"expertise": [
"Reviewer Expertise Comparative genomics"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Fatiah et al. is a descriptive study of the novel bacteria with antifungal activity, Serratia plymuthica UBCF_13 that was isolated from the leaf surface of Brassica juncea. The pangenome of this isolate along with another 17 Serratia plymuthica strains downloaded from GenBank was also performed by the authors.\nS. plymuthica is a cosmopolite species that have potential applications as a biocontrol agent due to its antifungal activity. Therefore comparative analyses of members of this species are useful to unveil the metabolic characteristics of this interesting microorganism.\nAlthough the manuscript is understandable for the most part, I would strongly recommend a further revision of the manuscript by a scientific editor as there are some sentences in the manuscript that are difficult to understand, hindering the readability of the entire manuscript.\nThere are also some important data and methodology that are lacking in the manuscript that would be useful from my point of view to better understand the complete context of the study and the reported findings.\nFor example, one of the main concerns is that when accessing the GenBank accession ID for the UBCF_13 strains provided by the authors, it can be observed in the taxonomy check performed by GenBank staff, that this strain is flagged as \"Inconclusive\". Thus, when checking the bottom of the Assembly QA tab from the GenBank webpage: https://www.ncbi.nlm.nih.gov/assembly/GCF_018336935.1#/qa, this strain is classified as a member of the species Serratia inhibens.\nThis species is also the one to which the strain PRI-2C was reclassified in 2020 as can be observed in the paper published in the International Journal of Systematic and Evolutionary Microbiology June 20201. Thus, it makes sense that these two strains are grouped together in the tree shown by the authors. The isolates NCTC8900 and NCTC8015 also failed their taxonomy check, being identified as well, as members of Serratia inhibens species, thus it makes sense that these four strains form a monophyletic group in the tree. These are important issues that I believe should be addressed by the authors. Also, this information could help clarify some of the information obtained by the authors in their pangenome analysis.\nOn the basis of the above, I think it is crucial to provide in the methodology how isolate UBCF_13 was identified as a member of S. plymuthica by the authors.\nAnother issue that I believe would help the authors increase the confidence of their analysis is to provide a quick explanation about the selection of the strains employed in their pangenome analysis. So far there are 29 available genomes classified as S. plymuthica in GenBank, however, the authors only utilized 18 strains (taking into account UBCF_13 ). It would be interesting to know what was the selection method of these strains performed by the authors.\nAlso, very importantly the sequence similarity cutoff for the pangenome analysis was provided (70%) but not the sequence coverage which is crucial to understand how strict the clustering performed was in the pangenome analysis. Also, it would interesting to know why these cut-offs were selected.\nFinally, a brief paragraph summarizing the conclusions obtained by the author after the result section would help wrap up the whole manuscript.\n\nIs the rationale for creating the dataset(s) clearly described? No\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? No\n\nAre the datasets clearly presented in a useable and accessible format? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-826
|
https://f1000research.com/articles/9-30/v1
|
20 Jan 20
|
{
"type": "Research Article",
"title": "The impact of the National Heart, Lung, and Blood Institute data: analyzing published articles that used BioLINCC open access data",
"authors": [
"Saif Aldeen AlRyalat",
"Osama El Khatib",
"Ola Al-qawasmi",
"Hadeel Alkasrawi",
"Raneem al Zu’bi",
"Maram Abu-Halaweh",
"Yara alkanash",
"Ibrahim Habash",
"Osama El Khatib",
"Ola Al-qawasmi",
"Hadeel Alkasrawi",
"Raneem al Zu’bi",
"Maram Abu-Halaweh",
"Yara alkanash",
"Ibrahim Habash"
],
"abstract": "Background: Data sharing is now a mandatory prerequisite for several major funders and journals, where researchers are obligated to deposit the data resulting from their studies in an openly accessible repository. Biomedical open data are now widely available in almost all disciplines, where researchers can freely access and reuse these data in new studies. We aim to assess the impact of open data in terms of publications generated using open data and citations received by these publications, where we will analyze publications that used the Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) as an example. Methods: As of July 2019, there was a total of 194 datasets stored in BioLINCC repository and accessable through their portal. We requested the full list of publications that used these datasets from BioLINCC, and we also performed a supplementary PubMed search for other publications. We used Web of Science (WoS) to analyze the characteristics of publications and the citations they received. Results: 1,086 published articles used data from BioLINCC repository, but only 987 (90.88%) articles were WoS indexed. The number of publications has steadily increased since 2002 and peaked in 2018 with a total number of 138 publications on that year. The 987 open data publications received a total of 34,181 citations up to 1st October 2019. The average citation per item for the open data publications was 34.63. The total number of citations received by open data publications per year has increased from only 2 citations in 2002, peaking in 2018 with 2361 citations. Conclusion: The vast majority of studies that used BioLINCC open data were published in WoS indexed journals and are receiving an increasing number of citations.",
"keywords": [
"Open Data",
"Publications",
"National Institute of Health",
"Bibliometrics"
],
"content": "Introduction\n\nRecent years have seen an increased call for data sharing in clinical studies, especially for research funded by international and governmental agencies1. The call originally aimed to maximize transparency for clinical trial results1, but the benefits of data sharing extended beyond its original aim. Open access data is frequently cited as a boon for researchers, where researchers can re-analyze already collected data to answer a new research question2,3. To organize and maximize the scientific use of open access data, researchers and funders store their data in open access data repositories4. The Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC), is a National Heart, Lung, and Blood Institute is one such data repository, initiated in 2000 with the aim of sharing data from observational and interventional studies supported by the institute5. The impact of open access data, in terms of publications generated and citations received is still unknown. In this study, we aim to analyze number of publications that used BioLINCC open access data, and the impact of these publications through the citations they received.\n\n\nMethods\n\nThere are a total of 205 studies listed on BioLINCC data repository, where four studies have their data stored in other repositories, and seven studies have only specimens available at the BioLINCC institution available upon request, but no datasets associated with them. We only included datasets stored in BioLINCC repository and can be accessed through their portal, which comprises 194 dataset.\n\nWe also contacted BioLINCC support to obtain an up to date list of published articles that used BioLINCC dataset, where we received a list of all publications up to 24th July 2019. Researchers accessing the BioLINCC datasets are requested to disclose any publication resulted from the use of the BioLINCC datasets. The BioLINCC also list published articles that used BioLINCC datasets on their website (https://biolincc.nhlbi.nih.gov/publications/). A manual search of PubMed was also carried out to confirm an updated full list of publications. We used the basic search of PubMed by inputting the title of the dataset in the search field. Any study that reported the use of the searched dataset as part of its results was included in our analysis. The included articles either used data stored in the BioLINCC repository alone, or used these datasets along with other datasets from other repositories.\n\nWe used Web of Science (WoS) database to analyze the characteristics of included publications. We prepared a list of digital object identifiers (DOIs) for the included articles. We inputted the DOI list into the WoS advanced search field, where only WoS indexed publications from the total included articles were analyzed further. The WoS database has a built-in analysis to provide data regarding the number of publications using the included dataset per year (yearly publications), topic of publication, affiliation of authors, and number of citations received6.\n\n\nResults\n\n1,086 published articles used data from BioLINCC repository, but only 987 (90.88%) articles were WoS indexed. All articles published were English language (see underlying data7). The first publication using BioLINCC open data was from 2002. Since then, the number of publications has steadily increased since 2002, as shown in Figure 1, and peaked in 2018 with a total number of 138 publications.\n\nThe 987 open data publications received a total of 34,181 citations from 27,904 published articles up to 1st October 2019. The average citation per item for the publications using BioLINCC data was 34.63. The total number of citations received by publications using BioLINCC data per year has increased from only 2 citations in 2002, to a peak of 2361 citations in 2018 (Figure 2).\n\nA total of 352 (35.66%) of the published articles related to cardiac and cardiovascular systems, 106 (10.74%) articles related to general internal medicine, and 92 (9.32%) related to public and occupational health. Figure 3 shows the 10 most common fields the studied publications using BioLINCC data published in. The American Journal of Cardiology had the highest number of publications using BioLINCC data (60; 6.08%), followed by the International Journal of Cardiology with 47 (4.76%), and American Journal of Medicine 25 (2.53%). Table 1 shows the top 10 journals that publications using BioLINCC data were published in. US authors participated in 842 (85.31%) of the publications using BioLINCC data, followed by Canadian and England authors, with 121 (12.26%), and 81 (8.21%), respectively (Figure 4). The top three affiliations in terms of publications using BioLINCC data were University of Alabama system, University of Alabama at Birmingham, and University of California system as shown in Table 2.\n\n\nDiscussion\n\nTremendous effort has been made by BioLINCC in preparing dataset to be used as open data since its establishment, where hundreds of studies have been published using BioLINCC open data6. The impact of these publications can be measured in terms of citations received, where citations of publications using BioLINCC data have exponentially increased. They received a total of 2361 citations in the year 2018. Cardiology is the main field, with more than third of publications are cardiology related, and the top two journals publishing articles using BioLINCC data are also cardiology journals.\n\nIn an analysis done in 2017, Coady and his colleagues analyzed the administrative records of investigator requests for BioLINCC data, they found that 35% of clinical trial data were associated with at least one publication within five years from data public release8. Where we previously pointed to the importance of open access data for underfunded researchers2, our results showed that the top three countries using open access data are USA, UK, and Canada. Researchers new to open data might be skeptical about the publishing opportunity of studies performed using open data. In our analysis the top 10 journals publishing open data studies, which also comprised around 27% of the total studied publications, had an impact factor of more than two. Regarding the clinical impact of publications using open data, an example would be the post-hoc analysis of the Digitalis Investigation Group trial using the open data of the original trial9, which showed that digoxin therapy is associated with an increased risk of death from any cause among women, but not men, a finding that the original study failed to find. The digitalis trial is an example of how cardiology researchers are using open data, with efforts of cardiology initiatives encouraging data sharing and use by cardiology researchers10. Clinical trial data sharing in cardiology has also been used to validate the reproducibility of published results11. In our study, we found a higher number of cardiology related publications using open access data compared to other specialties.\n\nSince 2003, the National Institute of Health mandated that data collected by studies receiving more than $500,000 be stored in a publicly available repository, with BioLINCC being the main repository for NIH-NHLB institute funded research12. This might explain the high impact of studies resulting from the BioLINCC stored data. On the other hand, data shared by platforms other than BioLINCC may lack sufficient description about the shared data, which will hamper its use by other researchers13. Moreover, repositories should focus on facilitating access to data and increasing awareness about it, so that more researchers can use the data from these repositories10,11. Our results are based on BioLINCC repository, where data of well-funded research projects undergo extensive processing before being publicly shared, resulting in well-curated, high quality data. Other studies should be done to validate our results, by evaluating data repositories that do not have the pre-sharing processing.\n\n\nData availability\n\nHarvard Dataverse: Publications that used Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) datasets. https://doi.org/10.7910/DVN/1TXA3C7\n\nThis project contains the following underlying data:\n\nBioLINCC Dataset.tab (Spreadsheet containing details of publications using BioLINCC datasets)\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\nGøtzsche PC: Strengthening and opening up health research by sharing our raw data. Circ Cardiovasc Qual Outcomes. 2012; 5(2): 236–237. PubMed Abstract | Publisher Full Text\n\nAldeen AlRyalat S: Open data are a boon for underfunded researchers. Nature. 2018; 563(7730): 184. PubMed Abstract | Publisher Full Text\n\nHlatky MA: RESPONSE: A Mentor's Perspective on Using Shared Research Data. J Am Coll Cardiol. 2018; 71(18): 2077–2078. PubMed Abstract | Publisher Full Text\n\nGiffen CA, Carroll LE, Adams JT, et al.: Providing Contemporary Access to Historical Biospecimen Collections: Development of the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biopreserv Biobank. 2015; 13(4): 271–279. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoady SA, Wagner E: Sharing individual level data from observational studies and clinical trials: a perspective from NHLBI. Trials. 2013; 14: 201. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlRyalat SAS, Malkawi LW, Momani SM: Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases. J Vis Exp. 2019; (152): e58494. PubMed Abstract | Publisher Full Text\n\nAlRyalat SA: Publications that used Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) datasets. 2019. http://www.doi.org/10.7910/DVN/1TXA3C\n\nCoady SA, Mensah GA, Wagner EL, et al.: Use of the National Heart, Lung, and Blood Institute Data Repository. N Engl J Med. 2017; 376(19): 1849–1858. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRathore SS, Wang Y, Krumholz HM: Sex-based differences in the effect of digoxin for the treatment of heart failure. N Engl J Med. 2002; 347(18): 1403–1411. PubMed Abstract | Publisher Full Text\n\nAcademic Research Organization Consortium for Continuing Evaluation of Scientific Studies--Cardiovascular (ACCESS CV), Patel MR, Armstrong PW, et al.: Sharing Data from Cardiovascular Clinical Trials--A Proposal. N Engl J Med. 2016; 375(5): 407–409. PubMed Abstract | Publisher Full Text\n\nGay HC, Baldridge AS, Huffman MD: Feasibility, Process, and Outcomes of Cardiovascular Clinical Trial Data Sharing: A Reproduction Analysis of the SMART-AF Trial. JAMA Cardiol. 2017; 2(12): 1375–1379. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNational Institutes of Health: NIH Data Sharing Policy. Accessed on 17th of November 2019. Reference Source\n\nHuser V, Shmueli-Blumberg D: Data sharing platforms for de-identified data from human clinical trials. Clin Trials. 2018; 15(4): 413–423. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "68865",
"date": "10 Aug 2020",
"name": "Christian Ohmann",
"expertise": [
"Reviewer Expertise clinical research",
"medical informatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting paper about the impact of data sharing for a non-commercial repository (BioLINCC). From the viewpoint of the reviewer, the manuscript should be improved:\nIn the section “data collection” the authors describe different data search methods for publications:\nUpdated list of publications received from BioLINCC directly.\n\nList of published articles on the BioLINCC website.\n\nManual search of Pubmed with the title of the dataset.\nThe authors should describe the overlap/differences between the results of the different search strategies, preferably in a figure. The authors could use the PRISMA flow diagram as an example (https://www.equator-network.org/reporting-guidelines/prisma/).\nThe authors state in the “bibliometric analysis” section that “Any study that reported the use of the searched data set as part of its results was included in our analysis”. It is not clear, how the datasets were identified in the publication. Was this performed via the registration number of the underlying study in a registry (e.g. NCT-number) or by the title/acronym of the data set from the BioLINCC database? The authors should clarify how this was performed.\nImportant to add would be a statistic describing the number of publications per data set (may be also dependent on the year of publication of the data set in BioLINCC). Are there many datasets without any or only very few publications? Is the majority of publications concentrated in a few datasets? This information is important because no requests for data sharing may not justify costs and resources for preparation of data sharing (e.g. de-identification, curation).\nOne of the factors that is relevant for the number of publications is the year when the data set was published in BioLINCC. A figure correlating the date of publication of the data set with the number of publications could illustrate that. This is similar with the relation between the year of publication and the number of citations. These relationships should be worked out in the paper.\nAnother aspect to be considered could be the role of outliers in the statistics. Are there datasets and/or publications with a very high number of citations (e.g. more than 100). Does the citation pattern mainly concentrate in a few outstanding datasets or is it more evenly distributed?\nThe authors should include and discuss a cross-sectional web-based survey about access to clinical research data from BioLINCC, covering the period from 2007 to 2014 (Ross JS et al. Data sharing through an NIH central database repository: a cross-sectional survey of BioLINCC users. BMJ open 2016;6(9):e012769)1.\nThe authors think that it would be good style to thank BioLINCC for providing datasets after contact.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "5958",
"date": "28 Sep 2020",
"name": "Saif Aldeen AlRyalat",
"role": "Author Response",
"response": "It is an honor to receive feedback from professor Ohmann, we performed almost all the changes suggested, and we hope the current version satisfies the quality required. Here are the detailed responses. This is an interesting paper about the impact of data sharing on a non-commercial repository (BioLINCC). From the viewpoint of the reviewer, the manuscript should be improved: Comment: In the section “data collection” the authors describe different data search methods for publications: The updated list of publications received from BioLINCC directly. List of published articles on the BioLINCC website. Manual search of Pubmed with the title of the dataset. The authors should describe the overlap/differences between the results of the different search strategies, preferably in a figure. The authors could use the PRISMA flow diagram as an example (https://www.equator-network.org/reporting-guidelines/prisma/). Response: Thank you for suggesting the PRISMA flow chart. We added a new flow chart detailing the steps of including datasets and the criteria of inclusion, with the number of datasets resulted after each exclusion step. While the list of publications provided by the BioLINCC was almost complete, the manual and Pubmed searches didn’t yield a significant addition, where only a few articles added only (we added this to the article). On the other hand, the detailed number of datasets included and excluded is of paramount importance, we used the flow chart for detailing its number. Comment: The authors state in the “bibliometric analysis” section that “Any study that reported the use of the searched data set as part of its results was included in our analysis”. It is not clear, how the datasets were identified in the publication. Was this performed via the registration number of the underlying study in a registry (e.g. NCT-number) or by the title/acronym of the data set from the BioLINCC database? The authors should clarify how this was performed. Response: Any author requested BioLINCC datasets for use in a study should explicitly mention the dataset used in the methods (i.e. the name of the dataset and the acronym if available), in addition to acknowledging the BioLINCC in the acknowledgment section. Comment: Important to add would be a statistic describing the number of publications per data set (may be also dependent on the year of publication of the data set in BioLINCC). Are there many datasets without any or only very few publications? Is the majority of publications concentrated in a few datasets? This information is important because no requests for data sharing may not justify costs and resources for preparation of data sharing (e.g. de-identification, curation). Response: Thank you for this insight. We analyzed the number of publications associated with each dataset. As the reviewer expected, there are many datasets with no publications associated with them, as well as datasets with high number of publications. We added these results and relevant tables, and we further discussed them in the discussion. Comment: One of the factors that is relevant for the number of publications is the year when the data set was published in BioLINCC. A figure correlating the date of publication of the data set with the number of publications could illustrate that. This is similar with the relation between the year of publication and the number of citations. These relationships should be worked out in the paper. Response: The publication year of datasets may vary according to the datasets, and may change with time if the study got updated (i.e. more data released with time). So it was difficult to study it, considering the unavailability of specific dates provided in the dataset we received from the BioLINCC. Comment: Another aspect to be considered could be the role of outliers in the statistics. Are there datasets and/or publications with a very high number of citations (e.g. more than 100). Does the citation pattern mainly concentrate in a few outstanding datasets or is it more evenly distributed? Response: As the author mentioned, we found several “outlier” datasets and we mentioned them in the results. These datasets were associated with higher number of publications compared to other datasets. Comment: The authors should include and discuss a cross-sectional web-based survey about access to clinical research data from BioLINCC, covering the period from 2007 to 2014 (Ross JS et al. Data sharing through an NIH central database repository: a cross-sectional survey of BioLINCC users. BMJ open2016;6(9):e012769)1. Response: Thank you for suggesting the article. We made good use of it. The authors think that it would be good style to thank BioLINCC for providing datasets after contact."
},
{
"c_id": "6329",
"date": "21 Apr 2021",
"name": "Saif Aldeen AlRyalat",
"role": "Author Response",
"response": "Dear Professor Ohmann, We hope our responses satisfy your comments, if so, we hope to receive your feedback. Thank you for your time. Sincerely, Saif Aldeen AlRyalat, MD. Corresponding author."
}
]
},
{
"id": "70339",
"date": "08 Sep 2020",
"name": "Lisa Federer",
"expertise": [
"Reviewer Expertise data science",
"data sharing and reuse"
],
"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 addressed an interesting question - what are the impacts of open data, specifically considering citations received by publications using open data sets. This question is very timely given the increasing number of funder and journal requirements that datasets be made open. However, my primary concern with this paper is that it doesn't really provide much context for understanding impact.\n\nThe authors have tracked citations to articles that reuse datasets over time. However, with nothing to compare these counts to, it's hard to contextualize what these citations really mean. Are these papers being cited more/less than similar articles that aren't reusing datasets? How do citations to these articles describing secondary reuse compare to the number of citations received by the articles describing the dataset originally and its primary use? It's evident that citations to these articles are going up over time, but that's to be expected to an extent. So I'm not really sure what to make of these numbers and how to use them to understand impact. While this article provides an overview of the state of citations to articles reusing BioLINCC data, it is unclear to me what conclusions can be reasonably drawn from this analysis about impact.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "5959",
"date": "28 Sep 2020",
"name": "Saif Aldeen AlRyalat",
"role": "Author Response",
"response": "We would like to thank Dr. Frederer, who is an expert in the field of data science, for the insight and thoughts she shared through her revision. While we agree with her comments on the gap between our study and the big aim of “studying the impact of open data”. Our study tried to answer a certain aspect of this aim, which we further specified in the current version, and added more data that will provide better insight on BioLINCC datasets, publications, and their impact. Here are our detailed responses: Comment: The authors have addressed an interesting question - what are the impacts of open data, specifically considering citations received by publications using open data sets. This question is very timely given the increasing number of funder and journal requirements that datasets be made open. However, my primary concern with this paper is that it doesn't really provide much context for understanding impact. Response: We totally agree with Dr. Federer, that the analysis of open data is most relevant during this time. One of the most important data repository in the biomedical field containing high quality datasets for well conducted studies is the BioLINCC repository. The interest to study the characteristics of this data repository is not new, as we pointed in the publications by Coady et al., Ross et al., and Giffen et al. While none of these papers alone provide the full picture of the impact of the BioLINCC repository and open data, they each provide knowledge on certain aspects. We chose to study the number of datasets that were used out of the total datasets in the BioLINCC repository, the number of publications generated (considering that this is the main reason for data requests as found by Ross et al), and number of citations these publications received. While this aim will cover a small aspect of the big question of “the impact of open data”, it will provide an important insight for better understanding of the characteristics of open data at the BioLINCC repository, what are the main datasets used, their fields, and the assurance that using an open dataset won’t compromise publishing potential of studies, if important findings found. We tried to stress further on this point. Comment: The authors have tracked citations to articles that reuse datasets over time. However, with nothing to compare these counts to, it's hard to contextualize what these citations really mean. Are these papers being cited more/less than similar articles that aren't reusing datasets? How do citations to these articles describing secondary reuse compare to the number of citations received by the articles describing the dataset originally and its primary use? It's evident that citations to these articles are going up over time, but that's to be expected to an extent. So I'm not really sure what to make of these numbers and how to use them to understand impact. While this article provides an overview of the state of citations to articles reusing BioLINCC data, it is unclear to me what conclusions can be reasonably drawn from this analysis about impact. Response: We agree with the author that comparing the number of citations received by publications that used open data with primary data articles would provide a better insight into the impact of open data compared to other articles. We amended the aim to narrow its scope so that it accommodates the aspects covered by our study: “The impact of open access data, in terms of the number of datasets used from a repository, publications generated from these datasets, and citations received by these publications are still unknown. In this study, we aim to study the BioLINCC datasets, the number of publications that used BioLINCC open access data, and the impact of these publications through the citations they received.” We added the point mentioned by the esteemed reviewer to the study limitations and as a suggestion for future studies. We further discussed the aspects regarding the BioLINCC use of datasets and the characteristics of its publications."
}
]
},
{
"id": "70340",
"date": "25 Sep 2020",
"name": "Colby Vorland",
"expertise": [
"Reviewer Expertise Meta-research"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The authors ask an interesting question as to what the impact of BioLINCC has been on the use of open data. However, the assessments of impact do not seem to appropriately contextualize the use of BioLINCC datasets as compared to growth of scientific publishing overall. Further, the authors include data in their analyses before the existence of BioLINCC, and the methods used to sample are unclear. -------------- Abstract\nIt is unclear why WoS indexing is in the conclusions, unless it is being used as a proxy for ‘impact.’ If so, the article does not make clear that WoS indexing is being used as a sign of impact.\n\nThe choice of ‘citations’ as a metric for ‘impact’ is questionable. Citations may best be considered a metric of ‘attention’.\n\nIntroduction BioLINCC was not initiated in 2000 as stated- it was 2008: https://www.nhlbi.nih.gov/science/biologic-specimen-and-data-repository-information-coordinating-center-biolincc The NHLBI had a different repository since 2000. However, since the authors focus on BioLINCC, this raises the question why the authors start their survey in 2002, and how this data came to be included in their sampling.\n\nMethods The methods as currently stated are not reproducible. For example, on what date were BioLINCC and PubMed sampled? What was the search string for PubMed?\n\nIt is not clear whether PubMed entries necessarily indicate that they use BioLINCC datasets. The authors mention “any study that reported the use of the searched dataset as part of its results was included”. Does that mean full texts were reviewed? If so, by what process and by which of the authors?\n\nIt is not clear what is meant by “title of the dataset in the search field”. Does this mean the study name? The study acronym? It seems likely that many publications would not use the exact dataset name in the title or abstract and this approach would therefore potentially miss papers. Were any new papers found beyond the BioLINCC list from the PubMed search? How many articles from the BioLINCC list were not confirmed in the PubMed search? This information is missing from the methods.\n\nResults It is indicated that over 9% of the articles using data from BioLINCC are not WoS indexed. If these articles are not evenly distributed over time, then it will skew the results of the trends. For example – were the papers not indexed more recent papers that WoS has not yet picked up? At minimum, the authors can manually extract the year, journal, and country of publication from these papers to include the in assessments.\n\nThe utility of the analyses as currently presented seem questionable. How does the increase in articles published and citations by year compare to trends in overall metrics of these measures? i.e. do these trends outpace or just reflect the growth of scientific publishing overall? The authors may also consider limiting such comparison to the specific fields that use BioLINCC data.\n\nThe authors note the values ‘peaked in 2018’, but that was the most recent year of full data, given their partial year in 2019. Thus, 2019 is likely artificially small by virtue of it being a partial year.\n\nThe University of Alabama at Birmingham is part of the University of Alabama System, and thus counting them separately does not seem to make sense.\n\nIt is unclear how fields of study were determined. Were these just extracted from WoS (is this “topic of publication” per methods or a separate extraction), or did the authors classify them? Regardless, the finding that cardiology is the top field is not surprising, given that BioLINCC is from the National Heart, Lung, and Blood Institute. This should be made clear.\n\nOne key point that may undermine the idea of ‘impact’ of the open datasets is that the study investigators appear to be included in these counts. For example, the University of Alabama at Birmingham is a key site for some studies (e.g., CARDIA), and thus they would be publishing from their datasets whether they were open in BioLINCC or not. So, what is the incremental contribution to investigators who are not part of the cohort? What difference is it making for how many papers would be published if the data were open or not?\n\nDiscussion In general, the discussion does not seem to flow logically. For example, in one paragraph, the authors discuss the percent of publications after data release, the top countries from which BioLINCC data are used and top journals, and then a single example of clinical impact from using BioLINCC data. The points in the discussion should be separated and connected to the purpose of the study. New results (e.g., impact factor) should not be introduced in the discussion. Further, have there been other studies that have examined these or related questions about BioLINCC or other repositories?\n\n“The impact of these publications can be measured in terms of citations received, where citations of publications using BioLINCC data have exponentially increased”\nExponential growth is a specific mathematical term whereas the growth in the figures appears to be roughly linear.\n“Researchers new to open data might be skeptical about the publishing opportunity of studies performed using open data.”\nThis statement does not seem relevant to the analysis nor supported by any citations.\nFinally, a limitations section is needed noting the sole focus on WoS and whether the inclusion of other indexes might alter conclusions. For example – to our knowledge, F1000Research is not indexed in WoS; would relevant studies published here be included in a different index?\n\nData We downloaded and inspected the data:\nThere is no data dictionary to interpret the dataset.\n\n‘Recid’ starts at 4 and not 1. Some ‘Recid’s are missing (for example, #5, #7). Were these entries those that were not indexed by WoS? Those DOIs would still be useful to include in the dataset so future researchers can use them.\n\nWere theses and other article types included in all analyses (include this information in the methods)?\n\nThere are missing data (e.g., funding; MESH terms; article types; study type; one publication was missing ‘study list’).\n\nThe authors state that they searched WoS by DOI, and yet DOIs are missing from some entries. How was this accounted for in the analysis? Are the missing DOIs counted as part of ‘not indexed in WoS’?\nGeneral The writing is generally clear, but it could benefit from a grammatical edit in some passages.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "6552",
"date": "21 Apr 2021",
"name": "Saif Aldeen AlRyalat",
"role": "Author Response",
"response": "I went through the manuscript and amended and responded to all comments. Here are the responses. Reviewer Colby Vorland and Andrew Brown It is an honor to receive a feedback from Drs Colby and Brown from Indiana university, we performed almost all the changes suggested, and we hope the current version satisfy the quality required. Here are the detailed responses. Summary: The authors ask an interesting question as to what the impact of BioLINCC has been on the use of open data. However, the assessments of impact do not seem to appropriately contextualize the use of BioLINCC datasets as compared to growth of scientific publishing overall. Further, the authors include data in their analyses before the existence of BioLINCC, and the methods used to sample are unclear. Response: Thank you. The study is mostly descriptive of the studies published using datasets stored at the BioLINCC repository, with a bibliometric analysis of these studies. We believe that such analysis will show the impact of open data and will encourage authors to further share their data publicly. So we agree with the reviewer that the current analysis lacks the comparison with the growth of overall scientific literature, but we will consider such analysis in the near future. The BioLINCC is basically a repository to store and facilitate the share of data collected by National Heart, Lung, and Blood Institute funded studies, where these studies and their data might have been done before the existence of the BioLINCC, but were stored in the BioLINCC repository afterward. -------------- Abstract It is unclear why WoS indexing is in the conclusions, unless it is being used as a proxy for ‘impact.’ If so, the article does not make clear that WoS indexing is being used as a sign of impact. Response: We used the WoS database as they have strict and high bar criteria to index publication, so it was used as a proxy for impact as the authors stated. We clarified this point in the abstract as suggested. The choice of ‘citations’ as a metric for ‘impact’ is questionable. Citations may best be considered a metric of ‘attention’. Response: we agree with the author that the issue of considering citation as the sole metric for impact is debatable, so we made this point clear in the limitation section. Introduction BioLINCC was not initiated in 2000 as stated- it was 2008: https://www.nhlbi.nih.gov/science/biologic-specimen-and-data-repository-information-coordinating-center-biolincc The NHLBI had a different repository since 2000. However, since the authors focus on BioLINCC, this raises the question why the authors start their survey in 2002, and how this data came to be included in their sampling. Response: Whereas the BioLINCC repository itself was made in 2008, the datasets deposited in it were developed before that, since 2000*, so the publications may date back to as early as 2002. * Coady SA, Wagner E. Sharing individual level data from observational studies and clinical trials: a perspective from NHLBI. Trials. 2013 Dec;14(1):1-3. Methods The methods as currently stated are not reproducible. For example, on what date were BioLINCC and PubMed sampled? What was the search string for PubMed? It is not clear whether PubMed entries necessarily indicate that they use BioLINCC datasets. The authors mention “any study that reported the use of the searched dataset as part of its results was included”. Does that mean full texts were reviewed? If so, by what process and by which of the authors? Response: The original dataset was extracted by contacting the BioLINCC personnel and asking them for the up to date list of publications that used repository’s datasets. Our supplementary PubMed search was carried out as follows, which we further elaborated in the methods section: “A manual search of PubMed was also carried out to confirm an updated full list of publications as follows: We used the basic search of PubMed by inputting the title of the dataset in the search field (e.g., Cooperative Study of Sickle Cell Disease or CSSCD), in order to retrieve results that mention the dataset in the title, abstract, or keywords. The searched articles were manually screened by one of the authors (SAA) to check if the dataset was used in the study to generate results, where authors either detail the name and acronym of dataset used in the methods section, usually with specific citation to relevant study, or in the acknowledgment section in their articles. The included articles either used data stored in the BioLINCC repository alone or used these datasets along with other datasets from other repositories We added the searched articles to the original dataset provided by the BioLINCC. We analyzed the number of studies published using each dataset (supplementary material).” It is not clear what is meant by “title of the dataset in the search field”. Does this mean the study name? The study acronym? It seems likely that many publications would not use the exact dataset name in the title or abstract and this approach would therefore potentially miss papers. Were any new papers found beyond the BioLINCC list from the PubMed search? How many articles from the BioLINCC list were not confirmed in the PubMed search? This information is missing from the methods. Response: Inputting the title and the acronym of the dataset in the PubMed search will retrieve all articles that mentioned the dataset in the title, abstract, keywords. The guidelines for reporting secondary analysis articles require the mention of the dataset used in the title or abstract*. Despite that, we agree with the reviewers that our search might miss few articles that did not mention the dataset there. We tried to limit the words for the methods and results, which is why these details are not provided the full manuscript. We directly added the results searched by the supplementary search directly on the original dataset provided by the BioLINCC, which is provided as supplementary material. * Swart E, Schmitt J. STandardized Reporting Of Secondary data Analyses (STROSA)-Vorschlag für ein Berichtsformat für Sekundärdatenanalysen. Zeitschrift für Evidenz, Fortbildung und Qualität im Gesundheitswesen. 2014 Jan 1;108(8-9):511-6. Results It is indicated that over 9% of the articles using data from BioLINCC are not WoS indexed. If these articles are not evenly distributed over time, then it will skew the results of the trends. For example – were the papers not indexed more recent papers that WoS has not yet picked up? At minimum, the authors can manually extract the year, journal, and country of publication from these papers to include the in assessments. Response: We analyzed the non-indexed articles manually to check if they were published in 2019, which if so might reflect a delay in the indexing. We found that they were distributed over the years with the majority were published in the year 2018. We could not perform detailed analysis as they could not be analyzed using the WoS database, so clarified this in the results: “For the 99 (9.12%) articles that were not indexed, they were distributed over the years with the majority (i.e. 42 articles) were published in 2018.” The utility of the analyses as currently presented seem questionable. How does the increase in articles published and citations by year compare to trends in overall metrics of these measures? i.e. do these trends outpace or just reflect the growth of scientific publishing overall? The authors may also consider limiting such comparison to the specific fields that use BioLINCC data. Response: Thank you for the important point. While we did not compare with the overall publishing trend in the field, we tried to show the increase in the number of publication using open access data in each field. The use of specific dataset might not be restricted to the field of the dataset itself, as a dataset that was originally a cardiovascular dataset might be used by researchers from other fields for other ideas. As an example, Radiological images in ACCESS datasets were used several times for Radiology publications. The authors note the values ‘peaked in 2018’, but that was the most recent year of full data, given their partial year in 2019. Thus, 2019 is likely artificially small by virtue of it being a partial year. Response: We agree with the reviewer, so we made this point clear in the methods. The University of Alabama at Birmingham is part of the University of Alabama System, and thus counting them separately does not seem to make sense. Response: We corrected according to reviewer suggestion, the WoS database have both as separate affiliation, which led to this confusion. It is unclear how fields of study were determined. Were these just extracted from WoS (is this “topic of publication” per methods or a separate extraction), or did the authors classify them? Regardless, the finding that cardiology is the top field is not surprising, given that BioLINCC is from the National Heart, Lung, and Blood Institute. This should be made clear. Response: These are WoS based classification, we changed in the text accordingly. One key point that may undermine the idea of ‘impact’ of the open datasets is that the study investigators appear to be included in these counts. For example, the University of Alabama at Birmingham is a key site for some studies (e.g., CARDIA), and thus they would be publishing from their datasets whether they were open in BioLINCC or not. So, what is the incremental contribution to investigators who are not part of the cohort? What difference is it making for how many papers would be published if the data were open or not? Response: We thank the reviewers for the important remarks, as it is difficult to performed such discrimination in the current study, we made this point clear in the limitation part, so that readers would consider this point upon interpreting the results. Discussion In general, the discussion does not seem to flow logically. For example, in one paragraph, the authors discuss the percent of publications after data release, the top countries from which BioLINCC data are used and top journals, and then a single example of clinical impact from using BioLINCC data. The points in the discussion should be separated and connected to the purpose of the study. New results (e.g., impact factor) should not be introduced in the discussion. Further, have there been other studies that have examined these or related questions about BioLINCC or other repositories? Response: We made several changes on the discussion to improve its flow. We removed some of the unrelated discussion part. We also removed the part related to impact factor. “The impact of these publications can be measured in terms of citations received, where citations of publications using BioLINCC data have exponentially increased” Exponential growth is a specific mathematical term whereas the growth in the figures appears to be roughly linear. Response: We changed accordingly, thank you. “Researchers new to open data might be skeptical about the publishing opportunity of studies performed using open data.” This statement does not seem relevant to the analysis nor supported by any citations. Response: We removed it through our effort to improve the discussion part, thank you. Finally, a limitations section is needed noting the sole focus on WoS and whether the inclusion of other indexes might alter conclusions. For example – to our knowledge, F1000Research is not indexed in WoS; would relevant studies published here be included in a different index? Response: We agree with the reviewer, we made clear that WoS database might not include all studies published using open access data from BioLINCC repository. Data We downloaded and inspected the data: There is no data dictionary to interpret the dataset. Response: We added a description at the dataset website: https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi%3A10.7910%2FDVN%2F1TXA3C&version=DRAFT ‘Recid’ starts at 4 and not 1. Some ‘Recid’s are missing (for example, #5, #7). Were these entries those that were not indexed by WoS? Those DOIs would still be useful to include in the dataset so future researchers can use them. Response: The entries did not use the BioLINCC data, so were not included in the dataset. Were theses and other article types included in all analyses (include this information in the methods)? Response: Thesis were not included, we added this to the methods. There are missing data (e.g., funding; MESH terms; article types; study type; one publication was missing ‘study list’). The authors state that they searched WoS by DOI, and yet DOIs are missing from some entries. How was this accounted for in the analysis? Are the missing DOIs counted as part of ‘not indexed in WoS’? Response: Missing doi were added to the manually to the WoS search for data analysis. They were not counted as part of the “not indexed in WoS”. After inputting doi to the databse, information about the study will automatically be retrieved from the WoS database, so missing data in the excel sheet won’t affect the analyzed data. Thank you for your consideration! Sincerely, Saif Aldeen AlRyalat, M.D. Corresponding author."
}
]
}
] | 1
|
https://f1000research.com/articles/9-30
|
https://f1000research.com/articles/10-825/v1
|
18 Aug 21
|
{
"type": "Research Article",
"title": "Incisional correction of corneal astigmatism during phacoemulsification – a randomized trial",
"authors": [
"Najah K. Mohammad",
"Tamer F. Elewa",
"Enas B. Aldehaimy",
"Tareq A. Almamoun",
"Tamer F. Elewa",
"Enas B. Aldehaimy",
"Tareq A. Almamoun"
],
"abstract": "Background: Phacoemulsification is regarded as a type of refractive surgery by which it is possible to reduce pre-existing corneal stigmatism. This study aimed to evaluate the efficacy and safety of on-axis corneal incision with or without opposite clear corneal incisions (OCCI) to correct preoperative corneal astigmatism during uncomplicated phacoemulsification surgeries. Methods: A randomized, prospective, parallel two-arm interventional study, which included a total 40 eyes from 40 patients, was conducted. Patients were divided into two groups: 20 patients as controls underwent phacoemulsification with on-axis incision (CCI group), and 20 patients underwent phacoemulsification with OCCI (OCCI group). Results: Mean astigmatic correction was significantly higher in the OCCI group (0.665 vs 0.265 diopters, p-value <0.001), compared to the CCI group. Most of the parameters (surgical induced astigmatism, magnitude of error, and correction index) were significantly higher in the OCCI group compared to the CCI group (p-value <0.01). There were no incision-related complications. Conclusions: Both incisional methods are useful methods for correction of preoperative corneal astigmatism but OCCIs correct a higher amount of astigmatism than the on-axis clear corneal incision. Registration: ClinicalTrials.gov NCT04418986 (05/06/2020).",
"keywords": [
"Phacoemulsification",
"Corneal astigmatism",
"Clear corneal incision",
"Opposite clear corneal incision",
"Vector analysis."
],
"content": "Introduction\n\nCurrently cataract surgery is considered to be a refractive surgery, with the main therapeutic goal of achieving emmetropia; as a result, correction of corneal astigmatism becomes essential for such an operation.1,2 The prevalence of corneal astigmatism of more than 1 diopter is as high as 45% of those who undergo cataract surgery.3\n\nIt is possible to reduce pre-existing corneal astigmatism by creating a clear corneal incision at the steep meridian of the cornea; however, astigmatism correction is limited to a maximum of 1 diopter (D) when corrected by a small incision. A possible limitation is the difficulty in performing the operation which is caused by the location of the steep meridian, such as the difficulty of creating superonasal or inferonasal incisions at the left eye. This approach is usually sufficient for correcting astigmatism less than 1 D in most eyes.1,4 An opposite side clear corneal incision (OCCI) could enhance the flattening effect on the cornea.5\n\nThe current work aims to evaluate the efficacy and safety of on-axis corneal incision with or without OCCIs to correct preoperative corneal astigmatism during uncomplicated phacoemulsification surgeries. The current work is based on the fact that the cornea is not a perfect sphere and many patients present with corneal astigmatism in addition to cataracts. In one procedure, phacoemulsification, cataracts and corneal astigmatism can be corrected based on the principle of releasing incision.\n\n\nMethods\n\nWritten informed consent was obtained from each participant for participation and publication of clinical information. The study was approved by the institutional regulation board committee of Faculty of Medicine – Baghdad University (Ref#0122-2019). The study followed the Declaration of Helsinki 2008 for research on human subjects.\n\nThis trial was registered with ClinicalTrials.gov (NCT04418986) on 5th June 2020. The trial was registered retrospectively, since mandatory clinical trial registration was only recently introduced to research policies in Iraq so after the study, we registered the trial to ensure transparency of the study.\n\nThis study was a randomized, parallel two-arm interventional study. The study included 40 eyes with visually significant cataract and preoperative corneal regular astigmatism between 0.75 and 2 D undergoing phacoemulsification surgery.\n\nPatients were divided into two groups in a 1:1 ratio: 20 patients as controls underwent phacoemulsification with on-axis incision (CCI group), and 20 patients underwent phacoemulsification with OCCIs (OCCI group).\n\nThe study was carried out in the ophthalmology clinic in Ghazi al-Hariri Surgical Specialties Hospital. The recruitment period was three months, from July 2019 until September 2019. All procedures took place in in the ophthalmology clinic in Ghazi al-Hariri Surgical Specialties Hospital, and all the procedures were carried out by NKM.\n\nThe participants were approached by the investigators during their visit to the ophthalmology clinic of Ghazi al-Hariri Surgical Specialties Hospital. The primary investigator, Dr. Najah K. Mohammad, examined each participant at admission to the center and conducted an initial interview to check the adherence of the patients to the inclusion and exclusion criteria, specifically age, previous ocular surgeries, and systemic diseases, and if the cataract intervention met their requirements. After obtaining their informed consent and confirming adherence of the participants to the inclusion and exclusion criteria they entered the study. Since this was a pilot study, the sample size was not determined by formal power analysis.\n\nComputer-based randomization was used in which the patients were randomly divided into two groups. After the initial interview, the patients were numbered consequently, then randomized into two groups using the online software Research Randomizer.\n\nNegative history of ocular surgery, clear cornea, and central corneal thickness (CCT) less than 640.\n\nPatients with lenticular astigmatism, corneal opacities or pathology like Fuch’s endothelial dystrophy, previous ocular surgeries like glaucoma surgery or PKP or pterygium excision, posterior segment diseases and pathology, and complicated phacoemulsification were excluded from this study.\n\nAll the patients had their complete history taken and underwent ophthalmic examination that included: manifest refraction; uncorrected distance visual acuity (UCDVA); best corrected distance visual acuity (BCDVA); intraocular pressure (IOP) measurement by non-contact air puff tonometry; detailed examination of the anterior segment using slit lamp biomicroscopy; posterior segment detailed examination using indirect ophthalmoscopy; corneal topography, mesopic pupil size and corneal pachymetry were done using Sirius Topographer (CSO, Italy); and ocular biometry to measure axial length, anterior chamber depth, and horizontal white to white (WTW) distance were done using partial coherence interferometry (PCI), the ZEISS IOLMaster® 500 (Carl Zeiss Meditec AG, Germany).\n\nCCI, clear corneal incision; OCCI, opposite clear corneal incision.\n\nThe procedure is similar to our previous study by Eliwa et al.,6 in which the steep meridian of the corneal topography was marked using a Whitehouse Gravity Axis Marker. This was done before local anesthesia was administered. Peribulbar anesthesia (lidocaine 2% [5 ml], bupivacaine 0.5% [5ml], and hyaluronidase 1,500 IU/mL [2 ml], all given via the peribulbar route) associated with mild sedation with midazolam was used in all cases.\n\nCoaxial small incision cataract surgery was performed for all cases of both groups using a 2.8 mm keratome placed at steep meridian and 1-mm paracentesis was made 90 degrees apart with a 20-gauge microvitrectomy blade (Alcon Laboratories, Inc., Fort Worth, TX). Surgery was performed with a 30-degree, 0.9-caliper phacoemulsification tip (microtip) with the divide-and-conquer technique using the INFINITI vision system (ALCON laboratories INC).\n\nThe AcrySof SN60WF (Alcon Laboratories, Inc.) intraocular lens (IOL) was loaded in cartridge C and then inserted using a Royale injector (ASISCO LLC, Westmont, IL). The tip of the cartridge was introduced into the external part of the incision, after which the IOL was injected into the capsular bag.\n\nIn the OCCI group, a single penetrating incision was created with a 2.8 mm keratome in clear cornea, 1.5 mm anterior to limbal blood vessels, centered over the steep meridian and opposite the phacoemulsification incision.\n\nPostoperative topical therapy included a combination of topical antibiotics (moxifloxacin drops 2% [1 – 2 drops every six hours for a two-week duration]), and steroid eye drops (prednisolone acetate 1% [1 – 2 drops every six hours for a two week duration, than tapered to twice daily for two weeks] and eye lubricants (Systane Ultra drops, 1 – 2 drops every six hours for four weeks).\n\nPrimary outcomes\n\nChange in surgically induced astigmatism (SIA) one month after the phacoemulsification. Corneal astigmatism was examined by corneal topography, preoperatively and four weeks after the surgery, by the same technician, and changes in astigmatism were assessed by Alpins vector analysis comparing the SIA pre- and postoperatively.\n\nSecondary outcomes\n\nTo investigate the differences between CCI and OCCI regarding the changes in corneal astigmatism assessed by corneal topography and SIA.\n\nThe Anderson-Darling test was used to assess the adherence of variables to normality, the paired t-test (or Wilcoxon median rank test if data did not follow normal distribution) was used to analyze the difference between preoperative and postoperative outcomes and the independent t-test (or Mann–Whitney U test if data did not follow normal distribution) was used to analyze the difference between two independent variables. The p-value was considered to be significant if <0.05 and all analysis was carried out using SPSS version 20.0.1 (IBM Corp, Armonk, NY).\n\n\nResults\n\nThe study included 40 eyes (Figure 1). The mean age of participants was 57.9 ± 13.25, and 52.5% were males (21/40).16 These cases were divided into two groups: CCI and OCCI groups. There was no statistically significant difference between the two groups regarding patient demographic data, as illustrated in Table 1.\n\nMean corneal power significantly reduced after one month postoperatively in the OCCI group, while the CCI group showed a slight reduction in mean corneal power postoperatively. The UCVA significantly improved in both groups after the procedure, from 0.114 ± 0.048 and 0.146 ± 0.102 preoperatively in CCI and OCCI groups, respectively (approximately 6/60, 1 LogMAR), to 0.35 (approximately 6/18, 0.48 LogMAR) in the CCI group and 0.45 (approximately 6/12, 0.3 LogMAR) in the OCCI group postoperatively. Mean BCVA significantly increased from 0.283 ± 0.097 (approximately 6/24, 0.60 LogMAR) preoperatively to 0.438 ± 0.146 (approximately 6/12, 0.3 LogMAR) postoperatively in the CCI group, and the OCCI group showed a statistically significant increase in BCVA from 0.375 ± 0.150 (approximately 6/18, 0.48 LogMAR) preoperatively to 0.564 ± 0.125 (approximately 6/9, 0.18 LogMAR) postoperatively, as illustrated in Table 2.\n\nThe mean change in topographic astigmatism was statistically significantly higher in the OCCI group (0.665 ± 0.268 D) than the CCI group (0.265 ± 0.142 D) (p-value < 0.001; Figure 2A), while there was no statistically significant difference between the two groups regarding the change in mean corneal power (see Figure 2B).\n\nCCI, clear corneal incision; OCCI, opposite clear corneal incision.\n\nMean magnitude of target induced astigmatism vector (TIA) of both groups was 1.37 D, which was similar to preoperative topographic astigmatism. Most of the parameters (surgical induced astigmatism, magnitude of error, and correction index) were significantly higher in OCCI group compared to the CCI group (p-value < 0.01), as illustrated in Table 3.\n\n\nDiscussion\n\nCataract surgery is considered to be a refractive procedure aiming for postoperative emmetropia, which required correction of spherical and astigmatic errors.2 Corneal astigmatism of more than 1 D has been reported in up to 45% of cataract surgery candidates,3 while 11.6% of eyes undergoing cataract surgery have more than 2 D of corneal astigmatism.7\n\nSince the astigmatic effect of CCIs on the steep meridian is well documented, it is reasoned that adding an CCI opposite to the first incision (OCCI) would enhance the flattening effect, providing a good method to manage the preexisting corneal astigmatism during cataract surgery. OCCIs are simple to perform, do not require additional skills or instruments, and since the additional incision is self-sealing, particularly when it is not used to introduce instruments, the added risk to the surgery is negligible compared to its benefit of astigmatism reduction.5,8\n\nThe topographic corneal astigmatism in the CCI group decreased by 0.265 ± 0.142 diopters, while OCCI reduced the topographic corneal astigmatism by 0.665 ± 0.268 diopters, which was in agreement with Bhalla’s study, which reported a reduction of 0.28 and 0.7 D in topographic astigmatism in CCI and OCCI groups, respectively,9 but these results were different to other studies.\n\nIn 2000, Lever and Dahn performed cataract surgery on 33 eyes of 26 patients with an OCCI ranging from 2.8 to 3.5 mm in length and they reported a mean corneal astigmatism correction of 2.06 D with this technique.5 Qammar and Mullaney in 2005 reported a mean astigmatic correction of 1.23 ± 0.49 D.10 In 2006, Khokhar and colleagues11 reported that a 3.2 mm CCI reduced topographic astigmatism by 0.59 ± 0.43 D at three months follow-up, which is more than our CCI group, which showed a 0.265 ± 0.142 D reduction in topographic astigmatism. The OCCI group of Khokhar’s study showed a reduction in preoperative corneal astigmatism of 1.60 ± 0.45 D versus 0.665 ± 0.268 D in our study.\n\nOn the other hand, our results were higher than Tadros’ study, which reported a 0.5 ± 0.73 D reduction in preoperative corneal astigmatism.12 They were also higher than Bazzazi’s study, which reported the mean topographic astigmatism change to be 0.003 D and 0.036 D in superior and temporal CCI groups, respectively, which was less than our CCI group (0.265 D), while in the OCCI groups topographic astigmatism was reduced by 0.505 D and 0.557 D in superior and temporal groups, respectively, versus 0.665 D in our study.13 In addition, Nemeth’s study found a 0.13 D reduction in topographic astigmatism in their CCI group, which was less than our CCI group (0.265 D), while Nemeth’s OCCI group showed a reduction in topographic astigmatism of 0.2 D versus 0.665 D in our study.14\n\nUsing vector analysis,15 we also evaluated the predictability of the astigmatic correction. The topographic data were analyzed. The mean magnitude of TIA was 1.370 ± 0.384 D in the CCI group and 1.370 ± 0.505 D in the OCCI group that was similar to preoperative topographic astigmatism. The mean magnitude of SIA was 0.403 ± 0.183 D in our CCI group, which was less than Khokhar’s study (0.85 ± 0.75 D)11 and Nemeth’s study (0.61 ± 0.43 D)14 but more than Bazzazi’s study (0.036 ± 0.51 D)13 and Bhalla’s study (0.33 ± 0.22 D).9 Regarding the OCCI group of our study, the mean magnitude of SIA was 0.849 ± 0.519 D, which was less than that of Lever and Dahn’s study (2.25 D),5 Tedros’ study (1.57 D),12 Qammar and Mullaney’s study (2.10 D),10 Nemeth’s study (0.99 D)14 and Khokhar’s study (1.66 D).11 On contrary, the mean SIA of our OCCI was higher than that of Bazzazi’s study (0.505 D), and Bhalla’s study (0.76 D).9\n\nAll the above differences in the resulted mean change in astigmatism and SIA could be the result of using 2.8 mm incisions in our study compared to 3.2 mm incisions used in most of the studies that corrected a higher astigmatism than we did, or may be due to different sample sizes, postoperative topographic astigmatism (1.37 D in our study versus 3.6 D in other studies), and follow up period (one month versus 2-3 months in others).\n\n\nConclusion\n\nBoth incisional methods are useful methods for correction of preoperative corneal astigmatism but OCCIs correct a higher amount of astigmatism than the on-axis CCIs. In addition, using a 3.2 mm incision in both ways may correct a higher amount of astigmatism than using a 2.8 mm incision.\n\n\nData availability\n\nZenodo: Corneal Astigmatism - excel. https://doi.org/10.5281/zenodo.4907691.16\n\nThis project contains the study data in XLSX format.\n\nZenodo: Incisional Correction Of Corneal Astigmatism During Phacoemulsification-proposal. https://doi.org/10.5281/zenodo.4907717.17\n\nThis project contains a copy of the study protocol in DOCX format.\n\nZenodo: CONSORT checklist for “Incisional correction of corneal astigmatism during phacoemulsification – a randomized trial”. http://doi.org/10.5281/zenodo.5028589.18\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nBuckhurst PJ, Wolffsohn JS, Davies LN, et al.: Surgical correction of astigmatism during cataract surgery. Clin Exp Optom. 2010; 93(6): 409–18. PubMed Abstract | Publisher Full Text\n\nEliwa TF, Elsamkary MA, Hamza I: Effect of biaxial versus coaxial microincision cataract surgery on optical quality of the cornea. Indian J Ophthalmol. 2015; 63(6): 487. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan MI, Muhtaseb M: Prevalence of corneal astigmatism in patients having routine cataract surgery at a teaching hospital in the United Kingdom. J Cataract Refract Surg. 2011; 37(10): 1751–5. PubMed Abstract | Publisher Full Text\n\nPrisant O, Hoang-Xuan T, Proano C, et al.: Vector summation of anterior and posterior corneal topographical astigmatism. J Cataract Refract Surg. 2002; 28(9): 1636–43. PubMed Abstract | Publisher Full Text\n\nLever J, Dahan E: Opposite clear corneal incisions to correct pre-existing astigmatism in cataract surgery. J Cataract Refract Surg. 2000; 26(6): 803–5. PubMed Abstract | Publisher Full Text\n\nEliwa TF, Abdellatif MK, Hamza II: Effect of limbal relaxing incisions on corneal aberrations. J Refract Surg. 2016; 32(3): 156–62. PubMed Abstract | Publisher Full Text\n\nCurragh DS, Hassett P: Prevalence of corneal astigmatism in an NHS cataract surgery practice in Northern Ireland. Ulster Med J. 2017; 86(1): 25. PubMed Abstract | Free Full Text\n\nTaneja M: Management of Astigmatism in cataract. Official Scientific J Delhi Ophthalmological Society. 2015; 25(4): 252–8. Publisher Full Text\n\nBhalla JS, Rani M, Gupta S: Evaluation of Opposite Clear Corneal Incision in Controlling Astigmatism in Cataract Patients Undergoing Phacoemulsification Surgery. Official Scientific J Delhi Ophthalmological Society. 2016; 26(4): 241–5. Publisher Full Text\n\nQammar A, Mullaney P: Paired opposite clear corneal incisions to correct preexisting astigmatism in cataract patients. J Cataract Refract Surg. 2005; 31(6): 1167–70. PubMed Abstract | Publisher Full Text\n\nKhokhar S, Lohiya P, Murugiesan V, et al.: Corneal astigmatism correction with opposite clear corneal incisions or single clear corneal incision: comparative analysis. J Cataract Refract Surg. 2006; 32(9): 1432–7. PubMed Abstract | Publisher Full Text\n\nTadros A, Habib M, Tejwani D, et al.: Opposite clear corneal incisions on the steep meridian in phacoemulsification: early effects on the cornea. J Cataract Refract Surg. 2004; 30(2): 414–7. PubMed Abstract | Publisher Full Text\n\nBazzazi N, Barazandeh B, Kashani M, et al.: Opposite clear corneal incisions versus steep meridian incision phacoemulsification for correction of pre-existing astigmatism. J Ophthalmic Vis Res. 2008; 3(2): 87. PubMed Abstract | Free Full Text\n\nNemeth G, Kolozsvari B, Berta A, et al.: Paired opposite clear corneal incision: time-related changes of its effect and factors on which those changes depend. Eur J Ophthalmol. 2014; 24(5): 676–81. PubMed Abstract | Publisher Full Text\n\nAlpins N: Astigmatism analysis by the Alpins method. J Cataract Refract Surg. 2001; 27(1): 31–49. PubMed Abstract | Publisher Full Text\n\nMohammad NK: Corneal Astigmatism - excel. Zenodo. 2021, June 7. Publisher Full Text\n\nMohammad NK: Incisional Correction Of Corneal Astigmatism During Phacoemulsification-proposal. Zenodo . 2021, June 7. Publisher Full Text\n\nMohammad NK: Incisional correction of corneal astigmatism during phacoemulsification – a randomized trial. Zenodo. 2021, June 24. Publisher Full Text"
}
|
[
{
"id": "93413",
"date": "24 Sep 2021",
"name": "Hesam Hashemian",
"expertise": [
"Reviewer Expertise Cornea",
"Keratoconus",
"ICRS",
"refractive 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 study is designed to compare two techniques of corneal incisional surgery to correct corneal astigmatism during cataract surgery. Incisional surgeries have been used for refractive correction on the cornea in LRI, AK, and RK surgeries. In all these surgeries a nearly full thickness incisions cut continuous collagen layers which are extended from limbus to limbus and violate the integrity of the cornea. As we see in all cases of incisional surgery inability of result prediction and regression or overcorrection in long run are drawbacks of this technique. Violation in biomechanical stability of cornea is the other concern that is due to near full thickness cutting of collagen strands.\nA decrease in corneal sensation caused by cutting nerve endings and secondary dry eye is another concern in these patients. So it was better to have a longer follow-up to address refractive stability; biomechanical changes and checking corneal sensation.\nIrregular astigmatism of any kind can not be predictably corrected by incisional surgery. And due to biomechanical deterioration, any kind of corneal ectasia should be considered as an exclusion. So the authors should mention these two conditions as an exclusion to study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "120077",
"date": "24 Jan 2022",
"name": "Lixia Luo",
"expertise": [
"Reviewer Expertise cataract"
],
"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 assess the efficacy and safety of on-axis cornea incision with or without opposite clear incisions to correct preoperative cornea astigmatism. Despite that this is an interesting topic, the current study had significant flaws in terms of protocol compliance, data analysis, and processing. I have listed a few comments for the authors’ reference:\nThe efficacy of on-axis corneal incision with or without OCCI to correct preoperative corneal astigmatism has been studied before, What are the innovation and necessity of this research?\n\nthe Method section of Abstract: has not been clarified clearly, such as the inclusion criteria, the range, and type of astigmatism, the follow-up time, and examination items. Besides, the methods of statistical analysis were not mentioned.\n\nthe Result section of Abstract: The data reported in the MS should strictly follow the protocol registered. The secondary outcome displayed in clinicaltrals.gov was the change in visual acuity, instead of the differences regarding the changes in cornea astigmatism between the two groups.\n\nAbstract: a spelling mistake: pre-existing corneal astigmatism; grammar mistakes, a total of 40 eyes of 40 patients.\n\nIntroduction: “however, astigmatism correction is limited to ……at the left eye”. Please list the references you have referred to here.\n\nIntroduction: “The current work is based on……releasing incision” is unnecessary. The author should explain the necessity of this study compared to previous research.\n\nthe Ethical statement in Method: Clinical trials are defined by the WHO as “any research study that prospectively assigns human participants or groups of humans to one or more health-related interventions to evaluate the effects on health outcomes.” Registration should be with an appropriate registry and should take place before the enrolment of the first participant. Regardless of any national policies that may exist, trials registered after the date of the first enrolment are considered to be retrospective.\n\nthe Participants in Method: The sample size was not determined by formal power analysis, and even lack a post-hoc power analysis, thus it was questionable whether such a small sample size was sufficient to evaluate this question.\n\nthe Exclusion criteria in Method: Why did you exclude patients with lenticular astigmatism?\n\nResults: The baseline BCVA was better in the OCCI group, instead of the authors’ claim that there was no statistical difference between the two groups at baseline.\n\nResults: The change in astigmatism is a vector, should be analyzed with the consideration of both magnitude and meridian. Thus, the mean vector or centroid is the proper value to use. The double-angle plots of the differences in corneal astigmatism measurements should be displayed.\n\nDiscussion: The first paragraph should summarize the main finding of the study, rather than repeat the Introduction.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-825
|
https://f1000research.com/articles/9-1106/v1
|
09 Sep 20
|
{
"type": "Study Protocol",
"title": "Impact of COVID-19 on utilization of maternal, newborn and child health services in Nigeria: protocol for a country-level mixed-methods study",
"authors": [
"Godwin Akaba",
"Osasuyi Dirisu",
"Kehinde Okunade",
"Eseoghene Adams",
"Jane Ohioghame",
"Obioma Obikeze",
"Emmanuel Izuka",
"Maryam Sulieman",
"Michael Edeh",
"Osasuyi Dirisu",
"Kehinde Okunade",
"Eseoghene Adams",
"Jane Ohioghame",
"Obioma Obikeze",
"Emmanuel Izuka",
"Maryam Sulieman",
"Michael Edeh"
],
"abstract": "Background: Battling with COVID-19 and providing essential services along the continuum of care could be challenging. This study will evaluate the impact of COVID-19 on utilization of maternal, newborn and child health (MNCH) services in Nigeria and explore the barriers being experienced by women and their families in getting access to MNCH services, as well as other contextual factors that may have shaped the utilization of MNCH services during the COVID-19 pandemic. Methods and analysis: The study will adopt an observational mixed-methods study design involving 18 health care facilities delivering MNCH services in six selected states across six geopolitical zones of Nigeria. We will retrieve longitudinal data on MNCH services from all selected hospitals three months before and after the first recorded case of COVID-19 in Nigeria. Qualitative data will be collected using in-depth interviews conducted via mobile phones or ZOOM meeting platforms among stakeholder participants (users of MNCH services, health workers and policymakers) to ascertain their perceptions on how COVID-19 has shaped the utilization of MNCH services. We will triangulate quantitative and qualitative data to better understand the impact of COVID-19 on the utilization of MNCH services in Nigeria. Ethics and dissemination: Ethics approvals have been obtained from the Health Research Ethics Committee of the tertiary hospitals involved in the study. Our findings will provide the first evidence from an African setting on the impact of COVID-19 on the utilization of MNCH services using a mixed-methods study design for policy formulation towards sustained MNCH service delivery.",
"keywords": [
"Impact",
"COVID-19",
"Utilization",
"MNCH",
"Healthcare",
"Services",
"Nigeria",
"Africa"
],
"content": "Introduction\n\nThe Sustainable Development Goals agenda is part of the global efforts to improve maternal, new-born and child health (MNCH) by challenging countries to make efforts to reduce the global burden of maternal, new-born and child mortality1. However, despite these efforts, global maternal mortality remains unacceptably high with about 303,000 women dying each year from pregnancy-related complications2, for which sub-Saharan Africa and Southern Asia accounts for about 86% of such deaths1. According to the World Health Organization (WHO) report, an estimated 5.3 million under-5 deaths and 2.5 million neonatal deaths were reported in 2020, which are equivalent to an under-5 mortality rate of 39 per 1,000 live births and neonatal mortality rate of 18 per 1,000 live births, while the maternal mortality rate is 211 per 100,000 live births3.\n\nIn Nigeria, MNCH outcomes have improved over the last decade. However, these outcomes are still rated as being among the worst in the world4. The under-5 mortality rate is 132 deaths per 1,000 live births while the infant mortality rate is 67 deaths per 1,000 live births4. On the other hand, the maternal mortality ratio in Nigeria is 512 per 100,000 live births and some of the main causes of maternal deaths include obstetric haemorrhage, infection, obstructed labour, unsafe abortion, preeclampsia/eclampsia, malaria, anaemia, and contributory factors such as lack of awareness about complications in pregnancy, inability to seek timely medical intervention, lack of utilization of health care services, lack of transportation and inability to pay for services4,5. With these indices, Nigeria is the second largest contributor to maternal mortality worldwide accounting for more than 10% of all cases2,5.\n\nIn order to improve child survival and maternal health, the continuum of care for MNCH was designed and this has gained so much attention because it is expected to reduce the burden of maternal deaths, neonatal deaths and deaths among under-5 children particularly in lower and middle-income countries6,7. The continuum of care includes healthcare services for mothers and children from pre-pregnancy to delivery, postnatal and childhood6,8. Furthermore, this depicts the link between maternal and child health, particularly as they seem to be affected by the same variables. Therefore, this makes it important that at every specific point in the continuum of care, every mother/child pair should receive the full package to attain maximum satisfaction6. Towards a positive impact on overall MNCH indicators, every woman is expected to continuously receive antenatal care (ANC), skilled birth attendance at delivery and postnatal care (PNC). The WHO recommends that every pregnant woman is expected to have a minimum of eight ANC contacts before delivery9. This is because ANC helps to identify pregnancy risks, provide appropriate care for women who might be at risk of potentially fatal conditions, provide opportunities for counselling these women and give access to health-promoting services (weight measurement, blood pressure measurement etc), and it also helps to increase subsequent use of maternal and child health services7,10. Even though the majority of maternal and neonatal deaths occur in the postpartum period, in Nigeria, only about 42% of mothers utilize PNC services within the first two days after delivery. Similar trends are seen in the utilization of ANC, the number of deliveries attended by skilled birth attendants and uptake of immunization and family planning services. According to the Nigerian Demographic and Health Survey 2018, only 57% of women had at least four ANC visits, deliveries by skilled birth attendants were 43%, immunization coverage for age-appropriate vaccinations was 21%, and modern contraceptive prevalence rate among currently married women was 12%4.\n\nLow utilization of MNCH services can be categorized into two major factors, which are the user factor and the health system factor. The user factor includes distance to a health facility, cultural beliefs and practices, economic factors and many other factors within the community and respective households. On the other hand, the health system factor includes the capacity of health staff, attitude of care providers, infrastructure and other forms of interactions that take place within the healthcare system1.\n\nWith the recent COVID-19 pandemic, the resilience of health systems’ and countries’ emergency preparedness and response have been tested. According to the WHO, over 200 countries, areas and territories have been affected and as such health systems have been critically affected11. As of May 17, 2020, there have been 4,534,731 cases of COVID-19 and over 307,537 deaths globally. In Africa, about 58,663 cases and 1,710 deaths have been recorded. On the other hand, in Nigeria, 5,621 cases and 176 deaths have been recorded12. COVID-19 pandemic and its devastating impact on the health systems, livelihood and economies of Nations have been likened to a “war” situation. Health care for women and children are usually disproportionally and negatively impacted at times of war and conflicts. Battling with COVID-19 and providing essential services along the continuum of care is critical and challenging4. To avert deaths, it is important to ensure that appropriate care is available to every woman and every child during the pandemic. We, therefore, hypothesized that COVID-19 pandemic in Nigeria may have further worsened the already poor maternal and child health services utilization in Nigeria. Thus, this study is designed to evaluate the impact of COVID-19 on the utilization of MNCH services in Nigeria using a mixed-method approach. The quantitative part of the study will involve the collection of longitudinal data on maternal and newborn health services, while the qualitative component will explore the barriers being experienced by women and their families in getting access to MNCH services as well as other contextual factors that may have shaped the utilization of MNCH services during the COVID-19 pandemic. It would also explore the level of preparedness of the Nigeria health system in responding to such pandemics and examine the available policies and action plans that are currently in place. Findings from this study will be beneficial in providing key stakeholders at all levels of the health care system with the necessary information that will provide new direction and policy for the country towards mitigating the negative impact of COVID-19 on the already fragile health system, and thus help in sustaining previous efforts towards attaining the third sustainable development goal of “achieving good health and well-being for all” in Nigeria.\n\n\nAim and objectives\n\nThe study aims to assess the rate of utilization of maternal and newborn child health (MNCH) services before and during the COVID 19 pandemic as well as to critically examine the various barriers and facilitators associated with accessing MNCH services during the COVID-19 pandemic in Nigeria. Specific objectives are to:\n\n1. Ascertain the trend in the utilization of MNCH services before and during COVID-19 pandemic.\n\n2. Determine the barriers and facilitating factors associated with access to MNCH services during the COVID-19 pandemic.\n\n3. Identify gaps in the MNCH continuum of care and the most affected level of care during the COVID-19 pandemic.\n\n4. Explore contextual factors that may have shaped the utilization of MNCH services during the COVID-19 pandemic\n\n\nProtocol\n\nThis study will be conducted in six states across the six geopolitical zones of the country. The states were purposively selected during the proposal development and categorized according to the number of reported COVID-19 cases as “high-burden states (high number of cases) and low-burden states (low number of cases)”. For this study, any state with at least 56 confirmed cases of COVID-19 as at May 17, 2020 (equivalent to approximately 1% of total cases of COVID-19 at that time) will be regarded as a high-burden state, while those with less than 56 confirmed cases will be classified as low-burden states. The high-burden states include Lagos in the South-west (n=2,373), Kano in the North-west (n=825) and Abuja FCT in the North-central (n=397), while the low-burden states are Enugu in the South-east (n=11), Taraba in the North-east (n=17) and Bayelsa in the South-south (n=6). The participating states and health facilities are shown in Table 1.\n\nThe study will use a mixed-methods design to evaluate the impact of the novel COVID-19 pandemic on the utilization of MNCH across six selected states of Nigeria. The quantitative part of the study will involve the collection of longitudinal data from hospitals in the participating States on maternal and newborn health services (antenatal clinic attendance, hospital deliveries, postnatal clinic attendance, family planning services and immunization uptakes) three months before (December 1, 2019, to February 28, 2020) and after (March 1 to May 31, 2020) the first recorded case of COVID-19 in Nigeria. The data from the three high-burden states (Abuja FCT, Lagos, Kano) will be compared with that of the three low-burden states (Enugu, Taraba and Bayelsa). The qualitative arm will assess the perceptions of users of healthcare facilities, health workers, and policymakers on how COVID-19 has shaped the utilization of MNCH services in their locality as well as other contextual factors contributing to the projected views.\n\nParticipants for the qualitative survey will be identified, screened for eligibility, and selected by purposive sampling method by the study coordinator in each of the selected states. The participants will include policymakers, service providers and service users from each of the participating states. Research collaborators in the six states who are all healthcare practitioners working in the tertiary health facilities will support the recruitment of policymakers and service providers in the states. The service providers will help in the recruitment of the service users who presented for MNCH services during the study period.\n\nInclusion and exclusion criteria for stakeholder enrolment are the same across all participating states. Eligible participants are those aged at least 18 years with adequate physical, mental, and cognitive capacity who give informed consent to participate in the study.\n\nDefinition of stakeholders\n\nPolicymaker – a healthcare professional who has been working within the health system for at least one year and is involved in defining policy on MNCH services.\n\nService provider – a healthcare professional who has been working within the health system for at least one year and involved in the direct provision of MNCH services in any of the study facility before and during the current COVID-19 pandemic.\n\nService user – someone who has accessed MNCH services during the COVID-19 pandemic.\n\nQualitative data will be collected by in-depth interviews (IDIs) from the three stakeholder groups comprising of one policymaker, health care worker and service user related to MNCH services from each of the three levels of the healthcare system in the six selected states. The interviews will be conducted using mobile phones or ZOOM application platforms depending on the choice of the respondents due to the social distancing regulations in Nigeria. Nationally, a total of fifty-four (54) IDIs will be conducted (comprising of 18 IDIs for each of the stakeholder groups).\n\nBefore the IDIs, the interviewers will be required to check if the participants meet the inclusion criteria. Stakeholders who failed to meet the inclusion criteria or those who declined consent will be excluded from participating in the study. The list of stakeholders to be interviewed and their distribution across the six participating states is as shown in Table 2.\n\nSeveral theoretical frameworks have been developed that may have relevance to exploring and understanding barriers to the utilization of health care services. We will use a hybrid of the social-ecological model (SEM) and the three delays model to investigate and explore how COVID-19 has impacted on utilization of MNCH services in Nigeria. The SEM provides a theory-based approach to understanding the complex interaction between individual, interpersonal, community, institutional and policy factors that influence behaviour and practice13. The delay model recognizes three phases (delay in deciding to seek care, delay in reaching healthcare facility and delay in receiving adequate care at the health facility) as contributing to women’s ability to receive care towards averting poor outcomes. These delays are shaped by several complex factors operating at the same or different levels of delays14–16. Figure 1 shows the theoretical frameworks to be used for this study.\n\nQuantitative data: Data for the three months preceding the first confirmed case of COVID-19 in Nigeria (December 1, 2019, to February 28, 2020) and the three months after (March 1 to May 31, 2020) will be collected from one facility each at the three different levels of the Nigerian healthcare system (primary, secondary and tertiary facilities) in each of the six selected states. The facilities are also to be spread across three different Local Government Areas in each of the participating states. Monthly data to be collected includes: total antenatal care (ANC) attendance, total facility deliveries, total postnatal clinic (PNC) attendance, total family planning services rendered, and the total number of babies who received immunization. These data will be used to evaluate the trends in the utilization of MNCH services in these states.\n\nQualitative data: The state study coordinators will schedule and confirm the dates and time of the planned IDIs with the study participants after obtaining informed written consent. The participants will also be informed that the interview will be recorded during the informed consent process. Interviews will then be facilitated by a trained interviewer over the phone or via ZOOM. The interviewers have expertise in the conduct of IDIs and will be working with members of the core research team to schedule interviews with the respondents while determining the best time for the interview to take place. The study participants will be informed about the purpose of the study and are invited to participate in the interview, which will last for approximately 20 to 30 minutes. The interviews will be conducted using an IDI guide designed specifically for each of the stakeholder groups. After the interview, the audio recordings would be transcribed verbatim. The transcripts will be compared with the audio recordings to ensure completeness and are then analysed and utilized to develop the study report. Table 3 shows examples of some of the question that will be asked for each of the stakeholder groups.\n\nMNCH, maternal and newborn child health.\n\nQuantitative data: This data will be entered into a computer and analysed using SPSS version 20.0 for Windows (Armonk, NY: IBM Corp.) to show the trends of the utilization of MNCH services over the six months review period. The differences in MNCH services utilization between the study period (before and during the COVID era) and COVID-19 infection burden (high- and low-burden states) within and across the different levels of the healthcare system will be tested using the independent sample t-test. The level of significance will be reported at P<0.05.\n\nQualitative data: Audio recorded interviews will be transcribed verbatim and transcripts will be anonymized with pseudonyms. Data analysis will begin with the reading of transcripts repeatedly to achieve immersion and derive codes by identifying words in the text that capture key concepts. Initial codes will be discussed by the study team and sorted into categories based on linkages between key concepts. The themes that represent key issues with MNCH services will be developed for initial coding and inductive analysis. The data will then be entered into NVivo software version 12 for organization and analysis. Each transcript will be coded by two members of the research team independently to reduce inter-coder variability.\n\nData protection: On completion of this study, transcripts will be stored in password-protected computers/laptops and only the core research team will have access to the data. All members of the team will sign a confidentiality agreement. All study participants will be assigned an identification code, which will be delinked from their identity at the data entry point. Audio recordings will be destroyed at the end of the project. Transcripts will be stored for a minimum of 5 years after the project ends and will only be destroyed afterwards if necessary.\n\n\nEthical considerations\n\nEthics approvals have been obtained from the Health Research Ethics Committee of the participating tertiary hospitals involved in the study: University of Abuja Teaching Hospital (UATH/HREC/PR/2020/001), Lagos University Teaching Hospital (LUTHHREC/EREV/0520/42), University of Nigeria Teaching Hospital, Enugu (NHREC/05/01/2008B-FWA00002458-1RB00002323), Mohammad Abdullahi Wase Teaching Hospital, Kano (MOH/Off/797/T.I/2060), Federal Medical Centre, Yenagoa, Bayelsa (FMC/ADM/017/Vol.1/138), Federal Medical Centre, Jalingo, Taraba (FMC/JL/ADM/330). Social approval and permission will be sought from the primary and secondary facilities selected for the study. The ethical review undertaken by all project investigators will ensure standard processes (dignity, autonomy, informed consent, confidentiality, anonymity, ability to adhere to protocol) and data security are maintained. Voluntary and informed participation, confidentiality and safety of participants will constitute key principles of researcher–respondent interaction. Written consent will be obtained from service users, service providers and policymakers prior to their enrolment in the study. The study will be conducted according to the Helsinki declarations on ethical principles for medical research involving human subjects.\n\n\nPatient and public involvement, and dissemination\n\nThe development of the research question was based on experiences of patients narrated in the media, as well as during medical consultations at the obstetric emergency services of the University of Abuja Teaching Hospital, Abuja. Their inputs were sought in designing the qualitative component of the study proposal.\n\nFindings from this study will be disseminated by delivering presentations at national and international conferences, organization of study dissemination meetings involving relevant stakeholders in Nigeria and publishing articles in peer-reviewed journals. Additionally, all participating institutions and patients will be notified of the key findings from the study. Data resulting from this study will be deposited in a data repository (Mendeley Data) and can be assessed by the public.\n\n\nStudy status\n\nThe study is currently collecting both longitudinal data and qualitative data.\n\n\nDiscussion\n\nThis paper reports a protocol for an observational mixed-methods study design aimed at collecting quantitative data showing the trend of utilization of MNCH services during the three months preceding and during the COVID-19 pandemic, and qualitative data from key stakeholders across the health systems in the six geopolitical zones in Nigeria to determine the barriers and facilitators associated with access to MNCH services during the COVID-19 pandemic. Additionally, the study will explore other contextual issues that have shaped service delivery along the MNCH continuum of care during the COVID-19 pandemic. The study findings will provide a timely contribution to the ongoing debate on the magnitude of impact on access and utilization of MNCH services across the different levels of the Nigeria health system following the COVID-19 outbreak and also help in identifying strategies that will assist Nigeria and other African countries in maintaining focus towards the realization of the third sustainable development goal of “ensuring good health and well-being for all” amidst the COVID-19 pandemic.\n\n\nConclusion\n\nThe identification of the state of MNCH continuum of care and the most affected components of care during the COVID-19 pandemic in Nigeria could lead to multiple benefits for service users, service providers, policymakers and other relevant stakeholders towards effective planning for the strengthening of national health systems during the COVID-19 pandemic.\n\n\nData availability statement\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nThe authors wish to acknowledge the management staff of the participating hospitals for approving the conduct of the study in their institutions, and also the patients who made inputs in the design of the qualitative study.\n\n\nReferences\n\nKisiangani I, Elmi M, Bakibinga P, et al.: Persistent barriers to the use of maternal, newborn and child health services in Garissa sub-county, Kenya: a qualitative study. BMC Pregnancy Childbirth. 2020; 20(1): 277. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYaya S, Okonofua F, Ntoimo L, et al.: Men's perception of barriers to women's use and access of skilled pregnancy care in rural Nigeria: a qualitative study. Reprod Health. 2019; 16(1): 86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: World health statistics 2020: monitoring health for the SDGs, sustainable development goals. Geneva: World Health Organization; 2020. Accessed June 1, 2020. Reference Source\n\nNational Population Commission (NPC) [Nigeria] and ICF: Nigeria Demographic and Health Survey 2018. Abuja, Nigeria, and Rockville, Maryland, USA: NPC and ICF. 2019. Accessed on July 2, 2020. Reference Source\n\nUneke CJ, Sombie I, Keita N, et al.: Improving maternal and child health policymaking processes in Nigeria: an assessment of policymakers' needs, barriers and facilitators of evidence-informed policymaking. Health Res Policy Syst. 2017; 15(Suppl 1): 48. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAkinyemi JO, Afolabi RF, Awolude OA: Patterns and determinants of dropout from maternity care continuum in Nigeria. BMC Pregnancy Childbirth. 2016; 16(1): 282. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYasuoka J, Nanishi K, Kikuchi K, et al.: Barriers for pregnant women living in rural, agricultural villages to accessing antenatal care in Cambodia: A community-based cross-sectional study combined with a geographic information system. PLoS One. 2018; 13(3): e0194103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nInternational Federation of Red Cross and Red Crescent Societies: Maternal, newborn and child health framework. 2013. Accessed on May 26, 2020. Reference Source\n\nWorld Health Organization: WHO recommendations on antenatal care for a positive pregnancy experience. 2016. Accessed on May 20, 2020. Reference Source\n\nDoctor HV, Bairagi R, Findley SE, et al.: Northern Nigeria Maternal, Newborn and Child Health Programme: Selected analyses from population-based baseline survey. Open Demography J. 2011; 4: 11–21. Publisher Full Text\n\nInternational Labour Organization: ILO Sectoral Brief. 2020. Accessed on May 26, 2020. Reference Source\n\nWHO: WHO Timeline - COVID-19. World Health Organization. Accessed on May 17, 2020. Reference Source\n\nHeise LL: Violence against women: An integrated, ecological framework. Violence Against Women. SAGE Periodicals Press Thousand Oaks. 1998; 4(3): 262–290. PubMed Abstract | Publisher Full Text\n\nThaddeus S, Maine D: Too far to walk: maternal mortality in context. Soc Sci Med. 1994; 38(8): 1091–1110. PubMed Abstract | Publisher Full Text\n\nThorsen VC, Sundby J: Piecing together the maternal death puzzle through narratives: the three delays model revisited. PLoS One. 2012; 7(12): e52090. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMgawadere F, Unkels R, Kazembe A, et al.: Factors associated with maternal mortality in Malawi: application of the three delays model. BMC Pregnancy Childbirth. 2017; 17(1): 219. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "71048",
"date": "05 Oct 2020",
"name": "Adedayo Tella",
"expertise": [
"Reviewer Expertise Fetomaternal medicine",
"infertility and assisted conception",
"reproductive health."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review this article at its proposal stage.\nSummary: This article seeks to evaluate the impact on utilization of maternal, newborn and child health (MNCH) services in Nigeria by the COVID-19 pandemic as battling with COVID-19 and providing essential health care services can be a real challenge. The study will adopt a mixed-methods study design involving 18 health care facilities delivering MNCH services at the 3 levels of care in six selected states across the six geopolitical zones of Nigeria over a six month period (pre and post first recorded case of COVID-19 in Nigeria). The findings from this study will aid policy formulation towards sustained MNCH services during the COVID-19 pandemic and beyond.\nComments to the authors: An interesting and well thought-out study. Three months before and during COVID-19 pandemic may not give the entire picture of MNCH services but to avoid recall bias, the duration covered is appropriate. In terms of use of the term ‘rates’ the duration is not up to a year, as such projections may be considered. We have few suggestions;\nGrammar:\nMany conjunctions are used erroneously. ‘However’ and ‘on the other hand’ should be used for divergent views and not for views with similar flow of information.\n\nSome sentences are too long Paragraph 3, lines 9 -13; also rephrase Paragraph 2; lines 3-7.\n\nParagraph 3, line 3; low income countries not lower.\n\nUse of past and future tenses need to be checked. A continuous check throughout the write up is required. This is a protocol but some events have taken place and some will take place in the future.\n\nIntroduction:\nMaternal, newborn and child health (MNCH) - What of the period of infancy? Infancy should be included because of the peculiarity of this disease that affects infants and their caregivers (usually mothers) during that period.\n\nParagraph 3, line 13; The sentence, 'Even though the majority of maternal and neonatal deaths occur in the postpartum period in Nigeria, only about 42% of mothers....' is contentious. Is majority of maternal death really postpartum or peri-partum? Give a reference for the 42%.\n\nRate of utilization – rate is usually with an annual denominator (time), yours is over 6 months or are you projecting?\n\nProtocol:\nUnder Study design, specify the type of study. This is a cross sectional study using a mixed-methods approach.\n\nUnder Study design, can the authors specify how the longitudinal data will be collected from hospitals in the participating states. Will the data be sampled or will data of all patients that access MNCH services in those states be collated? Is it in retrospect? We believe this should be addressed to make the article scientifically sound.\n\nUnder Study design, line 8; '....Contextual factors...' – Give some explanation or examples.\n\nWhat approach will you be using for the qualitative study? – phenomenological?\n\nUnder Methods of data collection (qualitative), check this sentence; 'The interview will be recorded during informed consent---' wording can be simply put as audio recording of informed consent.\n\nIn-depth interview for 20 minutes is regarded as short, about 30 minutes; or 30-40 minutes is preferable.\n\nWas the IDI guide tested and if yes, where and among which stakeholders?\n\nUnder Patient and public involvement and dissemination; dissemination to participants and other stakeholders should come first before disseminating to national and international conferences, because the activity serves as both a dissemination and verification exercise when it is among participants of a study.\n\nUnder Data management (Qualitative); Do you intend to code before entering the transcript into NVivo or import the transcript and code in NVivo?\n\nUnder Data Management (Quantitative); Use of t-test for proportions? Consider Chi-square test for proportion.\n\nUnder Data Protection; Audiotapes destroyed immediately after the project could be risky. Keeping in a safe place for 6 months before destruction may be safer.\n\nThank you.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
},
{
"id": "75059",
"date": "11 Jan 2021",
"name": "Marleen Temmerman",
"expertise": [
"Reviewer Expertise RMNCAH",
"clinical",
"epidemiological",
"health systems",
"policy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWell designed protocol to address an important public health issue that is the utilization of essential health services, more specifically mother and child health services.\nThe proposed methodology adopts quantitative and qualitative mixed-methods approach, addressing users of services, health care providers and policymakers.\nComments:\nThe proposed timeframe of 3 months before and e months after the first covid case seems short and probably does not allow the current status following the initial 'covid-19 shock'.\n\nThe voices missing are the women that do not attend the MCH services anymore; they should be included in FGDs.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "6266",
"date": "14 Jan 2021",
"name": "GODWIN AKABA",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for your comments. I wish to respond that our study received ethical approvals in the first and second weeks of June 2020 at which time Nigeria was only about 3 months into the COVID -19 pandemic and we commenced data collection on 22nd June 2020 to 30th September 2020. The objective of our study was to investigate the effect of lockdown due to the COVID-19 pandemic on the utilization of MNCH services in Nigeria. This protocol was first submitted to this Journal (F1000 Research) on 20th August 2020 at which time the authors had declared that we were already collecting both longitudinal and qualitative data which describes fully the situation of COVID-19 in Nigeria at that time during which Nigeria was still in lockdown. We believe that if this research protocol was reviewed at that time the comment may not have been made since the data were collected within 4- 6 months of the COVID-19 pandemic in Nigeria. Thank you Godwin.O.Akaba"
}
]
}
] | 1
|
https://f1000research.com/articles/9-1106
|
https://f1000research.com/articles/10-824/v1
|
17 Aug 21
|
{
"type": "Research Article",
"title": "Knowledge of infection prevention and control practices among health care workers caring for patients with suspected or confirmed COVID-19: a cross-sectional study",
"authors": [
"Eman H Elsebaie",
"Amany A Salem",
"Amal S Sedrak",
"Ahmed Ayad",
"Sahar A Ahmed",
"Bassante A El Razik",
"Noha M Abu bakr Elsaid",
"Eman H Elsebaie",
"Amany A Salem",
"Amal S Sedrak",
"Ahmed Ayad",
"Sahar A Ahmed",
"Bassante A El Razik"
],
"abstract": "Background: The COVID-19 pandemic is increasing rapidly. Hospital acquired infections enhance local outbreaks, impacting the vulnerable populations. Infection prevention and control practices (IPC) refer to all the activities used to reduce the risk of infection spread. This study aims to estimate the proportion of health care workers (HCWs) who acquired SARS-CoV2 infection, and evaluate their knowledge to IPC and suggest recommendations to reduce the risk of SARS-CoV2 infection.\n\nMethods: This is a cross-sectional study conducted in Egypt from June 8, 2020, till August 19, 2020. A purposive sample of 518 HCWs from different governorates was included in the study. HCWs filled a structured questionnaire developed by the World Health Organization on a Google Form and a printed copy. The questionnaire link was shared on social media forums including HCWs such as Facebook.\n\nResults: The mean age of HCWs was 33±7 and 65% were males. The majority of health care workers were affiliated with the Ministry of Health and Population (62.5%), recruited from Cairo (52.4%), and were physicians (78.2%). About 11% of the HCWs had been infected with SARS-CoV2. Their mean knowledge percent score regarding IPC was 36.19 ± 11.26. The highest rate of infection was among those with little experience (p=0.002), and those worked inside Cairo (p=0.018). About 89% mentioned that the leading cause of infection with SARS-CoV2 was the shortage in Personal Protective Equipment (PPE). About 42% recommended raising the awareness for the importance of IPC to decrease risk of infection.\n\nConclusions: HCWs had a low score of knowledge toward IPC. There was a considerable proportion of SARS-CoV2 infection among them. Lack of knowledge and shortage of PPE were the contributing factors. It is necessary to provide juniors with IPC training, and hospitals with sufficient PPE.",
"keywords": [
"Infection control",
"COVID-19 pandemic",
"health care workers",
"health care facilities"
],
"content": "Introduction\n\nA pandemic of SARS-CoV2 was proclaimed on March 11, 2020.1 As of March 26, 2020, more than 150 countries have registered more than half a million cases of COVID-19 globally. In all EU/EEA countries and the UK, the number of confirmed cases of COVID-19 is expanding, accounting for a growing share of the global cases.2-4\n\nHealthcare facilities associated infections is considered a serious public health problem.5 Nosocomial outbreaks accounts for a substantial share of local outbreaks, hurting elders and exposed populations disproportionately.6 Infection prevention and control practices (IPC) encompass all measures taken to limit the risk of infection spread. IPC practices could be clustered into two classes: standard precautions and transmission-based precautions.7 IPC practices are vital to protecting health systems’ functioning and mitigating the effects on vulnerable communities.8\n\nAccording to the COVID-19 Situation Report by World Health Organization (WHO) 82, 52 countries had identified a total of 22,073 health care workers (HCWs) had caught COVID-19.9 Among total cases, the median percentage of HCW infection was 10.04% (range 0–24.09%). HCWs had a median fatality rate of 0.8% (range 0-18.95%). Indonesia had the highest case fatality rate (18.95%), followed by Uzbekistan, Iran, and Egypt, which had a 6.52% case fatality rate. The United States had the lowest recorded case fatality rate, at 0.29%.10\n\nAccording to the Egyptian Medical Syndicate, since the outbreak of coronavirus in Egypt in mid-February, at least 68 frontline HCWs have died, and more than 400 have been confirmed positive, with a very high mortality rate of 15.8% which needs a clear justification by the health authorities.11,12\n\nIPC are considered a top priority for slowing infection transmission in healthcare facilities, reducing the demand for specialized healthcare, such as intensive care unit beds, protecting vulnerable groups, shielding healthcare workers, and finally preventing the spread of cases to other healthcare facilities and the general public.6\n\nCoronaviruses are mostly believed to be transmitted via large respiratory droplets, getting in contact with infected fomites and breathing the aerosols generated during Aerosol Generation Procedures (AGPs). Aside from the protection by the different components of PPE, the virus’ transmissibility at several stages of the disease remains uncertain. Consequently, attention should be applied when considering these elements.13,14 Except for AGPs, it is unknown if facial filtering piece (FFP) respirators offer the best protection against other coronaviruses and respiratory viruses such as influenza than surgical masks.15,16 As a result, a reasonable option would prioritize the use of Filtrating Face Piece (FFP2/3) respirators for therapeutic methods with a high risk of transmission, such as intensive care or AGPs.14,17\n\nCOVID-19 spread among HCWs is exacerbated by a lack of awareness and knowledge of infection control measures among these workers.18 Therefore, applying preventive measures is the most critical intervention to control COVID-19 infection. HCWs display a greater risk of infection, as explained by their constant contact with patients. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) recently released recommendations for COVID-19 prevention and control among HCWs.19,20\n\nThis study will estimate the proportion of SARS-CoV2 infection among HCWs at various health care facilities in Egypt, as well as assess healthcare workers’ knowledge toward IPC while taking care for suspected or confirmed COVID-19 patients, primarily in settings with wider community transmission, based on the facts mentioned above. Finally, this study will explore the association between infection prevention and control practices knowledge and the proportion of infection among HCWs.\n\nThe objectives of this study are:\n\n1. To determine the proportion of SARS-CoV2 infection among the participating HCWs.\n\n2. To assess knowledge of IPC among HCWs caring for suspected or confirmed COVID-19 cases.\n\n3. To discover the relationship between HCWs’ knowledge and the proportion of SARS-CoV2 infection among them.\n\n4. To suggest recommendations to reduce the risk of SARS-CoV2 infection among HCWs who care for confirmed or suspected COVID-19 cases.\n\n\nMethods\n\nStudy design: We conducted a cross-sectional analytical study to assess the knowledge of HCWs to infection control practices caring for confirmed or suspected COVID-19 cases.\n\nSample size and technique: Purposive sample of 518 participants was targeted mainly through electronic data collection. The sample size was estimated based on evidence from a previous study assessing knowledge and practice of HCWs toward infection prevention and control practices conducted in 2018 due to lack of studies assessing the same issue in context with COVID-19 pandemic at the time of conducting our study.21 Considering the knowledge percent score as a primary outcome, Epi-calc 2000 (version 1.01) was used to calculate the sample size of this study. Assuming 80% power, a 0.05 level of significance, and an estimated proportion of 85%,21 the sample size was estimated to be 469 participants. After adding a non-response rate of 10%, so the estimated sample size was 516, but the final sample included 518 participants.\n\nStudy population and setting: The study was conducted on HCWs from different Egyptian governorates, affiliated with the Ministry of Health and Population (MOHP), academia, police/military hospitals, as well as freelancers.\n\nInclusion criteria: All HCWs’ categories, physicians, pharmacists, and nurses, who approved participating in the study, were recruited.\n\nExclusion criteria: Non-HCWs and who were not fluent in English or could not complete the questionnaire were excluded.\n\nData collection tool: Based on the tool developed by WHO,22 a self-administered structured questionnaire composed of 29 questions was designed. Questions were presented in the English language. The authors checked content and face validity. The questionnaire was piloted on 26 HCWs who were excluded from the analysis. No modification in the questionnaire was needed based on the pilot testing. The internal consistency of the study questionnaire was assessed by calculating the Cronbach alpha. The value was 0.75 for the knowledge section. No potential sources of bias had been facing the investigators since data collection was mainly based on the electronic method. HCWs were asked to submit their e-mail address at the end of the survey to avoid duplicate entries; duplicate entries with the same e-mail address were excluded before analysis, and the first entry was maintained.\n\nAn online data collection method was used in line with lockdown measures conducted in Egypt to achieve social distancing. An online Google form was created, and participants were invited to complete and submit it. The questionnaire link was shared on social media forums including HCWs such as Facebook, Twitter, and What’s App. 488 questionnaires were done as Google forms. About 32 copies of the questionnaire have been printed and disseminated to HCWs who worked at health care facilities that lacked internet connections through the help of two house officers and two residents in these health care facilities. Data were collected from June 8, 2020, till August 19, 2020 (No follow-up was done).\n\nThe questionnaire enclosed the following sections: (I) Socio-demographic characters and history of getting SARS-CoV2 infection: age, gender, affiliation, specialty, education, years of experience, place of work, attendance of any IPC courses and getting SARS-CoV2 infection diagnosed by the Polymerase Chain Reaction (PCR) test; (II) Knowledge section entailed knowledge questions covering the primary general information of infection prevention and control practices, specifically a) Applying standard precautions for all patients. b) Contact and droplet precautions, airborne precautions for aerosol-generating procedures, using environmental and engineering controls; (III) Two questions assessing HCWs’ opinions and attitudes about underlying causes for widespread SARS-CoV2 infections among HCWs and their suggestions for improving adherence to IPC, improving infection control situation and decreasing the risk of SARS-CoV2 infections among them by answering an open-ended question.\n\nFor each of the 15 knowledge questions, a score of one point was assigned to the correct response, and a score of zero was assigned to the incorrect response. In the case of multiple-choice questions, choosing all the correct answers was scored one point while choosing some of the correct answers was scored 0 with the maximum score to be 15 (percent score = total score of every participant/15*100). Those attained ≥ 5.5 points (out of 15 points, the average for the score) were assigned as being knowledgeable, while those who attained < 5.5 points were assigned as being not knowledgeable.\n\nData analysis: The data were coded by two of the authors and exported on a data sheet prepared on Microsoft Excel program, version 2013. The data was analyzed using SPSS version 24. Simple descriptive statistics were used to create a summary and simple frequency of quantitative data. The bivariate analysis was carried out and displayed in cross-tabulations, with proportions being compared using the chi-square and Fisher’s exact tests as needed. To compare normally distributed data, an independent T-test was performed. P-value < 0.05 was used as the significance level.\n\nEthics approval and consent to participate: The Faculty of Medicine’s ethical committee, Suez Canal University approved the study protocol (IRB number 4189-5-2020). Throughout the analysis, we protected participants’ identities by keeping the data of the participants confidential and asking participants to provide truthful answers. The participation was non-compensated and voluntary. We put the informed consent in the first part of the online and printed questionnaire, and if participants refused to give consent to participate, they had been unable to complete the form. Participants had to choose by checking a box if they agree or refuse to participate in the study and publishing their result. Therefore, completion of the questionnaire denoted participant’s agreement to participate in the study and publish their results.\n\n\nResults\n\nA total of 518 HCWs (65% males and 35% females) were included in this study. The Age range was (23 – 69) years, with a mean age of 33±7 years and median (IQR) years of experience 7 (4–10). The majority of the participants were affiliated with the Ministry of Health and Population (MOHP) with a total percentage of 62.5%; 22.4% participants were affiliated to academia; and 3.1% were working at military hospitals. Our study included participants from 21 Egyptian governorate, the highest recruitment was from Cairo (52.4%), Giza (16.2%), Dakahlia (5.8%), Kafr Elsheikh (5%), and Alexandria governorates (3.9%). The majority of the participants were physicians (405/78.2%), followed by pharmacists (52/10%), dentists (39/7.5%), nurses (18/3.5%) and technicians (4/0.8%). The level of education obtained by the participants mainly were Bachelor and Master’s degrees (35.5% and 32.4%, respectively), followed by a doctorate (15.1%), diplomas (10.4%), and obtained fellowships and higher institutes graduates (6.6%). The majority of our participants were entry-level physicians considered the frontline HCWs against the COVID-19 pandemic. Our participants’ seniority level was mostly residents (32.4%) followed by participants who were specialists (27%), which corresponds to entry-level physicians with fewer years of experience. The specialties of physicians who took part in this survey were primarily internal medicine physicians (10.8%), clinical and chemical pathologists (8.9 %), followed by anesthesiologists (ICU) (8.5%), pediatric (6.6%) and radiologists (6.2%) of the sample.\n\nOut of the 518 HCWs, those who have taken infection prevention control courses were 54.4%. About two-thirds of HCWs working in Cairo governorate were infected compared to only 33.3% of those working outside Cairo (P-value = 0.018; OR = 1.965; 95% CI:1.113-3.466). Regarding the years of experience, 76.7% of those working less than seven years were infected compared to 23.3% of those working more than seven years (P-value = 0.002; OR = 2.650; 95% CI:1.416-4.958). About 93% of the infected group reported the presence of infected HCWs in their working facilities compared to 80% among the non-infected group (P-value = 0.014; OR = 3.422; 95% CI: 1.209-9.690) (Table 1).\n\nThe relation between socio-demographic characteristics and infection with SARS-CoV2 among the study population (n = 508).\n\n* Significant P-value (≤0.05).\n\n** Chi-square test.\n\nAs regards IPC knowledge association with infection among HCWs, less than 2% (10 participants) preferred not to declare if they had SARS-CoV2 infection, so they were excluded from the analysis. Wearing appropriate PPE while cleaning soiled bleeding toils and linens from patients with COVID-19 was significantly associated with lower proportion of infection (P-value = 0.011; OR = 2.318; 95% CI:1.193-4.504). The knowledge about importance of wearing boots, impermeable aprons as routine PPE for HCWs caring for patients with suspected or confirmed COVID-19 was significantly associated with lower proportion of infection (P-value = 0.042; OR = 1.997; 95% CI:1.016-3.546). The attitude towards the importance of specialized or referral hospitals for patients with suspected or confirmed COVID-19 infection when hospitalization is needed was significantly associated with lower proportion of infection (P-value = 0.005; OR = 2.298; 95% CI:1.277-4.149) (Table 2). The knowledge score among HCWs was 5.43 ± 1.69 (percent score = 36.19 ± 11.26) (Table 3). The score was not significantly different between physicians and other HCWs among the study population (P-value = 0.824) (Table 4).\n\nThe relation between IPC knowledge and infection with SARS-CoV2 among the study population (n = 508).\n\n* Significant P-value (≤0.05).\n\n** Chi-square test.\n\nParameters of knowledge score of IPC practices among the study population.\n\n* Significant P-value (≤0.05).\n\n** T-independent test.\n\nRegarding HCWs opinions about the high proportion of infection among them, they reported that the primary cause was PPE shortage (88.8%) and the least cause was their misbelief in the effectiveness of PPE (8.1%) (Figure 1). As for further suggestions to improve the infection control situation, adherence to IPC and decreasing the risk of SARS-CoV2 infection among HCWs taking care of patients with suspected or confirmed COVID-19 cases: the highest proportion of HCWs (42%) recommended raising the awareness for the importance of IPC among HCWs, an equal proportion of HCWs (12.9%) suggested both providing a proper system for IPC with punishment for the non-adherent, and advising to perform frequent testing every two weeks for HCWs in isolation hospitals, while the lowest proportion of HCWs (3.2%) suggested depending on CT for diagnosis of SARS-CoV2 infection (Figure 2).\n\n\nDiscussion\n\nThe novel COVID-19 pandemic is the center of attention worldwide, causing a massive burden on economies, health care systems, and HCWs.10 The cumulative number of infected cases is over 83 million reported cases and over 1.8 million deaths globally since the pandemic started.9 In Egypt, the cumulative number of cases is over 148 thousand reported cases and over eight thousand deaths since the pandemic, with a case fatality rate of 5.5%.11 The infection rate among HCWs is 2.37% of the total confirmed cases, with a case fatality rate 6.52% with 244 tests per million.10\n\nHCWs displays amplified occupational risk of acquiring COVID-19 infection and higher mortality rates due to a shortage of PPE and inapplicable social distancing within the healthcare work environment.23,24 Evidence concerning the burden of COVID-19 infection in HCWs is still insufficient.10 Strengthening and applying infection control measures in all health facilities is crucial to limit the spread of COVID-19 infection among HCWs.25\n\nHere, our aim was to explore the proportion of SARS-CoV2 infection among HCWs in Egypt, to assess their knowledge of infection control practices, its relation with the proportion of SARS-CoV2 infection among them, and to suggest recommendations for decreasing the risk of SARS-CoV2 infection among HCWs caring for confirmed or suspected COVID-19 cases.\n\nWe found that 82.2% of respondents have reported having a colleague within their working facility tested positive for COVID-19. In contrast, around 11% of HCWs themselves were admitted because of testing positive for COVID-19. However, these percentages could be underestimated because COVID-19 infection causes many asymptomatic and subclinical cases.23 Compared to other studies in Egypt, showing the incidence of HCWs infection was 2.37%, 11%, and 13.5%10,26,27 respectively. Another cross-sectional study in New York City23 reported a 19.4% infection rate. Furthermore, 4.3% was estimated in a cross-sectional study in a hospital in Muscat, Oman28 and 30.35% in a study in Mexico.24\n\nWe found that HCWs infection rate was significantly higher in Cairo governorate (P-value = 0.018, OR = 1.965); it could be due to the highest population distribution, or that this governorate has specialized fever hospitals which were more exposed to infection burden on its health care systems. Also, a higher infection rate was found among workers with ≤7 years of experience (P-value = 0.002, OR = 2.650) which may be due to lack of experience and higher workload for junior physicians than senior ones. This goes in agreement with Vindrola et al.25 However, the infection rate did not differ significantly with age. Among those who were ≤ 32 years, 20% were infected, and 14.7% were not infected by COVID-19 (P-value = 0.288). As regards the affiliation, the highest proportion of infection was among those affiliated to MOHP (46.7%), but the result was not statistically significant, this might be due to unpreparedness for such a pandemic, higher flow rate of patients with a shortage of PPE compared to military/police hospitals (3.3%) (P-value = 0.062), and this goes following Papoutsi et al.10 Regarding HCWs categories, there was no statistically significant difference between them regarding the proportion of SARS-CoV2 infection (p = 0.23). This may be explained by the fact that all HCWs were responsible for the fight against COVID-19 due to lack of health care personal, increased workload and the huge number of cases during the wave. This was contradictory to a recent systematic review that reported the most frequently affected personnel were nurses and non-emergency wards during screening.25\n\nRegarding the knowledge, although 54.4% of our participants took infection control courses, their mean knowledge percent score was 36.19 ± 11.26, which is surprisingly low. It could be due to poor course content or not following the courses by proper practice. Therefore, they did not retain much information.\n\nWe noticed that the non-infected group of respondents got higher percentages of correct answers and significantly higher percent to the choice “wear PPE” to the question “How to clean soiled bedding, towels, and linens from patients with COVID-19” (P-value = 0.011, OR = 2.318). For the question “wearing PPE in the form of boots, impermeable aprons, or coverall suits while dealing with suspected or confirmed COVID-19 infection patients” (P-value = 0.042, OR = 1.997) while “knowing that specialized or referral hospitals required for suspected or confirmed COVID-19 patients when hospitalization is needed” (P-value = 0.05, OR = 2.298) and with the choice of “using sodium hypochlorite at 0.5% for cleaning the environment” (P-value = 0.002, OR = 2.650). These findings showed an inverse association between IPC knowledge and proportion of COVID-19 infection that was statistically significant, this was in accordance with recent studies.29-32\n\nRegarding the HCWs’ opinions about the high proportion of infection among them in Egypt, they thought this could be due to shortage of PPE (88.8%) inconsistent with recent studies,9,25,33 work overload (84.2%) in agreement with recent studies32 and lack of knowledge on how to use PPE as estimated by Houghton systematic review,25,33 and the HCWs recommended raising the awareness for the importance of IPC (41.9%).\n\nWe recommend strengthening policies for applying IPC with proper supervision and providing junior physicians with mandatory IPC training. Besides, extending the surveillance within the facilities for early detection of infected workers and isolation of cases will minimize transmission risk. It was also supplying hospitals with sufficient PPE. It is crucial to consider the years of experience of workers while dealing with COVID-19 patients.\n\n\n\n• The study included representatives from all health care workers’ classes (physicians, pharmacists, dentists, and nurses), as well as physicians from different specialties (clinical pathologists, pediatric, radiologists, ophthalmologists, anesthesiologists, and internal medicine physicians).\n\n• Up to our knowledge, this is one of the earliest papers examining infection prevention and control practices among HCWs caring for patients with suspected or confirmed COVID-19 during the pandemic peak in Egypt.\n\n\n\n• Even though the study included different occupational classes, their distribution was not equal.\n\n• Although the study included HCWs from 21 Egyptian governorate and from almost all central Egyptian governorates (Cairo, Giza, Dakahlia, Kafr Elsheikh, and Alexandria governorates), further studies will be in need on a larger scale including all Egyptian governorates using a probability sample.\n\n\nConclusion\n\nWe concluded that HCWs had low score of knowledge of infection prevention and control practices. There was a considerable proportion of SARS-CoV2 infection among HCWs in Egypt, especially among those working in Cairo governorate with experience less than seven years; due to lack of knowledge about IPC measures and shortage of PPE in their working facilities.\n\n\nData availability\n\nDryad: Knowledge and attitude of Infection prevention and control practices among health care workers caring for patients with suspected or confirmed COVID-19. https://doi.org/10.5061/dryad.ht76hdrg2.34\n\nThis project contains the following underlying data.\n\n- Dataset (xlsx)\n\nData are available under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.",
"appendix": "References\n\nWorld Health Organization: WHO Director-General’s opening remarks at the media briefing on COVID-19e March 11 2020.Geneva: WHO; 2020. [Last accessed April 2020]. Reference Source\n\nEuropean Centre for Disease Prevention and Control (ECDC): Infection prevention and control for COVID-19 in healthcare settings 2020 [updated 12 March 2020; cited 26 March 2020].Reference Source\n\nEuropean Centre for Disease Prevention and Control (ECDC): COVID-19[cited 8 March 2020]. Reference Source\n\nWorld Health Organization (WHO): Coronavirus disease (COVID-19) outbreak 2020.Reference Source\n\nAllegranzi B, Bagheri Nejad S, Combescure C, et al.: Burden of endemic health-care-associated infection in developing countries: systematic review and meta-analysis. Lancet (London,England). 2011; 377(9761): 228–241. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization (WHO): Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19).2020 [cited 1 March2020]. Reference Source\n\nWorld Health Organization: Practical guidelines for infection control in health care facilities.SEARO Regional Publication No. 41 Manila: WHO Regional Office for the Western Pacific; 2004. [Last accessed on 2017 May 26] Reference Source\n\nIstituto Superiore di Sanita’ (ISS): Sorveglianza Integrata COVID-19 in Italia 2020.[updated 26 March 2020; cited 26 March 2020]. Reference Source\n\nWorld Health Organization: Coronavirus disease (COVID-19) situation reports. Date last accessed: 17 April 2020. Date last updated: 1 June 2020 Reference Source\n\nPapoutsi E, Giannakoulis VG, Ntella V, et al.: Global burden of COVID-19 pandemic on healthcare workers. ERJ Open Res. 2020 Apr; 6(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nEgyptian statistics. Retrieved May 2, 2020. Reference Source\n\nRetrieved June 15, 2020. Reference Source\n\nRothe C, Schunk M, Sothmann P, et al.: transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOng SWX, Tan YK, Chia PY, et al.: Air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a symptomatic patient. JAMA. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSmith JD, MacDougall CC, Johnstone CRA, et al.: Effectiveness of N95 respirators versus surgical masks in protecting healthcare workers from acute respiratory infection: a systematic review and meta-analysis. Cmaj. 2016; 188(8): 567–574. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTran K, Cimon K, Severn M, et al.: Aerosol generating procedures and risk of transmission of acute respiratory infections to healthcare workers: a systematic review. PLoS One. 2012; 7(4): e35797. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi R, Pei S, Chen B, et al.: Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). Science. 2020: eabb3221. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu Z, McGoogan JM: Characteristics of and important lessons from the coronavirus disease 2019 (COVID-19) outbreak in China: Summary of a report of 72314 cases from the chinese center for disease control and prevention. JAMA. 2020. Publisher Full Text\n\nWorld Health Organization 2020: Infection prevention and control during health care when novel coronavirus (nCoV) infection is suspected: interim guidance.January 2020. [accessed 2020-02-12] Reference Source\n\nCenters for Disease Control and Prevention: Update and interim guidelines on outbreak of 2019 Novel coronavirus (2019-nCoV).2019. [accessed 2020-02-12] Reference Source\n\nDesta M, Ayenew T, Sitotaw N, et al.: Knowledge, practice and associated factors of infection prevention among healthcare workers in Debre Markos referral hospital, Northwest Ethiopia. BMC Health Serv Res. 2018; 18(1): 465. Published 2018 Jun 18. Publisher Full Text\n\nWHO Infection prevention and control during health care when novel coronavirus (nCoV) infection is suspected: Interim guidance 25 January 2020. http\n\nStock Ariel D, Bader Edward R, Cezayirli P, et al.: Eskandar Emad: COVID-19 Infection Among Healthcare Workers: Serological Findings Supporting Routine Testing. Front Med VOLUME=7,2020. Reference Source\n\nAntonio-Villa NE, Bello-Chavolla OY, Vargas-Vazquez A, et al.: Assessing the burden of COVID-19 amongst healthcare workers in Mexico City: A data-driven call to action. medRxiv. 2020.07.02.20145169.\n\nVindrola-Padros C, Andrews L, Dowrick A, et al.: Perceptions and experiences of healthcare workers during the COVID-19 pandemic in the UK. BMJ Open. 2020; 10: e040503. Publisher Full Text\n\nMostafa AS, Abdalbaky A, Fouda EM, et al.: Practical approach to COVID-19: An Egyptian pediatric consensus. Egypt Pediatric Association Gaz . 2020; 68: 28. Publisher Full Text | Free Full Text\n\nKassem AM, Talaat H, Shawky S, et al.: SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility. Arab J Gastroenterol: The Official Publication of the Pan-arab Association of Gastroenterology. 2020 Sep; 21(3): 151–155. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl Maskari Z, Al Blushi A, Khamis F, et al.: Characteristics of healthcare workers infected with COVID-19: A cross-sectional observational study. Int J Infectious Dis . 2021; 102: 1201-9712. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLai X, Wang X, Yang Q, et al.: Will healthcare workers improve infection prevention and control behaviors as COVID-19 risk emerges and increases, in China? Antimicrob Resist Infect Control . 2020; 9: 83. Publisher Full Text\n\nWHO: About the Infection Prevention and Control Course Series. Last accessed January 2021. Reference Source\n\nAssefa J, Diress G, Adane S: Infection prevention knowledge, practice, and its associated factors among healthcare providers in primary healthcare unit of Wogdie District, Northeast Ethiopia, 2019: a cross-sectional study. Antimicrob Resist Infect Control . 2020; 9: 136. Publisher Full Text\n\nEjeh FE, Saidu AS, Owoicho S, et al.: Knowledge, attitude, and practice among healthcare workers towards COVID-19 outbreak in Nigeria. Heliyon . 2020; 6(11): e05557. 2405-8440. Publisher Full Text\n\nHoughton C, Meskell P, Delaney H, et al.: Barriers and facilitators to healthcare workers’ adherence with infection prevention and control (IPC) guidelines for respiratory infectious diseases: a rapid qualitative evidence synthesis. Cochrane Database Syst Rev . 2020; 4: CD013582. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElsebaie EH, et al.: Knowledge and attitude of infection prevention and control practices among health care workers caring for patients with suspected or confirmed COVID-19. Dryad, Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "92220",
"date": "25 Aug 2021",
"name": "Eman Omar Khashaba",
"expertise": [
"Reviewer Expertise Occupational medicine & Environmental 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\nReviewer comments:\nThe title is not reflecting the study objectives or the results as the title is knowledge of IC practice and the analysis focused on knowledge according to Covid-19 infection.\n\nSample size was calculated according to knowledge of infection control measures in general not Covid-19. A pilot study could be done to calculate relevant sample size.\n\nMethods:\nStudy tool:\nA self-administered structured questionnaire composed of 29 questions, however the knowledge score was 15 items. The tool needs detailed description for included sections in the questionnaire (number of questions in each section).\n\nStat analysis paragraph:\nHow were the quantitative variables described with simple frequency?\n\nResults:\nGeneral comment:\nThe sentences used for describing variables are too long; it would be better to summarize these variables, for example \"Have you ever taken any infection control courses or certificates?\" (Yes responses).\n\nReceived previous IC courses;\nThe first objective is not highlighted in the results. Please demonstrate that in your results.\n\nTable (1-2):\nUsing reference category for polytomous variables and calculation of OR and 95%CI is recommended.\n\nThe interpretation of total knowledge score was not used in tables.\n\nThe score ≤5 &>5 can be associated with different demographics, occupational and infection statuses.\n\nWeak presentation of data in tables 3 and 4.\n\nComparison of total knowledge score in infected and non-infected can be done (Tables 3 and 4).\n\nHow did the authors describe that there is a high proportion of infection although the percentage of infected HCWs is 11.6%?\n\nFig 1:\nProvide a proper system for IPC with punishment for the...incomplete variable in figure (please complete the sentence).\n\nHCWs recommendations to decrease the risk of SARS-CoV2 infection: How is the recommendation to depend on CT in diagnosis? The recommendation is related to CT in diagnosis (Fig 2).\n\nDecision: major revision is required.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "101251",
"date": "17 Dec 2021",
"name": "Eman T. Ali",
"expertise": [
"Reviewer Expertise clinical immunology",
"immunology."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI think the idea of the paper is excellent and is an important addition to the literature. This study aims to estimate the proportion of health care workers who acquired SARS-CoV2 infection, and evaluate their knowledge to IPC. This in itself is very important as long as it adds something novel, although the method used is a well-known organized questionnaire. Despite the rather small temporal and spatial extent of the study, it makes an important contribution to reducing the prevalence of disease, as the idea of the study addresses the problem of lack of knowledge and lack of personal protective equipment among health care workers.\nIn more detail, this study is cross-sectional but the authors provide novel experimental data which demonstrates that lack of knowledge and shortage of PPE were the contributing factors, and it is necessary to provide juniors with IPC training, and hospitals with sufficient PPE.\nThe article was written in a clear and sequential manner and the work is technically sound, and the research idea is clearly and accurately presented, in addition to choosing the appropriate study design for the main idea. Despite the small sample size taken from health care workers compared to the population of Egypt, this study included participants from 21 Egyptian governorate. Even though the study included different occupational classes, their distribution was not equal. As for the statistical analysis, it depends on simple descriptive statistics that were used to create a summary and simple frequency of quantitative data; this is because of the type of study, and I believe that the results were interpreted well. It is possible to adopt the results of this study because the OR values are within the limits of the internal confidence IC and therefore are considered real and not extreme values. One of the most important outcomes that they touched on:\nWearing appropriate PPE while cleaning soiled bleeding toils and linens from patients with COVID-19 was significantly associated with lower proportion of infection.\n\nThe knowledge about importance of wearing boots, impermeable aprons as routine PPE for HCWs caring for patients with suspected or confirmed COVID-19, was significantly associated with lower proportion of infection, and regarding the years of experience.\nThrough their results, the authors suggest recommendations to reduce the risk of SARS-CoV2. Moreover, the conclusion highlights the main objective of the work. I think this is one of the earliest papers examining infection prevention and control practices among HCWs caring for patients with suspected or confirmed COVID-19 during the pandemic peak in Egypt.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-824
|
https://f1000research.com/articles/10-823/v1
|
17 Aug 21
|
{
"type": "Research Article",
"title": "A better approach to discuss medical science and engineering data with a modified Lehmann Type – II model",
"authors": [
"Muhammad Zafar Iqbal",
"Muhammad Zeshan Arshad",
"Gamze Özel",
"Oluwafemi Samson Balogun",
"Muhammad Zafar Iqbal",
"Gamze Özel",
"Oluwafemi Samson Balogun"
],
"abstract": "Background: Modeling with the complex random phenomena that are frequently observed in reliability engineering, hydrology, ecology, medical science, and agricultural sciences was once thought to be an enigma. Scientists and practitioners agree that an appropriate but simple model is the best choice for this investigation. To address these issues, scientists have previously discussed a variety of bounded and unbounded, simple to complex lifetime models. Methods: We discussed a modified Lehmann type II (ML-II) model as a better approach to modeling bathtub-shaped and asymmetric random phenomena. A number of complementary mathematical and reliability measures were developed and discussed. Furthermore, explicit expressions for the moments, quantile function, and order statistics were developed. Then, we discussed the various shapes of the density and reliability functions over various model parameter choices. The maximum likelihood estimation (MLE) method was used to estimate the unknown model parameters, and a simulation study was carried out to evaluate the MLEs' asymptotic behavior. Results: We demonstrated ML- II's dominance over well-known competitors by modeling anxiety in women and electronic data.",
"keywords": [
"Power Function Distribution",
"Lehmann Type I",
"II Distribution",
"Failure Rate Function",
"Moments",
"Maximum Likelihood",
"Order Statistics",
"Quantile",
"Rényi Entropy."
],
"content": "Introduction\n\nOver the last two decades, researchers' increasing interest in the development of new models has explored the remarkable characteristics of the baseline model. As a result, new models open new avenues for theoretical and applied researchers to address real-world problems, allowing them to fit asymmetric and complex random phenomena more proficiently and adequately. As a result, several modifications, extensions, and generalizations have been developed and discussed in the literature, with the Lehmann1 type – I (L – I) and Lehmann type – II (L – II) models being among the simplest and most useful. The simple exponentiation of any arbitrary baseline model is given by L – I.\n\nwhere 0<x<1, and α>0 is a shape parameter.\n\nGupta et al.2 are credited with the use of L–I on exponential distributions. On the other hand, Cordeiro et al.3 established the L–II–G class of distributions and developed a dual transformation of L–I, which is given by\n\nwhere Gxξ is cumulative distribution function (CDF) of the arbitrary baseline model, based on the parametric vector ξ with α>0 as a shape parameter.\n\nThe closed-form feature of L–II allows one to derive and study its numerous properties, and in the literature, both approaches (L–I and L–II) have been extensively used in favor of the power function (PF) model, to study the unexplored characteristics of the classical and modified models. Recently, Arshad et al.4,5 developed bathtub-shaped failure rate and PF models followed by L–II and L–I families, respectively, and explored their applications in engineering data. Awodutire et al.6 generalized the half-logistic via L–II class, and Akilandeswari et al.7 proposed the Laplace L–I reliability growth model and discussed its application in the early detection of software failure based on time between failure observations.\n\nThe PF is a special case of the beta distribution in distribution theory, and its significance can be evaluated using statistical tests such as the likelihood ratio test. The PF's simplicity and utility has compelled researchers to investigate its further generalizations and applications in various fields of science. For this, we recommend that the reader look at Dallas's illustrious work.8 He discovered an intriguing relationship between PF and Pareto models when the inverse transformation of the Pareto variable explored the PF.8 Meanwhile, Meniconi and Barry9 discovered the PF as a best-fit model on electronic component data. Characterization is based on the independence of record values and order statistics, with lower record values attributed to Chang10 and Tavangar,11 respectively. Cordeiro and Brito12 created the beta version of the PF and discussed its use in petroleum reservoir and milk production data. The PF was characterized by Ahsanullah et al.13 using lower record values. Zaka et al.14 discussed techniques for estimating PF parameters such as least square (LS), relative least square (RLS), and ridge regression (RR). Tahir et al.15 generalized the PF via the Weibull-G class and applied it to bathtub-shaped data. Shahzad et al.16 used the techniques of L-, TL-, LL-, and LH moments to calculate the PF moments. Haq et al.17 generalized the PF via the QRTM-G class and investigated its application in two-lifetime data. Okorie et al.18 generalized the PF via the Marshall-Olkin-G class (Marshall and Olkin19) and investigated its application in data on anxiety in women and evaporation. Usman et al.20 proposed an exponentiated version of transmuted PF and investigated its application in biological and engineering data. Hassan et al.21 generalized the PF by following the odd exponential-G class (Tahir et al.22) and discussed its application in three-lifetime data. Zaka et al.23 developed a new reflected PF and investigated its application in medical sciences data, while Al-Mutairi24 discussed the weighted PF via the QRTM G-class and investigated its application in the engineering sector.\n\n\nModified Lehmann type II model\n\nWe developed a potentiated lifetime model known as the modified Lehmann type II (ML-II) model. It is constrained by the interval (0, 1). The ML-II is extremely well suited to modeling asymmetric and bathtub-shaped phenomena. By including a scale parameter (α>0), in the baseline model, it begins to outperform its competitors in terms of fit and robustness of the tail weight/skewness of the density function.\n\nThe ML-II is said to follow a random variable X if its associated CDF and corresponding probability density function (PDF) are given by\n\nand\n\nwhere 0<x<1, and α>−1,β>0 are the scale and shape parameters, respectively. For α = 0, the ML-II reduces to the L–II (baseline model).\n\nBalogun et al.,25,26 has developed the generalized version and G-class of ML-II (Equation (1)), respectively, and explored their applications in multidisciplinary areas of science.\n\nWe had the following objectives:\n\n(i) to develop a two-parameter model with an approach that had not been studied and discussed in the past;\n\n(ii) For the new model to have attractive closed-form features for CDF, PDF, and a likelihood function that is simple to interpret,;\n\n(iii) PDF and HRF to hold J, reversed-J, and bathtub shapes;\n\n(iv) To provide comparative results and a better fit than competing models.\n\nThis article is divided into the following sections:’Linear representation’ presents a mixture representation as well as numerous structural and reliability measures. ‘Estimation’ includes the estimation of model parameters using the maximum likelihood estimation (MLE) method, as well as a simulation study. ‘Application’ discusses real-world applications, and the final section summarizes the conclusion.\n\n\nLinear representation\n\nThe linear representations of CDF and PDF make the calculations much easier than the traditional integral computation for determining the mathematical properties. We consider the binomial expansion for this.\n\nHence, the mixture representation of CDF is given as\n\nPDF is given as follows\n\nor\n\nwhere ϕij=βi−βj−1iαj,α>−1,β>0,ηij=αj−1iβ−1iβ+1j,α>−1,β>0\n\nThe probability model plays an important role in reliability engineering by analyzing and predicting the lifespan of a component. Notable contributions include the survival function S(x), hazard rate function h(x), cumulative hazard rate function hc(x), reverse hazard rate function hr(x), Mills ratio M(x), and odd function O(x)).\n\nThe reliability function can be defined as the probability that a component will survive at time x. It is defined analytically as Sx=1−Fx. The survival/reliability function of X is denoted by\n\nTerms such as “failure rate function”, “hazard rate function”, and “force of mortality” are frequently discussed in the literature. These terms are used to describe the failure rate of a component over a specific time period (say x). It is mathematically defined as hx=fx/Rx.\n\nThe failure rate function of X is denoted by\n\nThe mechanical components/parts of some systems are frequently assumed to follow the bathtub-shaped failure rate phenomenon. To discuss the significance of the MLII, several well-established and useful reliability measures are available in the literature. One of them is the cumulative hazard rate function, which is defined as hcx=−logSx. The cumulative hazard rate function of X is denoted by\n\nThe reverse hazard rate function is defined by hrx=fx/Fx. The reverse hazard rate function of X is given by\n\nMills ratio is defined by Mx=Sx/fx. Mills ratio of X is given by\n\nThe odd function is defined by Ox=Fx/Sx. The odd function of X is given by\n\nAs mentioned above, we can obtain the linear expression for reliability characteristics. In terms of linear expression, the reliability and failure rate functions of X are given by\n\nand\n\nPropositions 1 and 2 discuss the limiting behavior of the ML-II's cumulative distribution (CDF), density (PDF), reliability (S(x)), and failure rate (h(x)) functions for x →0 and x →1.\n\nProposition-1. The limiting behavior of the CDF, PDF, S(x), and h(x) of the ML-II at x →0 is given below.\n\nProposition-2. The limiting behavior of CDF, PDF, S(x), and h(x) of the ML-II at x →1 is given as follows, respectively.\n\nThe possible shapes of the ML-II's density and failure rate functions are sketched over various model parameter choices shown in Figures 1 and 2. Figure 1 depicts the J, reverse-J, and bathtub shapes of the density function, while Figure 2 depicts the U, bathtub, and reverse-J shapes of the failure rate function.\n\nThe concept of quantile function was introduced by Hyndman and Fan.27 Inverting the CDF yields the pth quantile function of ML-II (Equation (1)). The quantile function is defined as follows: p=Fxp=PX≤xp,p∈01. Then, the quantile function of X is given by\n\nPut p = 0.25, 0.50, and 0.75 in Equation (3) to get the first quartile, median, and third quartile of X. To generate random numbers in the future, we will assume that the CDF in Equation (1) follows a uniform distribution u = U. (0, 1).\n\nThe mode of X is calculated by taking the first derivative of PDF (Equation (2)) and equating it to zero, as shown by\n\nAs a result, a simplified form of the mode is given by\n\nMeasures of skewness and kurtosis based on quartiles and octiles are less sensitive to outliers and work well against models, but they are deficient in moments.\n\nAccording to Figures 3 and 4, the skewness and kurtosis plots of the ML-II may be positively skewed.\n\nMoments play a significant role in distribution theory, where they are used to discuss the various characteristics and important features of the probability model.\n\nTheorem 1. Let X ∼ ML-II (x;α,β), with α>−1,β>0, then the r-th ordinary moment (say μr′) of X is given by\n\nwhere E = β1+α,Di=αi−β−1i\n\nProof: r-th ordinary moment can be written by following Equation (2) as\n\nAs a result, the above integral reduces to the r-th moment, which is given by\n\nwhere B(x;α,β) = ∫0xtα1−tβ−1dt is the beta function, E = β1+α,Di=αi−β−1i and α>−1,β>0\n\nThe r-th moment is quite helpful in the development of several statistics. For instance, the mean of X can be obtained by setting r =1 in Equation (6) and is given by\n\nMoment generating function MXt is defined as MXt=∑r=0∞trr!μr′. It is obtained by following Equation (6) and is given by\n\nCharacteristic function is defined as ∅Xt=∑r=0∞itrr!μr′. It is obtained by following Equation (6) and is given by\n\nThe factorial generating function of X is defined as Fxt=E1+tx=Eexln1+t=∑r=0∞ln1+trr!μr′. It is obtained by following Equation (6) and is given by\n\nThe Fisher index VarXEX may play a supportive role in the discussion of variability in X and it is given by\n\nFor the negative moments of X, substitute r by – w in Equation (6) and it is given by\n\nFurthermore, for fractional positive and fractional negative moments of X, substitute r by mn and −mn in Equation (6), respectively.\n\nThe Mellin transformation is well-known in statistics as a product distribution as well as a quotient for independent random variables. The Mellin transformation is presented by Mxm=Exm−1=∫xm−1fxdx. The Mellin transformation of X is given by\n\nwhere B(x;α,β) = ∫0xtα1−tβ−1dt is the beta function, E = β1+α,Di=αi−β−1i and α>−1,β>0.\n\nOne may perhaps further determine the well-established statistics such as skewness (τ1=μ32/μ23), and kurtosis (τ2=μ4/μ22), of X by integrating Equation (6). A well-established relationship between the central moments μs and cumulants (Ks) of X may easily be defined by ordinary moments by μs=∑k=0ssk−1kμ1/sμs−k/. Hence, the first four cumulants can be calculated by K1=μ1/, K2=μ2/−μ1/2, K3=μ3/−3μ2/μ1/+2μ1/3, and K4=μ4/−4μ3/μ1/−3μ2/2+12μ2/μ1/2−6μ1/4.\n\nSome numerical results of the first four ordinary moments (μ1/,μ2/,μ3/,μ4/), mode (a value that appears frequently in data), ε2 = variance (a measure of dispersion), τ1= skewness (measure of asymmetry), and τ2= kurtosis (a measure to discuss the heaviness of the distribution tails) for some chosen parameters are presented in Table 1 for S-I (α=0.5,β=0.9), S-II (α=0.9,β=1.5), S-III (α=1.2,β=1.9), S-IV (α=3.2,β=0.9), and S-V (α=0.2,β=3.9). Note that the results of moments and variance decrease gradually, while skewness falls between 0 and 1, mode increases, and kurtosis can be negative subject to the model parameter combinations.\n\nNumerical results of moments (μs/), variance (ε2), skewness (τ1), and kurtosis (τ2).\n\nIncomplete moments\n\nLower incomplete (LI) and upper incomplete moments are the two types of incomplete moments. LI moments are defined by Φrt=∫0txrfxdx. The LI moments of X are given as\n\nThe residual life function of random variable X, Rt=X−t/X>t, is the likelihood that a component whose life says x, survives in the different time intervals at t≥0. Analytically, it can be written as follows:\n\nResidual life function of X\n\nwith the associated CDF is given as follows\n\nThe mean residual life function of X is given by\n\nFurther, the reverse residual life can be defined as R¯t=t−X/X≤t\n\nReverse residual life function of X\n\nwith the associated CDF is given as follows\n\nThe mean reversed residual life function/mean waiting time is given by\n\nwhere B(x;α,β) = ∫0xtα1−tβ−1dt is the beta function, E = β1+α,Di=αi−β−1i, and α>−1,β>0\n\nOrder statistics and its moments play an important role in reliability analysis and life testing of a component in quality control. Let X1, X2, X3 , ..., Xn be a random sample of size n following the ML-II model and {X(1) < X(2) < X(3) < ... < X(n)} be the corresponding order statistics. The random variables X(i) , X(1) , X(n) are the i-th, minimum, and maximum order statistics of X, respectively.\n\nThe PDF of the i-th order statistics is given by\n\nBy incorporating Equations (1) and (2), the PDF of the i-th order statistics is given by\n\nEquation (8) can be written as\n\nStraightforward computation of Equation (9) leads to the w-th moment order statistics of X and it is given by\n\nwhere Gij=βi−αβ+α+ij,α>−1,β>0. Further, the minimum and maximum order statistics of X follow directly from Equation (8) with i = 1 and i = n, respectively.\n\nLet X1 and X2 represent a component's strength and stress, respectively, following the same univariate distribution. The inadequacy or effectiveness of a component is dependent on whether X2>X1 and X2<X1, respectively. Stress – strength reliability can be written as R=PX2<X1.\n\nTheorem 2. Let X1∼ ML-II (x;α,β1) and X2∼ ML-II (x;α,β2) be independent ML-II distributed random variables; then the reliability R is defined as β2β1+β2\n\nProof: Reliability R is defined as\n\nReliability of X is given by\n\nHence the above integral reduces R in terms of β1 and β2, refers to the stress-strength reliability of the ML-II, and it is given by\n\nThere are a number of schools of thought about defining entropy measures. Entropy can be the quantity of disorderedness, randomness, diversity, or sometimes an uncertainty in a system.\n\nThe Rényi30 entropy of X is defined by\n\nFirst, we simplify fx in terms of fδx by considering Equation (2)\n\nby applying the binomial expansion to this equation, we get\n\nand by placing this information in IδX, we get\n\nhence, by integrating the last equation we obtain the reduced form of the Rényi entropy of X and it is given by\n\nwhere Ai=−δβ+1iαi,α>−1,β>0.\n\nA generalization of the Boltzmann-Gibbs entropy is the η – entropy, although in physics, it is referred to as the Tsallis entropy. The Tsallis31 entropy/η – entropy is described by\n\nThe Tsallis Entropy of X is given by\n\nwhere Ci=−ηβ+1iαi,α>−1,β>0.\n\nHavrda and Charvat32 introduced ω− entropy measure. It is presented by\n\nThe Havrda and Charvat entropy of X is given by\n\nwhere Fi=−ωβ+1iαi,α>−1,β>0.\n\nArimoto33 generalized the work of32 by introducing ε− entropy measure. It is presented by\n\nThe Arimoto entropy of X is given by\n\nwhere Gi=−1εβ+1iαi,α>−1,β>0.\n\nBoekee and Lubba34 developed the τ− entropy measure. It is presented by\n\nBoekee and Lubba entropy of X is given by\n\nwhere Ii=−τ−1β+1iαi,α>−1,β>0.\n\nMathai and Haubold35 generalized the classical Shannon entropy known as ζ− entropy. It is presented by\n\nThe Mathai and Haubold entropy of X is given by\n\nwhere Ji=−2−ζβ+1iαi,α>−1,β>0.\n\nTable 2 presents the flexible behavior of the entropy measures for some chosen model parameters for S-VI (α=1.1,β=2.1), S-VII (α=1.1,β=1.5), and S-VIII (α=2.1,β=3.5).\n\nNumerical results of Rényi, Tsallis, Havrda and Charvat, Arimoto, Boekee and Lubba, and Mathai and Haubold entropy measures.\n\n\nEstimation\n\nIn this section, we estimate the parameters of the ML-II by following the method of MLE as this method provides the maximum information about the unknown model parameters. Let X1,X2,X3,…,Xn be a random sample of size n from the ML-II, then the likelihood function Lϑ=∏i=1nfxαβ of X is given by\n\nThe log-likelihood function LogLϑ=lϑ of X is\n\nNow, we are concerned about obtaining the MLEs of the ML-II. For this, first, we maximize the Equation (12) and second, we calculate the partial derivatives w.r.t., the unknown parameters (α,β) and equate to zero, respectively. The score vector components are given by\n\nPartial derivatives w.r.t. α,β are given as follows, respectively\n\nThe last two non-linear equations do not provide the analytical solution for the MLEs and the optimum value of α, and β. The Newton-Raphson (an appropriate) algorithm plays a supportive role in these kinds of ML estimates. Numerical solutions and estimates of the parameters are calculated using R version 3.6.2 (statistical software).\n\nIn this sub-section, to observe the asymptotic performance of MLE's φ̂=α̂β̂, we discuss the following algorithm.\n\nStep - 1: A random sample x1, x2, x3 , ..., xn of sizes n = 150, 200, 250, 300, 350, 400, 450, and 500 from Equation (5).\n\nStep - 2: The required results are obtained based on the different combinations of the model parameters placed in S-IX (α = 3.2, β = 2.5), S-X (α = 0.2, β = 0.9), and S-XI (α = 0.2, β = 1.5).\n\nStep - 3: Results of mean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) are calculated via nlmib in R. These results are presented in Tables 3 to 8.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (α) for S-IX.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (β) for S-IX.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (α) for S-X.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (β) for S-X.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (α) for S-XI.\n\nMean, variance (Var.), bias, mean square error (MSE), coverage probability (CP), and average width (AW) of (β) for S-XI.\n\nStep - 4: Each sample is replicated 1000 times.\n\nStep - 5: A gradual decrease with the increase in sample size is observed in mean, biases, MSEs, and Var.\n\nStep - 6: CPs of all the parameters φ=αβ are approximately 0.975, approaching the nominal value, and AW decreases when sample sizes increases.\n\nFurthermore, the frequent use of the measures in the development of average estimate (AE), bias, MSE, CP, AW, are given as follows:\n\n\nApplication\n\nIn this section, we explore the application of ML-II in medical science and engineering data. For this, we consider two lifetime datasets. The first dataset was originally reported by Smithson and Verkuilen.36 They studied a group of 166 healthy women's anxiety performance, i.e., outside of a pathological clinical setting, from Townsville, Queensland, Australia; data points are 0.01, 0.17, 0.01, 0.05, 0.09, 0.41, 0.05, 0.01, 0.13, 0.01, 0.05, 0.17, 0.01, 0.09, 0.01, 0.05, 0.09, 0.09, 0.05, 0.01, 0.01, 0.01, 0.29, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.09, 0.37, 0.05, 0.01, 0.05, 0.29, 0.09, 0.01, 0.25, 0.01, 0.09, 0.01, 0.05, 0.21, 0.01, 0.01, 0.01, 0.13, 0.17, 0.37, 0.01, 0.01, 0.09, 0.57, 0.01, 0.01, 0.13, 0.05, 0.01, 0.01, 0.01, 0.01, 0.09, 0.13, 0.01, 0.01, 0.09, 0.09, 0.37, 0.01, 0.05, 0.01, 0.01, 0.13, 0.01, 0.57, 0.01, 0.01, 0.09, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.05, 0.01, 0.01, 0.01, 0.13, 0.01, 0.25, 0.01, 0.01, 0.09, 0.13, 0.01, 0.01, 0.05, 0.13, 0.01, 0.09, 0.01, 0.05, 0.01, 0.05, 0.01, 0.09, 0.01, 0.37, 0.25, 0.05, 0.05, 0.25, 0.05, 0.05, 0.01, 0.05, 0.01, 0.01, 0.01, 0.17, 0.29, 0.57, 0.01, 0.05, 0.01, 0.09, 0.01, 0.09, 0.49, 0.45, 0.01, 0.01, 0.01, 0.05, 0.01, 0.17, 0.01, 0.13, 0.01, 0.21, 0.13, 0.01, 0.01, 0.17, 0.01, 0.01, 0.21, 0.13, 0.69, 0.25, 0.01, 0.01, 0.09, 0.13, 0.01, 0.05, 0.01, 0.01, 0.29, 0.25, 0.49, 0.01,0.01.\n\nThe second dataset was recently reported by Rahman et al.37 They studied the lifetime (in days) of 30 electronic devices and the dataset was as follows: 0.020, 0.029, 0.034, 0.044, 0.057, 0.096, 0.106, 0.139, 0.156, 0.164, 0.167, 0.177, 0.250, 0.326, 0.406, 0.607, 0.650, 0.672, 0.676, 0.736, 0.817, 0.838, 0.910, 0.931, 0.946, 0.953, 0.961, 0.981, 0.982, 0.990.\n\nThe ML-II is compared with its competing models (presented in Table 9) based on a series of criteria, namely, -Log-likelihood (-LL), Akaike information criterion (AIC), Bayesian information criterion (BIC), consistent Akaike information criterion (CAIC), and Kolmogorov Smirnov test (K-S) test statistics. Table 10 presents a set of descriptive statistics and Tables 11 and 12 present the parameter estimates and standard errors (in parenthesis) along the goodness-of-fit test. As seen in Tables 11 and 12, the performance of the ML-II abundantly satisfies the criteria of a better fit model. Consequently, we declare that the ML-II is a better fit among all competing models on the anxiety in women data. Moreover, Figures 5 and 6 present the empirically fitted plots comprising PDF (a), CDF (b), Kaplan-Meier Survival (c), Probability-Probability (P-P) (d), Box (e), and total test time (TTT) (f) plots (see Aarset38), which confirm the close fit to the data as well.\n\nFitted Probability density function (PDF) (a), Cumulative distribution function (CDF) (b), Kaplan-Meier survival (c), Probability – Probability (PP) (d), Box (e), and Total Test Time (TTT) (f) Plots for women’s anxiety data.\n\nFitted Probability density function (a), Cumulative distribution function (b), Kaplan-Meier survival (c), Probability-Probability (d), Box (e), and Total Test Time (f) Plots for 30 electronic devices data.\n\nKum = Kumaraswamy distribution ; L–I = Lehmann type I distribution; L–II = Lehmann type II distribution ; T-Kum = transmuted Kumaraswamy distribution ; Mostafa type-II distribution ; T-GPW = transmuted generalized power Weibull distribution; T-Lin = transmuted Lindley distribution.\n\n\nConclusion\n\nWe developed a potentiated lifetime model that exhibited the bathtub-shaped failure rate and addressed the most efficient and consistent results over complex random phenomena in this article. We called the proposed model a modified Lehmann type II (ML-II) model because it was a modified version of the Lehmann type II model. Several structural and reliability measures were developed and discussed. We used the maximum likelihood estimation method to estimate model parameters, and we also ran a simulation study to investigate the asymptotic performance of the MLEs. Data on anxiety in women from Smithson and Verkuilen36 and data on 30 electronic devices from Rahman et al.,37 were modeled to reveal the dominance ML-II over its competitors. It is hoped that in the future, the ML-II will be regarded as a superior alternative to the baseline model.\n\n\nData availability\n\nFigshare: two_dataset.doc, https://doi.org/10.6084/m9.figshare.14903142.45\n\nThis project contains the following extended data:\n\n• Smithson and Verkuilen dataset: anxiety test scores from a group of 166 healthy women\n\n• Rahman et al., dataset: lifetime (in days) of 30 electronic devices\n\nThe authors of this work sought and obtained consent to use the dataset from the respective authors. The dataset from Smithson and Verkuilen37 was originally published on Smithson's website and saved under Example 2.text. Rahman et al.'s dataset is available in their publication.38 The dataset was published in an open repository with the authors' permission.\n\n\nGrant information\n\nThis work was supported by Digiteknologian TKI-ymparisto project A74338 (ERDF, Regional Council of Pohjois-Savo).\n\n\nCompeting interests\n\nNo competing interests were disclosed.",
"appendix": "References\n\nLehmann EL: The power of rank tests. Ann. Math. Stat. 1953; 24: 23–43. Publisher Full Text\n\nGupta RC, Gupta P, Gupta RD: Modeling failure time data by Lehmann alternatives. Communications in Statistics-Theory and Methods. 1998; 27: 887–904. Publisher Full Text\n\nCordeiro GM, De Castro M: A new family of generalized distributions. J. Stat. Comput. Simul. 2011; 81: 883–893. Publisher Full Text\n\nArshad MZ, Iqbal MZ, Anees A, et al.: New Bathtub Shaped Failure Rate Model: Properties, and Applications to Engineering Sector. Pak. J. Statist. 2021; 37: 57–80.\n\nArshad MZ, Iqbal MZ, Ahmad M: Exponentiated Power Function Distribution: Properties and Applications. JSTA. 2020; 19: 297–313. Publisher Full Text\n\nAwodutire PO, Nduka EC, Ijomah MA: Lehmann Type II Generalized Half Logistic Distribution: Properties and Application. 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PubMed Abstract | Publisher Full Text\n\nRahman MM, Al-Zahrani B, Shahbaz SH, et al.: Cubic Transmuted Uniform Distribution: An Alternative to Beta and Kumaraswamy Distributions. EJPAM . 2019; 12: 1106–1121. Publisher Full Text\n\nAarset MV: How to identify bathtub hazard rate. IEEE. Trans. Reliab. 1987; 36: 106–108. Publisher Full Text\n\nKumaraswamy P: A generalized probability density function for double-bounded random processes. J. Hydrol. 1980; 46: 79–88. Publisher Full Text\n\nKhan MS, King R, Hudson IL: Transmuted Kumaraswamy distribution. SiT. 2016; 17: 1–28. Publisher Full Text\n\nMuhammad M: A New Lifetime Model with a Bounded Support. Asian J. Math. 2017; 7: 1–11. Publisher Full Text\n\nKhan MS: Transmuted Generalized Power Weibull Distribution. Thailand. Stat. 2018; 16: 156–172.\n\nKhan MS, King R, Hudson IL: Some Structural Properties of the Transmuted Lindley Distribution with Application to Women's Anxiety Data. 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}
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[
{
"id": "119893",
"date": "17 Jan 2022",
"name": "Lazhar Benkhelifa",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe linear representations of CDF and PDF are based on some infinite sums. The authors need to prove that these sums converge for all or some values of the parameters.\n\nIn page 6, it is better to present the proofs of the propositions 1 and 2.\n\nIn page 6, is it possible to give mathematical proof about the shapes of the pdf and hazard rate function?\n\nIn pages 7-8, what are the ranges of the skewness and kurtosis for the new model?\n\nIn order to check the accuracy of the expressions of the rth moments, the authors need to compare the obtained results with the numerical results based on Monte Carlo approximations.\n\nThe authors need to show that the introduced distribution is identifiable with respect to parameter vector ϑ=(α,β)^{T}.\n\nThe authors discussed only one estimation methods. Can they attempt others estimation methods and compare their performances?\n\nThe description of the estimation procedure is a little bit too brief. It would be good to expand on the algorithm used to estimate the model parameters (are they using a Newton-Raphson algorithm with the exact Hessian matrix?).\n\nThe likelihood equations are given in page 15. Obviously, they have not got an explicit solution and the MLE must be numerically calculated. At this point, the authors should do a study (theoretical or at least numerical): have these equations always got a solution? if so, is it unique? In this context, the authors must give more details about this issue, considering some plots of the log-likelihood (profile log-likelihood) function.\n\nConfidence intervals for the parameters were based on asymptotic normality. In page 15, the authors should add the asymptotic normality of ϑ=(α,β)^{T}. Also, the authors should add the interval estimates for ϑ in real data sets.\n\nAt the end of Section (Application), more information about the numerical computation will be useful. For example, does the procedure involve iteration and/or initialization? What statistical package was used to obtain the results in this paper?\n\nThe comparison between the AIC, BIC and CAIC are important but not sufficient to decide between one or another distribution. The authors should use the Cramer-von Mises and Anderson-Darling statistics with their p-values to decide which is the best distribution.\n\nA standard tool to evaluate the fit of a distribution is the P-P plot. Add this plot, in the application section.\n\nIn practice, much lifetime data is subject to censoring, but there is no discussion of this.\n\nAt least a short discussion on the estimation under Bayesian paradigm would be really nice. This would really strengthen the content of the paper.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "314601",
"date": "10 Sep 2024",
"name": "Matthew Iwada Ekum",
"expertise": [
"Reviewer Expertise Probability distributions and Linear model. Theory and 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\nResearch Paper Review The authors' work title is appropriate as “A better approach to discuss medical science and engineering data with a modified Lehmann Type – II model”. The work is well organized and follows a logical sequence as expected. However, the following comments are very necessary and important before the paper can be indexed.\nThe literature review, especially the empirical review needs more work on Power Function distribution and its applications. So, it is advisable to include more empirical works in the study to strengthen the background of the study. See the following work. Ref 1, Ref 2 , Ref 3, Ref 4 Write the objective in prose. Do not itemize it; it is not a seminar paper or project. Explain who would benefit from this study, i.e. the significance of the Study. Include this after the objectives, before the last paragraph. Major properties and characterization of the distributions have been established but to improve this work as a specific distribution from a new family, you are expected to show the stochastic ordering of the distribution. Also, show the relationship of this distribution with existing distributions or at least how it can be transformed to its parent distributions. See this work for a guide Ref 5 Also include areas of further study such as its regression model and inferences using the new distribution. See this distribution. See this paper as an example of a further study Ref 6 This present work developed a new distribution by combining Power Function (PF) distribution with Lehmann Type II. All the suggested references are based on combining PF with other distributions. So, they can have more arguments to support the usefulness of PF.The stochastic ordering is very important for a new distribution. I also referred the authors to a work where stochastic ordering was used as a guide. They may decide to use other materials as guide for the stochastic ordering. The stochastic ordering is very important.The essence of developing a model is to apply it in Statistical inferences like regression and hypothesis testing using real life data. So, even if this present work does not extend to regression model, suggestions can be given to extend it to regression in further studies. Normal-PF was also shown as an example.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-823
|
https://f1000research.com/articles/10-822/v1
|
17 Aug 21
|
{
"type": "Software Tool Article",
"title": "Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality",
"authors": [
"Davide Albanese",
"Claudio Donati",
"Claudio Donati"
],
"abstract": "Metagenomic sequencing allows large-scale identification and genomic characterization. Binning is the process of recovering genomes from complex mixtures of sequence fragments (metagenome contigs) of unknown bacteria and archaeal species. Assessing the quality of genomes recovered from metagenomes requires the use of complex pipelines involving many independent steps, often difficult to reproduce and maintain. A comprehensive, automated and easy-to-use computational workflow for the quality assessment of draft prokaryotic genomes, based on container technology, would greatly improve reproducibility and reusability of published results. We present metashot/prok-quality, a container-enabled Nextflow pipeline for quality assessment and genome dereplication. The metashot/prok-quality tool produces genome quality reports that are compliant with the Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard, and can run out-of-the-box on any platform that supports Nextflow, Docker or Singularity, including computing clusters or batch infrastructures in the cloud. metashot/prok-quality is part of the metashot collection of analysis pipelines. Workflow and documentation are available under GPL3 licence on GitHub.",
"keywords": [
"metagenome-assembled genome",
"MAG",
"genome quality",
"MIMAG",
"dereplication",
"completeness",
"contamination",
"nextflow",
"docker"
],
"content": "Introduction\n\nGenome-resolved metagenomics is one of the most promising approaches to identify and characterize novel microbial species. Large-scale environmental and host-associated studies demonstrated how metagenomics can expand our knowledge of uncultivated prokaryotes, recovering thousands of metagenome-assembled genomes (MAGs) of new archaeal and bacterial species.1,2 For this reason, automated and reproducible methods for assessing the quality of MAGs play a critical role.\n\nTo recover MAGs, metagenomic sequence reads are first assembled into contigs using specific algorithms.3 Contigs are then processed by tools like MetaBAT 24 or VAMB5 that use tetra-nucleotide frequency (TNF) profiles and abundance patterns to group sequences that are likely to belong to the same organism (binning). Binning improves the interpretability of metagenomic data, but at the same time represents (together with assembly) a significant source of error.6 Manual refinement7 can increase the quality of resulting MAGs, but undermines the reproducibility of the analysis and is unfeasible for large-scale studies.\n\nThe recently introduced Minimum Information about a Metagenome-Assembled Genome (MIMAG) standard8 recommends a set of measures for assessing the quality of MAGs. This comprises basic assembly statistics (e.g. N50), genome completeness, contamination and the presence of ribosomal RNA (rRNA) and transfer RNA (tRNA) genes.\n\nRecovering this information involves computational pipelines composed of a series of specialized tools that are often difficult to use and install. Moreover, each task can require parameters and custom scripts that are often poorly documented, making reproducibility of results challenging. Tools and standards such as Galaxy,9 Nextflow10 and the Common Workflow Language,11 coupled with container technologies like Docker, allows researchers to circumvent these issues, providing a way to build, run and share reproducible computational workflows.12\n\nWe present metashot/prok-quality, a comprehensive and easy-to-use Nextflow pipeline for assessing the quality of draft prokaryotic genomes. Metashot/prok-quality reports the quality statistics and estimates recommended by the MIMAG standard. Basic assembly statistics, completeness, both redundant and non-redundant contamination, rRNA and tRNA genes are reported in a single, comprehensive table.\n\n\nMethods\n\nMetashot/prok-quality is written using the Nextflow domain-specific language. Nextflow is a framework for building scalable scientific workflows using containers, allowing implicit parallelism on a wide range of computing systems. Reproducibility is guaranteed by versioned Docker images, which enclose software applications together with their dependencies, allowing isolation from the host environment and portability across platforms. metashot/prok-quality v1.2.0 is composed of five main modules (Figure 1) and includes several custom scripts, designed to manipulate the output of the different tasks.\n\nThe workflow takes a series of genomes (input bins) in FASTA format and returns: i) a tab-separated values (TSV) file including, for each input genome, the quality information recommended by the MIMAG standard (genome info table); ii) a directory containing the bins filtered according the completeness and contamination thresholds; iii) a TSV file listing the cluster membership of each genome after the dereplication (optional) and iv) a directory containing the cluster representatives. The original outputs of each task (e.g. Barrnap’s GFF output) are also reported in dedicated folders.\n\nSoftware included in version 1.2.0:\n\nCheckM v1.1.2. Several tools have been developed for the assessment of completeness and contamination of MAGs. The proposed workflow includes the widely used CheckM13 which estimate these metrics using ubiquitous and lineage-specific, single-copy core genes (SCGs) catalogs. CheckM is also used to recover the basic assembly statistics.\n\nGUNC v1.0.1. SCG-based tools like CheckM can have very low sensitivity towards contamination by fragments from unrelated organisms (non-redundant contamination).6 In order to circumvent this problem, the recent GUNC14 tool was added to the pipeline. GUNC quantifies the lineage homogeneity of contigs with respect to the full gene complement, accurately detecting chimerism induced by both redundant and non-redundant contamination.\n\nBarrnap v0.9. The presence of 5S, 23S and 16S rRNA genes is predicted by the BAsic Rapid Ribosomal RNA Predictor (Barrnap) using Hidden Markov models (HMM). Both bacteria and archaea databases are used.\n\ntRNAscan-SE v2.0.6. tRNA genes are searched using tRNAscan-SE,15 using bacteria and archaea covariance models. The number of tRNAs and tRNA isotypes found is reported.\n\ndRep v2.6.2. Dereplication is a procedure that groups the input genomes according to their whole-genome similarity, using metrics such as the Average Nucleotide Identity16 (ANI). Dereplication dramatically simplifies downstream analysis when the input genomes come from different sources.17 In the proposed workflow, filtered genomes (genomes that pass completeness, contamination and GUNC filters) are optionally dereplicated using dRep.18 For each cluster, dRep reports, as the cluster representative, the best-scoring MAG using the CheckM’s quality estimates. The score is computed using the following formula:\n\nscore = completeness − 5 × contamination + 0.5 × log(N50)\n\nPython3 custom scripts. The workflow includes three Python3 custom scripts, designed to manipulate the output of the different steps. The scripts make use of NumPy,17 Pandas and scikit-learn libraries.\n\nmetashot/prok-quality v1.2.0 requires Docker and Nextflow (tested on v20.07.1). Alternatively, the Singularity container engine can be used in place of Docker. At least 70 GB of RAM is required, a limit imposed by CheckM (v1.1.2). The workflow can run in a workstation with 16 GB of RAM using the options --reduced_tree and --max_memory 16.GB.\n\n\nUse case\n\nAs mentioned above, metagenome assembly tools combine the sequence reads into larger regions called contigs. Recently, many metagenomic assembly tools have been proposed. Amongst these, metaSPAdes3 and MEGAHIT19 have been shown to be able to efficiently handle large-scale short read sequencing data, producing high-quality contigs. Metagenomics contigs are then processed by tools like MetaBAT 24 in order to group sequences that are likely to belong to the same organism (binning). After binning, it is essential to assess the quality of the resulting candidate draft genomes.\n\nIn this section, we will show how to assess the quality of draft prokaryotic genomes using metashot/prok-quality. Given a series of candidate genomes in FASTA format stored in the “bins” directory, the version 1.2.0 of the workflow can be run with the following command line:\n\nA series of files and directories are created in the output directory results. The main output file is “genome_info.tsv”. This TSV file contains, for each input genome, a set of quality statistics, including completeness, contamination, GUNC filter, N50, rRNA genes found, number of tRNA and tRNA types. The columns included in this file are:\n\n• Genome: the genome filename;\n\n• Completeness, Contamination, Strain heterogeneity: CheckM estimates;\n\n• GUNC pass: if a genome does not pass GUNC analysis it means it is likely to be chimeric;\n\n• Genome size (bp), ... , # predicted genes: basic genome statistics (see https://github.com/Ecogenomics/CheckM/wiki/Genome-Quality-Commands#qa);\n\n• 5S rRNA, 23S rRNA, 16S rRNA: “Yes” if the rRNA gene was found;\n\n• # tRNA, # tRNA types: the number of tRNA and tRNA types found, respectively.\n\nThe directory “filtered” contains the genomes (in FASTA format) filtered according to --min_completeness, --max_contamination and --gunc_filter options (see below). The TSV file “genome_info_filtered.tsv” includes the same information as “genome_info.tsv”, but for the filtered genomes only. Representative (dereplicated) genomes (default ANI threshold 0.95) are reported in the “filtered_repr” folder. The companion file “derep_info.tsv” contains the summary of the dereplication procedure, including the genome filename, the cluster ID and the representativeness. A set of secondary directories contains the original output of each tool included in the pipeline:\n\n• checkm: contains the original CheckM's “qc” file;\n\n• gunc: contains the original GUNC output file;\n\n• barrnap: includes the predicted rRNA sequences for bacteria (.bac) and archaea (.arc) models in GFF and FASTA formats;\n\n• trnascan_se: includes the predicted tRNA sequences for bacteria (.bac) and archaea (.arc) models in TSV and FASTA formats;\n\n• drep: dRep original data tables, figures and log file.\n\nThe command options are:\n\nInput and output\n\n• --genomes: input genomes/bins in FASTA format (default “data/*.fa”);\n\n• --ext: FASTA files extension, files with different extensions will be ignored (default “fa”);\n\n• --outdir: output directory (default “results”);\n\n• --gunc_db: the GUNC database. If “none” the database will be automatically downloaded and will be placed the output folder (gunc_db directory) (default “none”);\n\n• --reduced_tree: reduce the memory requirements to approximately 14 GB, set --max_memory to 16.GB (default false);\n\n• --checkm_batch_size: run CheckM on “checkm_batch_size” genomes at once in order to avoid memory issues, see https://github.com/Ecogenomics/CheckM/issues/118 (default 1000);\n\n• --gunc_batch_size: run GUNC on “gunc_batch_size” genomes at once (default 100);\n\n• --min_completeness: discard sequences with less than “min_completeness” % completeness (default 50);\n\n• --max_contamination: discard sequences with more than “max_contamination” % contamination (default 10);\n\n• --gunc_filter: if true, discard genomes that do not pass the GUNC filter (default false);\n\n• --skip_dereplication: skip the dereplication step (default false);\n\n• --ani_thr: ANI threshold for dereplication (> 0.90) (default 0.95);\n\n• --min_overlap: minimum required overlap in the alignment between genomes to compute ANI (default 0.30);\n\n• --max_cpus: maximum number of CPUs for each process (default 8);\n\n• --max_memory: maximum memory for each process (default 70.GB);\n\n• --max_time: maximum time for each process (default 96.h).\n\n\nSoftware availability\n\nSource code available from: https://github.com/metashot/prok-quality\n\nArchived source code at time of publication: http://doi.org/10.5281/zenodo.4475355.20\n\nLicense: GPL-3.0\n\nDocker image definitions available from: https://github.com/metashot/docker\n\n\nData availability\n\nZenodo: metashot/prok-quality v1.2.0 with test data, v1.2.0, http://doi.org/10.5281/zenodo.4475355.3\n\nThis project contains test data and workflow documentation.\n\nData are available under the terms of GNU General Public License version 3 (GPL-3).\n\nDocker Hub: metashot docker images, https://hub.docker.com/u/metashot\n\nThis registry contains the pre-built Docker images\n\nGitHub: metashot/docker, https://github.com/metashot/docker\n\nThis project contains Docker image definitions.",
"appendix": "Acknowledgements\n\nThe authors wish to thank Giuseppe Cossu and the Information Technology team of the Fondazione Edmund Mach for technical support.\n\n\nReferences\n\nPasolli E, Asnicar F, Manara S, et al.: Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell. 2019 Jan 24; 176(3): 649–62.e20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParks DH, Rinke C, Chuvochina M, et al.: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017 Nov; 2(11): 1533–1542. PubMed Abstract | Publisher Full Text\n\nNurk S, Meleshko D, Korobeynikov A, et al.: metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017 May; 27(5): 824–834. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKang DD, Li F, Kirton E, et al.: MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019 Jul 26; 7: e7359. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNissen JN, Johansen J, Allesøe RL, et al.: Improved metagenome binning and assembly using deep variational autoencoders. Nat Biotechnol. 2021 Jan 4; Publisher Full Text\n\nChen L-X, Anantharaman K, Shaiber A, et al.: Accurate and complete genomes from metagenomes. Genome Res. 2020 Mar; 30(3): 315–333. Publisher Full Text\n\nShaiber A, Eren AM: Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories. MBio. 2019 Jun 4; 10(3). PubMed Abstract | Publisher Full Text | Free Full Text\n\nBowers RM, Kyrpides NC, Stepanauskas R, et al.: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017 Aug 8; 35(8): 725–731. Publisher Full Text\n\nAfgan E, Baker D, Batut B, et al.: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 2018 Jul 2; 46(W1): W537–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11; 35(4): 316–319. PubMed Abstract | Publisher Full Text\n\nStrozzi F, Janssen R, Wurmus R, et al.: Scalable Workflows and Reproducible Data Analysis for Genomics. Methods Mol Biol. 2019; 1910: 723–745. PubMed Abstract | Publisher Full Text\n\nEwels PA, Peltzer A, Fillinger S, et al.: The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar; 38(3): 276–278. PubMed Abstract | Publisher Full Text\n\nParks DH, Imelfort M, Skennerton CT, et al.: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul; 25(7): 1043–1055. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOrakov A, Fullam A, Coelho LP, et al.: GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes. bioRxiv. 2020. Reference Source\n\nChan PP, Lowe TM: tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019; 1962: 1–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoris J, Konstantinidis KT, Klappenbach JA, et al.: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007 Jan; 57(Pt 1): 81–91. PubMed Abstract | Publisher Full Text\n\nEvans JT, Denef VJ: To Dereplicate or Not To Dereplicate? mSphere. 2020 May 20; 5(3). Publisher Full Text\n\nOlm MR, Brown CT, Brooks B, et al.: dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017 Dec; 11(12): 2864–2868. Publisher Full Text\n\nLi D, Liu C-M, Luo R, et al.: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.2015. PubMed Abstract | Publisher Full Text\n\nAlbanese D, Donati C: metashot/prok-quality v1.2.0 with test data (Version 1.2.0). Zenodo. 2021, January 28. Publisher Full Text"
}
|
[
{
"id": "100039",
"date": "24 Nov 2021",
"name": "Thomas S. B. Schmidt",
"expertise": [
"Reviewer Expertise metagenomics",
"microbiome"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present ‘prok-quality’, a one-stop-shop Nextflow workflow for prokaryotic genome quality assessment, wrapping several state-of-the-art tools into a user-friendly pipeline. prok-quality fills two relevant niches: it provides an easy to install, easy to use interface to relevant bioinformatics tools for non-expert users; and a portable, scalable workflow to process datasets of increasing sizes.\nThe code is available on github. We were able to download, install and use the workflow as advertised. We have only very minor comments, to be addressed at the authors’ discretion:\n\nThe authors restrict their discussion to metagenome-assembled genomes. However, there is no inherent reason why the prok-quality workflow shouldn’t be used for reference genomes or isolate sequencing as well, and this may be worth emphasizing. In practice, many users work on large integrated datasets of MAGs and reference genomes, where fast, consistent quality control and clustering using a workflow such as prok-quality is highly relevant.\n\nIn the bigger picture of an entire genome-resolved metagenomics workflow, from raw reads to biological analyses, prok-quality covers a reasonable chunk: the quality control and ‘dereplication’ (clustering) of genomes. That way, it can be used as a module, independently of upstream (assembly & binning) and downstream (annotation, analysis) tool choices. However, in our view, prok-quality would benefit from the addition of a taxonomic classifier, e.g. GTDB-tk. Taxonomic information would fit in very well with the reported quality metrics; but in particular, the workflow could (optionally) provide consensus taxonomies for dRep 95% ANI clusters which would greatly add value for non-expert users.\n\nMinor: the GUNC preprint has in the meantime been peer reviewed and published (Orakov et al. (20211)).\n\nMinor: An option to switch from running with docker to running with singularity (e.g. '-profile singularity' with config profiles) would greatly enhance the ease of using this workflow as some clusters prohibit use of docker.\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": "100040",
"date": "31 Jan 2022",
"name": "Denis Baurain",
"expertise": [
"Reviewer Expertise bioinformatics",
"including genomic contaminations"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 tool is useful and works as advertised by the authors. The manuscript reads well and I only have very minor comments.\nFunctionality:\nI tested metashot/prok-quality on a HPC facility running the SLURM grid engine. The authors' instructions were nearly enough to make it work on my first attempt. However, getting right the Singularity options was a little trickier than expected. In this regard, Docker is easier to use but generally not available in HPC environments. I contacted the authors by email (posing as a regular user) and they replied immediately, confirming that the reported issue was on my side and not a bug in their package. Unfortunately, I had to attend more pressing matters and only got back to the issue recently, hence this delayed review report. I apologize for this. For the record, here are the lines required to run the tool successfully on my system:\n# in prok-quality/nextflow.config singularity.enabled = true singularity.cacheDir = \"$PWD\" singularity.autoMounts = false singularity.runOptions = \"-B /path-to-user-home/prok-quality-1.2.0_with_test_data/ -B /tmpscratch/username\"\nThe interface of metashot/prok-quality is straightforward and well designed, with attention to details, such as the possibility to deal with limited RAM (--reduced_tree option for CheckM) and to economize resources (--gunc_db option to avoid downloading the GUNC database multiple times). I only have a minor complaint: the --genomes option expects input filenames but if these do not match the --ext option (e.g., .fasta instead of .fa), infiles are silently ignored. In my view, the --ext option would make more sense with a --genomes option expecting an input directory. Indeed, when infiles are specified, there is no real need for filtering.\nThe tool's outputs are easy to understand and well documented. Testing it with default thresholds on a chimerical bacterial genome (Cornet and Baurain 2022, Genome Biology, in press) indeed flags it as contaminated and excludes it from the downstream dereplication step. In contrast, the two corresponding clean genomes undergo through all the steps of the pipeline, as expected.\nManuscript:\nAbstract:\nEukaryotic sequences can be found in metagenomic samples. These are more difficult to deal with, but should be mentioned in the second sentence.\n\nabstract: \"... platform that supports Nextflow, Docker or Singularity\" should read \"... platform that supports Nextflow and either Docker or Singularity\".\n\nIntroduction: I would suggest adding a small paragraph about the need to use multiple tools when assessing genomic contaminations. This paragraph could include (and slightly expand) the rationale for GUNC (presently located in the Methods). For some ideas, see Lupo et al. (20211).\n\nMethods:\nSome sentences are either too much or too little, for example those about the rationale for dRep. I think that one more sentence would help and it would be better to move the whole idea of dereplication at the end of the Introduction. Indeed, Methods should not explain concepts.\n\nFigure 1: The figure is nice. If I had to quibble, I would say that \"filtered bins\" can be misleading: here, the authors mean \"bins satisfying their criteria of completeness and contamination\" whereas one could imagine that they mean \"bins cleaned up from contaminating sequences\" (i.e., bins are passed \"as is\" and are not modified by the pipeline). Moreover, showing on the figure the parameters controlling the thresholds would help the reader to realize that they can be user-specified. Finally, a word is missing in the legend: \"according the completeness..\" should read \"according to the completeness...\"\n\nThe score formula should specify if completeness and contamination metrics are computed in percentage or not. Moreover, it might be interesting to make it user-tweakable (only a suggestion).\n\nUse case: I am not sure about the position of the backslash chars in the code snippet. I would have put them at end of lines.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-822
|
https://f1000research.com/articles/10-821/v1
|
17 Aug 21
|
{
"type": "Research Article",
"title": "Cost-effectiveness of hydroxychloroquine versus placebo for hand osteoarthritis: economic evaluation of the HERO trial",
"authors": [
"Sarah J Ronaldson",
"Ada Keding",
"Puvan Tharmanathan",
"Catherine Arundel",
"Sarah R Kingsbury",
"Philip G Conaghan",
"David J Torgerson",
"Ada Keding",
"Puvan Tharmanathan",
"Catherine Arundel",
"Sarah R Kingsbury",
"Philip G Conaghan",
"David J Torgerson"
],
"abstract": "Background: An economic evaluation alongside the Hydroxychloroquine Effectiveness in Reducing symptoms of hand Osteoarthritis (HERO) trial was undertaken to assess the cost-effectiveness of hydroxychloroquine compared with placebo for symptomatic treatment of hand osteoarthritis for patients with at least moderate hand pain and inadequate response to current therapies.\nMethods: A trial-based cost–utility analysis was undertaken from the perspective of the UK National Health Service and Personal Social Services over a 12-month time horizon, using evidence from 248 participants included in the HERO trial, conducted in England. Patient-level data were collected prospectively over a 12-month period, using participant-completed questionnaires and investigator forms, to collect healthcare utilisation, costs and quality-adjusted life years (QALYs) using the EQ-5D-5L. The base-case analysis was conducted on an intention-to-treat basis and used multiple imputation methods to deal with missing data. Results were presented in terms of incremental cost-effectiveness ratios (incremental cost per QALY) and net health benefit, with uncertainty surrounding the findings explored using cost-effectiveness acceptability curves.\nResults: The base-case analysis estimated slightly lower costs on average (−£11.80; 95% confidence interval (CI) −£15.60 to −£8.00) and marginally fewer QALYs (−0.0052; 95% CI −0.0057 to −0.0047) for participants in the hydroxychloroquine group versus placebo group at 12 months. The resulting incremental cost-effectiveness ratio of £2,267 per QALY lost indicated that although costs were saved, health-related quality of life was lost. Even assuming symmetrical preferences regarding losses and gains for health benefits, the findings do not fall within the cost-effective region. Similar findings arose for analyses conducted from the societal perspective and using complete cases only.\nConclusions: This economic evaluation indicates that hydroxychloroquine is unlikely to provide a cost-effective pain relief option for improving health-related quality of life in adult patients with moderate-to-severe hand osteoarthritis.",
"keywords": [
"economic evaluation",
"hand osteoarthritis",
"hydroxychloroquine",
"randomised controlled trial",
"cost-effectiveness analysis",
"cost-utility analysis"
],
"content": "Introduction\n\nHand osteoarthritis (OA) is a common, chronic disease, with newly diagnosed cases of hand OA estimated to occur in 2.4 per 1000 at-risk adults aged 45 and over in England each year.1 More generally, OA poses an increasing burden to health services,2 and is associated with substantial costs.3–5 These high costs arise as direct health-related costs, in the form of long-term pain control treatments, surgery and rehabilitation, and also indirect costs, such as productivity loss and costs relating to home care or childcare.4,5 The annual cost in the UK for topical nonsteroidal anti-inflammatories (NSAIDs) and oral NSAIDs, two of the most commonly used pharmacological therapies for OA, was estimated to be £19.2 million and £25.7 million respectively, in 2010 prices.3 In addition to the financial burden, OA also poses a considerable burden in terms of morbidity, sometimes considered as ‘intangible costs’, through a reduction in health-related quality of life experienced by OA patients.3\n\nIn order to improve the quality of life of hand OA patients, different management options are available; however, there is a paucity of effective treatments, with side effects often accompanying treatment.6–8 An option that has been explored in the past leading to unlicensed use is hydroxychloroquine (HCQ), which is established as a treatment for rheumatoid arthritis with acceptable safety.9,10 The Hydroxychloroquine Effectiveness in Reducing symptoms of hand Osteoarthritis (HERO) trial assessed the use of HCQ versus placebo as a treatment for people with at least moderate symptomatic and radiographic hand OA and inadequate response to current therapies (including NSAIDs and opioids). The clinical findings of the HERO trial demonstrated that HCQ was no more effective than placebo for pain relief when added to usual care, shown using a primary outcome of hand pain severity over the past two weeks as measured on an eleven-point (0 to 10) numerical rating scale (NRS) at six months.11 Despite the lack of clinical effectiveness, it is useful to summarise the economic findings to provide evidence that can help guide the efficient allocation of healthcare resources, and also to present the healthcare resource use and health-related quality of life associated with the population of patients included in the trial. Such findings may be useful for future evaluations.\n\nThe aim of this economic analysis was to evaluate the cost-effectiveness of HCQ versus placebo as a symptomatic treatment for patients over the age of 18 with at least moderately symptomatic hand OA and inadequate response to current therapies. The economic analysis was conducted over a 12-month time horizon from the perspective of the UK National Health Service (NHS) and Personal Social Services (PSS), and comprised (i) a cost-utility analysis, in terms of the cost per quality-adjusted life year (QALY) and (ii) a cost-effectiveness analysis, in terms of the cost per unit of reduction in pain score.\n\n\nMethods\n\nThe HERO trial was a randomised, double-blind, placebo-controlled trial with an economic evaluation conducted alongside. Patients with symptomatic and radiographic hand OA aged 18 years or over were recruited from 13 primary and secondary care centres in England; description of the study design and interventions are available in full elsewhere.11,12 A total of 248 participants were included in the trial; participants were aged 62.7 years on average (ranging from 40 to 88 years), with 81.9% being female. The trial involved 12-month follow up of the use of HCQ (200–400 mg) or placebo, in addition to ongoing usual care, where participants were randomised on a 1:1 basis. The study was registered with International Standard Randomised Controlled Trial Number ISRCTN91859104 on 17 October 2012, and received approval by Leeds East Research Ethics Committee (12/YH/0151) and the UK Medicines and Health Regulatory Authority. All participants provided written informed consent prior to screening and involvement in the trial.\n\nA within-trial economic analysis was undertaken from the perspective of the UK NHS and PSS, with results presented in terms of the incremental cost per QALY (cost–utility analysis), and the cost per unit of reduction in pain score (cost-effectiveness analysis), which used the trial’s primary outcome of hand pain severity. Patient-level data were collected for costs (healthcare resource use, medication use, and of HCQ drug) and health outcomes (EuroQol EQ-5D-5L and hand pain severity) over the 12-month follow up period, using questionnaires completed by participants at baseline, six months and 12 months. The base-case analysis was undertaken using multiple imputation to deal with missing data, with complete case analysis explored as a sensitivity analysis. A secondary analysis from the broader societal perspective was also conducted.\n\nQALYs were estimated by participants’ completion of the EQ-5D-5L (EuroQol Group, Rotterdam, The Netherlands)13,14 in self-completed questionnaires at baseline, six and 12 months follow up. The EQ-5D-5L is a preference-based measure that provides a descriptive profile of an individual’s health state15 and comprises five dimensions (mobility, self-care, usual activities, pain/discomfort and anxiety/depression) which each have five possible levels of response (no, slight, moderate, or severe problems, or unable to/extreme problems). The crosswalk value set developed by van Hout et al.16 was utilised for the estimation of utilities. A utility score of one indicates perfect health, a utility of zero indicates states equivalent to death, and negative scores indicate states considered to be worse than death. QALYs were calculated by plotting the utility scores at each of the three time points and estimating the area under the curve,17,18 with adjustment made for baseline utility.19 In addition to the evaluation of QALYs via a cost-utility analysis, the primary clinical outcome of the trial, hand pain severity, was also investigated via a cost-effectiveness analysis. Specifically, the reduction in hand pain severity was measured using a NRS (0 to 11, where higher scores represent worse levels of pain) and assessed by calculating the difference in hand pain NRS at 6 months and hand pain NRS at baseline.\n\nParticipants were asked about their utilisation of healthcare services in relation to their hand or hand pain via self-completed questionnaires at baseline, six and 12 months. Resource use items included in the questionnaire aimed to represent relevant services used by patients with hand OA, specifically within primary care (visits to the general practitioner (GP), nurse, and other primary care services), community care (physiotherapist and occupational therapist visits, and other community care services) and in the hospital setting (outpatient attendances, day case visits, and accident and emergency attendances). Total resource use per participant for the duration of the 12-month trial period was calculated by multiplying each resource use item by the corresponding unit cost (Table 1); unit costs were derived from established national costing sources.20,21 Participants were also asked via the study questionnaires about personal expenses, namely travel and childcare costs relating to healthcare appointments and over-the-counter medication costs, which fed into the secondary analysis, undertaken from a broader societal perspective. Unit costs were not required for these costs, as participants were asked to specifically state the amount of money spent on these, rather than the number of resources used.\n\nParticipants received a daily dose of HCQ in either 200, 300 or 400 mg (for 300 mg, alternating doses of 200 mg and 400 mg were taken); for costing purposes, participants were assumed to continue on the same dose throughout the study period (which was, in fact the case, with the exception of one participant). Unit costs of HCQ and medications used by participants, as recorded by study investigators, were obtained from the British National Formulary.22 The HCQ costing was based on the net price of HCQ sulfate 200 mg (60-tablet pack) being £5.15.23 The cost of HCQ use over the 12-month period was applied, unless there was information recorded regarding the participant stopping/withdrawing from treatment. The cost of placebo tablets represented a research cost and hence excluded from the costings. Information regarding participants’ use of oral and topical medication was recorded by study investigators at regular intervals during the trial period; investigator forms at 3, 6, 9 and 12 months were used for the medication costing. To attach costs to participants’ medication use, each medication was categorised (e.g. oral opioid, topical NSAID, antidepressant/neuropathic therapy), and within each category the average cost of the most commonly occurring medications was applied. A total medication cost per participant was generated by summing the cost of all medications used by the participant.\n\nThe base-case analysis was conducted on an intention-to-treat (ITT) basis; the two groups (HCQ versus placebo) were compared according to their initial random allocation, regardless of whether protocol deviations or withdrawals took place. Cost and outcome data were collected prospectively during the study and compared for the two groups over 12 months, hence discounting was not required. Costs are presented in UK £ sterling at 2015 prices and the analysis was undertaken in Stata 13© (StataCorp 2013, TX, USA) (RRID:SCR_012763); an open-access alternative is R (RRID:SCR_001905). The base-case analysis utilised a dataset generated via multiple imputation with chained equations and predictive mean matching to deal with missing data, based on the assumption that data were missing at random. The imputation model included baseline hand pain severity, concomitant analgesic use, average grip strength, body mass index (BMI), age and gender (all consistent with the clinical primary analysis model), baseline costs and baseline utility. A complete case analysis was also undertaken as a sensitivity analysis, where patients with any missing data were excluded, and available case analysis was used for initial exploration of the data.\n\nMean differences in costs and QALYs were compared for the two groups to assess the cost-effectiveness of HCQ versus placebo; estimates were produced using seemingly unrelated regression equations, with 95% confidence intervals estimated using bias corrected and accelerated bootstrap methods. The regression model adjusted for baseline utility and covariates consistent with those used in the trial’s statistical analysis. Differences between the groups were found to be statistically significant if P<0.05 and are presented alongside confidence intervals around the differences in costs and outcomes. Incremental cost-effectiveness ratios (ICERs) were used to present the findings, where appropriate, thereby indicating the additional cost per extra unit of benefit, calculated by dividing the mean difference in costs between trial groups by the mean difference in health outcomes. An ICER is compared with cost-effectiveness threshold values, to determine whether the intervention represents value for money. The NICE cost-effectiveness threshold for the UK ranges between £20,000 and £30,000 per QALY,24 hence both of these thresholds featured in the analysis. Results are also presented in terms of net health benefit (NHB)25 to aid interpretation of the findings; a positive NHB indicates an intervention is cost-effective, based on the cost-effectiveness threshold under consideration. The decision uncertainty surrounding the cost-effectiveness findings was explored using cost-effectiveness planes and cost-effectiveness acceptability curves (CEACs).26 A total of 5,000 estimates of incremental costs and incremental effects were generated, using non-parametric bootstrapping, and plotted on the cost-effectiveness plane. CEACs have been used to depict the probability of HCQ being cost-effective relative to placebo for a range of cost-effectiveness thresholds.\n\nIn addition to the cost-utility analysis described above, the cost-effectiveness analysis that explored the cost per unit of reduction in hand pain score utilised a mixed model, in line with the statistical model used for the clinical effectiveness analysis. This model accounted for baseline covariates and used an exchangeable covariance structure to account for the correlation of observations from the same patients over time.\n\n\nResults\n\nA total of 248 patients were recruited to the trial, of whom, 124 were randomised to receive HCQ and 124 to placebo. Complete utility data were available for 183 (73.8%) participants: 88 (71.0%) HCQ participants and 95 (76.6%) placebo participants, that is, all five dimensions of the EQ-5D-5L were completed at the three timepoints. Complete economic data, i.e. for both utilities and costs, were available for 76 participants (30.7%; 42 (33.9%) HCQ participants and 34 (27.4%) placebo participants). No deaths were reported during the trial period.\n\nMean healthcare resource use is summarised in Table 2 by group and timepoint, for all available cases. Most notable health services used by participants over the duration of the trial (sum of 6 month and 12 month resource use) were for: 2.7 GP visits (at GP practice), 2.2 outpatient clinic visits, 1.1 nurse visits (at GP practice), and 0.7 physiotherapist visits per participant, on average. At 12 months, participants in the HCQ group had fewer hospital outpatient visits, GP visits and nurse visits, but higher physiotherapist, occupational therapist, and accident and emergency (A&E) visits. In terms of the total mean cost for each resource use item, Table 3 summarises this according to group and the mean difference between groups, based on all available cases. Costs were found to be lower for the HCQ group, on average, for visits to the GP (at GP practice), nurse, A&E and hospital outpatient attendances, but were higher for GP visits (at home), physiotherapist and occupational therapist visits. However, none of the differences between groups were statistically significant.\n\nThe mean (standard deviation, SD) cost of HCQ for the 12-month period was £42.14 (£16.23), with HCQ costs estimated based on the following: seven participants prescribed a daily dose of 200 mg, 85 receiving 300 mg and 32 receiving 400 mg HCQ daily. A total of 90 HCQ participants received HCQ for the 12-month trial duration, whilst 34 received HCQ for durations less than this (ranging from 15 days to 308 days). Mean (SD) medication costs over the 12-month period were £282 (£235) for HCQ participants and £300 (£232) for placebo participants, for all available cases over the 12-month follow up. Hence, larger components of the total cost derived from hospital outpatient clinic appointments, GP visits (at GP practice) and medication costs, with costs of the drug, occupational therapist and physiotherapist visits being smaller cost drivers.\n\nUtility and quality-adjusted life years\n\nEstimation of the proportion of participants who reported the EQ-5D-5L levels (1 to 5) by dimension and group identified that the majority of participants (at least 95%) reported having problems in terms of pain/discomfort at all time points in both groups, whereas problems with self-care were reported for approximately a quarter to a third of participants (Table 4). Baseline utility was slightly higher in the HCQ group (0.615 versus 0.612 for HCQ and placebo, respectively) and the differences found between the groups at both 6 and 12 months were found to be very small (Table 5). The difference in QALYs at 12 months (HCQ−placebo), controlling for baseline utility, was 0.0012 (95% CI: −0.0251 to 0.0276), for available cases (n = 88 HCQ, n = 95 placebo). EQ-5D visual analogue scale (VAS) scores were found to be similar at baseline on average (72.4 for HCQ; 73.9 for placebo), and by 6 months, there was an increase for the HCQ group (to 74.5) compared with a slight reduction for the placebo group (73.6). However, by 12 months, the VAS score increased for both groups: 74.1 and 75.1 for the HCQ and placebo groups, respectively.\n\na The difference at 6 and 12 months is adjusted for baseline utility.\n\nHand pain score\n\nThe differences between treatment groups in terms of hand pain score were found to be small at each follow up time point and not statistically significant. At the primary endpoint of 6 months, patients in the HCQ group scored on average 0.16 points higher on the pain scale than those in the placebo group, therefore indicating worse pain for HCQ than placebo patients. As there was not a reduction found in terms of pain, it was not considered meaningful to calculate the ICER as originally intended, as it would have instead represented the cost per additional unit of pain.\n\nThe use of HCQ versus placebo was associated with a cost saving of £11.80 per participant, on average, in the base-case analysis (Table 6). In terms of the effect of HCQ on health-related quality of life, only marginal differences in QALYs were demonstrated. The base-case analysis found 0.005 fewer QALYs for participants in the HCQ group compared to the placebo group, on average, over the 12-month time horizon. It was therefore appropriate to report the results in terms of the cost per QALY lost, rather than per QALY gained that is more commonly seen; the resulting ICER showed cost savings of £2,267 per QALY lost, which implies that £2,267 would need to be saved in order to justify a loss of one QALY, i.e. costs are being saved but health is being lost. The NHB was found to be negative: −£92.30 (95% CI: −£102.11 to −£82.49) and −£144.34 (95% CI: −£158.67 to −£130.02) for the £20,000 and £30,000 cost-effectiveness thresholds, respectively.\n\na Adjusted for all covariates, including baseline utility & cost.\n\nb Difference between groups (HCQ – placebo) and 95% bias corrected and accelerated confidence intervals were estimated using seemingly unrelated regression.\n\nc Cost per QALY lost, which implies that £2,267 would need to be saved in order to justify a loss of one QALY, i.e. costs are being saved but health is being lost.\n\nFigure 1 illustrates the 5,000 bootstrap sample estimates, which are spread across the four quadrants of the cost-effectiveness plane quite evenly. The probability of HCQ being cost-effective for different willingness to pay thresholds is shown in Figure 2. For the NICE threshold of £20,000 per QALY, the probability of HCQ being cost-effective (under the base-case scenario) is 0.40, and similar at 0.39 for a threshold of £30,000 per QALY.\n\nThe secondary analysis undertaken from a societal perspective (incorporating personal costs for over-the-counter medication, childcare and travel for appointments) showed participants in the HCQ group incurred marginally lower mean costs (−£2.66; 95% CI: −£6.14 to £0.81), and slightly fewer QALYs (−0.010; 95% CI: −0.011 to −0.010) compared with placebo. The marginal cost saving for the HCQ group was not statistically significant. The resulting ICER was £265 per QALY lost, with a negative NHB at both the £20,000 threshold (−£199) and the £30,000 threshold (−£299).\n\nThe findings of the cost-utility analysis remained in the same direction for the complete case analysis, which comprised 76 participants (31% of total participants) who had complete economic data profiles, although a larger cost difference was found than in the base-case. Participants in the HCQ group incurred costs that were £50.95 lower than those in the placebo group, and 0.005 fewer QALYs, i.e. similar to the QALY difference in the base-case. However, the cost and QALY differences were not found to be statistically significant for the complete case analysis.\n\n\nDiscussion\n\nThis economic evaluation found that HCQ was associated with lower costs (mean cost reduction of −£11.80; 95% CI: −£15.60 to −£8.00), produced a marginally smaller mean QALY gain (−0.005 QALYs; 95% CI: −0.006 to −0.005 QALYs) and scored a worse level of pain on the hand pain scale at 6 months than placebo, on average. Hence, the differences in both costs and effectiveness were very small between the two groups. The corresponding ICER indicated a cost saving of £2,267 per QALY lost, implying that £2,267 would need to be saved in order to justify a loss of one QALY. Since the results showed a saving of £2,267 per QALY lost, HCQ is unlikely to be recommended from an economic perspective for hand OA management. The decision rule used in the UK is that where an intervention costs less than £20,000 per QALY when compared to its comparator, it is considered cost-effective. If we assume that decision makers have symmetrical preferences regarding losses and gains,27 then (where findings are in terms of the cost per QALY lost) an intervention would be considered cost effective if it could achieve cost savings greater than £20,000 per QALY forgone, when compared with the alternative. Considering this on the cost-effectiveness plane, a larger ICER in the south-west quadrant of the plane indicates that a larger cost saving is associated with each unit of forgone health benefit, therefore an ICER that exceeds the cost-effectiveness threshold is preferred.28\n\nThe study adds to the evidence base around management of hand OA, in finding that HCQ was not a cost-effective option and no more effective compared with placebo for pain relief of radiographic OA patients who have moderate-to-severe hand pain. Thereby, providing further evidence to reconsider continued use of HCQ in this patient group in line with the clinical findings of the trial.11 Additionally, the more detailed data regarding healthcare utilisation and health-related quality of life for the hand OA patients included in this study is of potential use for future studies or models. Hence the detailed breakdown of the EQ-5D-5L responses and resource use at the different time points have been provided. The economic evaluation considered costs and outcomes encountered over a 12-month time horizon. Analysis over a longer period of time may identify further costs that occur in the long-term, such as drug monitoring costs. For instance, if HCQ is used in the long-term, patients require regular ophthalmology screening over time due to the associated risk of retinopathy.29 Hence there are other potential costs that were not captured in the present analysis.\n\nA low proportion of participants (31%) had complete economic data profiles. The cumulative nature of the costs and QALYs that constitute the complete case analysis means that the economic profile is considered incomplete if only one cost item is missing. The study included several resource use items, and the ‘other’ resource use responses were often left blank (i.e. classed as missing), hence all data for the participant is lost using complete case analysis. The occurrence of missing data is, however, likely in economic evaluations that involve patient-level data,30 and was dealt with in this economic evaluation using multiple imputation.\n\nThe analysis applied costs as accurately as possible to generate the overall costs for both study groups. However, assumptions were made where necessary, for example by applying medications categories in order to simplify the medication costing, rather than micro-costing at the individual medication level due to the high volume of medications reported. We acknowledge that for the secondary analysis there is the possibility of double counting with the over-the-counter medications and the separate medication costs included. A further point to note about the secondary analysis, which took a societal perspective, is that it did not cover an extensive list of items that could potentially feed into this perspective. This was due to keeping the questionnaire to a manageable length rather than including further questions which may have deterred participants from completing the questionnaire and reduced the questionnaire response rate. The key cost areas were therefore selected and included.\n\n\nConclusion\n\nThis trial-based economic evaluation found that the use of HCQ for pain relief of patients with hand OA and moderate to severe pain was not a cost-effective management option when compared with placebo. Data from our study can be used to inform future studies in the area, regarding the use of healthcare services and the health-related quality of life of patients with hand OA.\n\n\nData availability\n\nFull underlying (non-aggregated) data cannot be made publicly available since the ethics approval of this study does not cover openly publishing non-aggregated data.\n\nIn order to access this data, it must be requested from the corresponding author. Data requestors will have to provide: i) written description and legally binding confirmation that their data use is within the scope of the study; ii) detailed written description and legally binding confirmation of their actions to be taken to protect the data (e.g., with regard to transfer, storage, back-up, destruction, misuse, and use by other parties), as legally required and to current national and international standards (data protection concept); and iii) legally binding and written confirmation and description that their use of this data is in line with all applicable national and international laws (e.g., the General Data Protection Regulation of the EU).\n\n\nReporting guidelines\n\nOpen Science Framework: CHEERS checklist for ‘Cost-effectiveness of hydroxychloroquine versus placebo for hand osteoarthritis: economic evaluation of the HERO trial’, https://doi.org/10.17605/OSF.IO/AQNWV.31\n\nData are available under the terms of the Creative Commons Attribution 4.0 International License (CC-BY 4.0).\n\n\nConsent\n\nAll participants gave written informed consent prior to entering the trial.\n\n\nEthical approval\n\nEthical approval was given by Leeds East Research Ethics Committee (reference number 12/YH/0151).",
"appendix": "Acknowledgements\n\nThe authors would like to thank the participants who took part in the HERO trial; the clinicians, research nurses, radiographers, ultrasonographers, and administrators at the trial sites and Sarah Hogg, Lema Vernon, Michelle Watson, and Illary Sbizzera for their work on the trial; and the York Trials Unit and the NIHR, through the Comprehensive Clinical Research Network, for their support of the HERO trial.\n\n\nReferences\n\nYu D, Peat G, Bedson J, et al.: Annual consultation incidence of osteoarthritis estimated from population-based health care data in England. Rheumatology (Oxford). 2015; 54(11): 2051–60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorgan OJ, Hillstrom HJ, Ellis SJ, et al.: Osteoarthritis in England: Incidence Trends From National Health Service Hospital Episode Statistics. ACR Open Rheumatol. 2019; 1(8): 493–8. 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PubMed Abstract | Publisher Full Text\n\nMurray D, MacLennan G, Breeman S, et al.: A randomised controlled trial of the clinical effectiveness and cost-effectiveness of different knee prostheses: the Knee Arthroplasty Trial (KAT). Health Technol Assess. 2014; 18(19). PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaulden M: Calculating and Interpreting ICERs and Net Benefit. Pharmacoeconomics. 2020; 38(8): 785–807. PubMed Abstract | Publisher Full Text\n\nMarmor MF, Kellner U, Lai TY, et al.: Recommendations on Screening for Chloroquine and Hydroxychloroquine Retinopathy (2016 Revision). Ophthalmology. 2016; 123(6): 1386–94. PubMed Abstract | Publisher Full Text\n\nDrummond M, Sculpher MJ, Torrance GWO, et al.: Methods for the economic evaluation of health care programmes. 3rd edition.Oxford, UK: Oxford University Press; 2005.\n\nRonaldson SJ: CHEERS checklist: HERO cost-effectiveness analysis. 2021."
}
|
[
{
"id": "92218",
"date": "21 Sep 2021",
"name": "Elizabeth A. Stokes",
"expertise": [
"Reviewer Expertise Health economics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper reports a within-trial cost-utility analysis (CUA) and cost-effectiveness analysis (CEA). The paper is clearly written, and appropriate methods have been used to conduct analyses. The text around interventions being cost-effective where findings are reported in terms of cost per QALY lost is very well explained.\nI have the following comments:\nA CUA and a CEA were planned, did you pre-specify which was the primary analysis?\n\nIntroduction – first sentence – who is at-risk?\n\nResource use was captured at baseline, 6 and 12 months. Did the questionnaires at each of these time points ask participants to recall their resource use over the previous 6 months? Was resource use captured at baseline solely for the purpose of including baseline costs in the multiple imputation models?\n\nDid you explore the missing at random assumption?\n\nCosts – resource use was captured on day cases, but no unit cost for this is reported in Table 1. Were there no participants who reported a day case admission? Were hospital admissions not captured as there is no chance that this patient group would be admitted for hand OA? In the introduction, surgery is cited as one of the high costs in this patient group.\n\nThe mean difference between groups and 95% CI is presented in Table 3 for costs and Table 5 for EQ-5D utilities, but not in Table 2 for resource use? It would help the reader to include this.\n\nTable 3 – did you consider separating medication costs into HCQ and other medications?\n\nThe time horizon for the CUA was 12 months but for the CEA was 6 months? While the primary clinical outcome of hand pain severity was measured at 6 months, this was also captured at 12 months. Why was your analysis for this outcome based on a shorter time horizon than the CUA analysis? Was a CEA over 12 months a pre-planned sensitivity analysis?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "100806",
"date": "10 Dec 2021",
"name": "David Mark Epstein",
"expertise": [
"Reviewer Expertise Economic evaluation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors conduct an economic evaluation alongside the RCT. There were no differences found between the groups in terms of hand pain or quality-of-life and no significant differences in costs. Although there were no differences, it is nevertheless worthwhile publishing these results, in order to avoid \"publication bias\" and guide future research in this area. The study, in general, is well conducted and I have no comments on technical matters. Rather than calculate an ICER, which implies some measurable difference in outcomes and costs, personally, I would interpret the results in the abstract and conclusions that there were no meaningful or statistically significant differences in any outcomes or costs at 1 year.\n\nThe authors do not discuss other therapies or research in this area and this contextual comparison would be useful.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-821
|
https://f1000research.com/articles/10-518/v1
|
30 Jun 21
|
{
"type": "Method Article",
"title": "Modeling the impact of early interventions on the transmission dynamics of coronavirus infection",
"authors": [
"Christopher Saaha Bornaa",
"Baba Seidu",
"Yakubu Ibrahim Seini",
"Baba Seidu",
"Yakubu Ibrahim Seini"
],
"abstract": "A deterministic model is proposed to describe the transmission dynamics of coronavirus infection with early interventions. Epidemiological studies have employed modeling to unravel knowledge that transformed the lives of families, communities, nations and the entire globe. The study established the stability of both disease free and endemic equilibria. Stability occurs when the reproduction number, R0, is less than unity for both disease free and endemic equilibrium points. The global stability of the disease-free equilibrium point of the model is established whenever the basic reproduction number R0 is less than or equal to unity. The reproduction number is also shown to be directly related to the transmission probability (β), rate at which latently infected individuals join the infected class (δ) and rate of recruitment (Λ). It is inversely related to natural death rate (μ), rate of early treatment (τ1), rate of hospitalization of infected individuals (θ) and Covid-induced death rate (σ). The analytical results established are confirmed by numerical simulation of the model.",
"keywords": [
"Coronavirus",
"stability",
"simulation",
"reproduction number",
"interventions",
"transmission"
],
"content": "Introduction\n\nAccurate detection of the underlying agent that causes a disease is very important. Globally, many infections remain undetected and therefore untreated, causing complications and major human and economic consequences. Managing diseases in our modern world requires strategic interventions at particular points during the infection cycle. These are before the infection, early stages of the infection (asymptomatic) and later stages of the infection (symptomatic). Before the infection, individuals may be immunized as a control measure. Immunization is a cost-effective and highly successful health intervention used to manage emerging infectious diseases such as coronavirus. This is a process where a person, through vaccination, becomes protected against an emerging disease. Early treatment of the disease can also be a good strategy in managing infectious diseases. It is therefore important to identify infected persons early enough to put them on treatment. Early treatment of SARS-CoV-2 would speed up the recovery process, reduce the likelihood of developing severe outcomes and reduce demand on health care systems [Kim et al., 2020; Strain et al., 2005]. Strain et al. [2005] studied the effect of early treatment of primary infection on cellular reservoir clearance of HIV-1 and noted a positive effect. The question arises of whether this will be the case for coronavirus infections. Individuals should also be encouraged to go for voluntary testing as this will increase case detection, thereby reducing the number of secondary infections [Kim et al., 2020]. In every infection, the exposure of an individual to the source of infection is followed by an incubation period which varies from one infectious disease to the other. For example, the incubation period for coronavirus disease 2019 (Covid-19) is 14 days. During the incubation period the infected individual may be asymptomatic and unaware of their infection. This is followed by the onset of symptoms and varied health behaviours of the infected individual. Some researchers support the notion that antiviral therapy hastens viral clearance in asymptomatic infection [Strain et al., 2005; Hu et al., 2020] thereby halting the progression to symptomatic infection and the subsequent impact on the health system and the society at large.\n\nIsolating persons who have been exposed to a coronavirus disease in order to prevent transmission has been a long established public health strategy [Kim et al., 2020]. This is done either in isolation homes or at hospitals in severe cases. Treatment interventions are offered in such circumstances.\n\nThis paper looks at the effect of early interventions on the transmission dynamics of coronavirus infection by employing mathematical modelling. Several mathematical models have been used as an engine to unravel knowledge in many epidemiological studies [Asamoah et al., 2017, 2020a, 2020b; Bornaa et al., 2017, 2020; Seidu et al., 2020; Agusto et al., 2015; Ivorra Benjamin and Ramos, 2015]. Most of these studies have yielded exceptional results that transformed the lives of families, communities, nations and the entire globe. Mathematical models have also been used to study pest and worm infestation in agriculture and aquaculture. Mathematical modeling is used in economics to observe, understand, and make predictions about human economic behavior.\n\n\nModel formulation\n\nConsider N(t) as the size of the total population at time t. The population is then subdivided into five classes: Susceptible, S(t), the latently infected (Exposed) E(t), the clinically symptomatic (Infected), I(t), the hospitalized in a facility (Hospitalized) H(t) and Recovered R(t) Classes. Thus, the population is given as\n\nPeople are recruited into the susceptible population through birth and immigration at rate Λ and leave by having active contact with the viral source and being infected at rate β. These individuals progress to the latently infected class E(t). The susceptible population also decreases by natural death at the rate μ. Thus;\n\nThe population of the latently infected (exposed) class decreases whenever an exposed individual begins to show clinical symptoms and is moved into the infected class I(t) at rate δ. This may be due to lack of intervention or intervention failure. It also decreases through natural and disease induced deaths, and recovery from early intervention (treatment) at rates μ, σ and τ1 respectively. Thus;\n\nThe population of clinically infected individuals decreases due to hospitalization, natural death and disease induced death at rates θ, μ and σ respectively. Thus;\n\nThe population of the individuals that are hospitalized increases whenever the clinically infected individuals are taken to the hospital at rate θ, then decreases due to natural death, disease induced death and recovery at rate τ2. Thus;\n\nThe population of the recovered individuals increases whenever there is recovery from the exposed class due to early treatment, and also from hospitalized individuals due to recovery after treatment at rates τ1 and τ2 respectively, and decreases by natural death. For the period under consideration, the recovered is assumed to have permanent immunity.\n\nThe description of the dynamics of the disease infection is depicted by following set of equations.\n\nFor purposes of analysis, let k1 = τ1 + δ + σ + μ, k2 = θ + σ + μ, and k3 = τ2 + σ + μ.\n\nWe begin to discuss some basic properties of model (1) in the next section. This includes the positivity and boundedness, equilibrium states, local and global stability of the equilibria and sensitivity analysis. Numerical simulation is also employed to confirm the analytical results. Finally, the results are discussed and are conclusions drawn.\n\n\nQualitative properties of the model\n\nLemma 0.1. If only all solutions of model (1) start in Ω, they remain in it for all t ≥ 0.\n\nAlso, for the model (1), the region Ω=S,E,I,H,R∈R≥05N≤Λμ is a positively invariant set.\n\nProof. Define ζ(x)=x(t)=0 andS,E,I,H,R∈R≥05, ∀x∈S,E,I,H,R.\n\nThe following therefore is obtained from model (1);\n\nAs stated in Lemma 2 of Yang et al. [1996], a solution of model (1) is always such that S(t),E(t),I(t),H(t),R(t)∈R≥05. The first part of the lemma is therefore proved.\n\nWe have\n\nfrom N = S + +E + I + H + R. Thus, N(t)≤N(0)e−μt+Λμ1−e−μ.\n\nTherefore if 0≤N(0)≤Λμ then ≤limsupt→∞N(t)≤Λμ.\n\nThus, all solutions of the model remain in Ω whenever they start in it. The second part of the lemma is also proved and hence the whole Lemma is proved.\n\nWe therefore conclude that model (1) is mathematically and epidemiologically well-posed within Ω [Hethcote, 2000].\n\nThere are basically two equilibria for model (1); the disease-free, E0 and endemic, E* equilibria. The solution of the system\n\ngives the equilibrium points of the model.\n\nAssume that an equilibrium point of the model is typically S*,E*,I*,H*,R*, then model (1) gives;\n\nTheorem 0.1. The model (1) has unique endemic and disease free equilibria.\n\nProof. The solution of 2 for I* = 0 is E0=S0,0,0,0,0, where S0=Λμ. When I*=δβΛ−μk1k2β is substituted into (2), the endemic equilibrium is obtained, thus proved.\n\nNow, the basic reproduction number is obtained by employing the next-generation matrix method of Zhisheng and Van den Driessche [2012]. Thus;\n\nThe stability of an equilibrium point is determined by considering all the roots of the characteristic equation of the Jacobian Matrix of model (1). If all the roots are negative then the equilibrium point is said to be locally asymptotically stable. The Jacobian Matrix J of the model is given as\n\nIt can be shown that at E, − μ and − k3 are roots of the characteristic equation of the Jacobian Matrix J. Clearly all these roots are negative. The roots that remain must therefore satisfy equation 3 at E0. This is the characteristic polynomial of the Jacobian Matrix J∈,\n\nwhere\n\nThe roots of equation 3 are the eigenvalues of J∈.\n\nwhere\n\nWhenever R0<1, all the coefficients Φi, i = 0, 1, 2, are positive. This suggests lemma 2 by using Descartes rule of signs.\n\nLemma 0.2. The E0 is locally asymptotically stable whenever R0<1 and unstable whenever R0>1.\n\nAgain, the roots that remain must, after establishing that −μ and −k3 are roots of the characteristic equation of the Jacobian Matrix J, satisfy equation 4. This is the characteristic polynomial of the Jacobian Matrix J∋ at E*, where\n\nThe roots of equation 4 are the eigenvalues of J∋.\n\nwhere\n\nWhenever R0≤1, all the coefficients Πi, i = 0, 1, 2, 3 are positive. This also suggests lemma 3 by using Descartes rule of signs.\n\nLemma 0.3. The E* is locally asymptotically stable whenever R0≤1 and unstable whenever R0>1.\n\nThe technique of Castillo-Chavez et al. [2002] is employed to study the global stability of E0. If we let Y=S,R and X=S1,Q,I,H, model (1) can now be re-written as\n\nwhere\n\nand\n\nAccording to Castillo-Chavez et al. [2002], the following conditions establish the global stability of E0.\n\nwhere L=DXG(Y*,0) is the Jacobian of G(Y,X) with respect to X at E0.\n\nIf the reduced system of (1) given by\n\nis considered, then disease-free equilibrium point Y*=E0 is clearly a globally asymptotically stable point of the reduced system. Also, let G(Y,X)=LX−G^(Y,X), where\n\nand\n\nSubstituting E0, into G^(Y,X) gives zero components and condition H2 is satisfied. Whenever R0≤1 the E0 is globally asymptotically stable hence establishing the following results.\n\nLemma 0.4. The disease-free equilibrium point E0 of the model is globally asymptotically stable whenever R0≤1.\n\nIn this section, we try to find out whether or not the endemic equilibrium is globally stable using Lyapunov functions technique.\n\nTheorem 0.2. The endemic equilibrium of model (1) is globally asymptomatically stable whenever R0>1.\n\nProof. Consider the Lyapunov function\n\nIf we take the derivative of V we obtain\n\nAfter some algebraic manipulation dVdt=A−B, where\n\nand\n\nTherefore whenever A<B⇒dVdt<0, and also A−B=0⇒dVdt=0, this is possible if S = S*, E = E*, I = I*,H = H*, R = R*. Therefore, the largest compact invariant set for model (1) is {E*}. Hence the global asymptotic stability of E* is established in the positive region R≥05 if A < B for R0>1 as in Lyapunov-LaSalle’s stability theorem [LaSalle, 1968],\n\nParameters play a very important role in the dynamical behaviour of models; therefore the study of the impact of changes in the values of these parameters cannot be underestimated [Seidu et al., 2020; Bornaa et al., 2021; Chitnis et al., 2008]. The influential parameters of the model are considered by beginning to value the changes that occur in their values. Sensitivity analysis is therefore employed to help identify such influential parameters of the model. The normalized forward sensitivity technique is employed to study the sensitivity of R0 to model parameters.\n\nDefinition: Let model output R0 be differentiably dependent on model parameter x. The normalized forward sensitivity index of R0 with respect to x is defined by\n\nThe model parameter values in Table 1 are carefully selected as baseline values for the purposes of the sensitivity test and numerical simulation only. The local sensitivity indexes are therefore recorded in Table 2 taking R0 as a model output.\n\n\nNumerical simulation\n\nConsidering the baseline parameter values in Table 1, numerical experiments are performed, with initial values of S = 0.411e + 5, E = 0.493e + 2, I = 0.243e + 2, H = 0.318e + 2, R = 0.97e + 3, from literature to verify the analytical results established. The simulation is carried out using matlab version 1.0 for MathWorks R2017a release.\n\nSimulation to illustrate the local stability of the disease free equilibrium of model (1) is run for R0<1.\n\nFigure 2 depicts the bar graph of the sensitivity of R0 to marginal changes in each of the parameters that constitute R0.\n\nTo illustrate the impact of early treatment on the dynamics of coronavirus infection, we now present the early treatment parameter τ1, which is varied (from initial value of 0.5 at 0.5 intervals) and observe its impact on the spread of coronavirus infection, with all other parameters kept constant (see Figure 4a, b, c, d and e).\n\nEach parameter under consideration is varied (from initial value at 0.5 intervals) to observe its impact on the spread of Covid-19 infections, with all other parameters kept constant (see Figure 5a, b, c, d and e for δ; Figure 6a, b, c, d and e for θ; Figure 7a, b, c, d and e for β).\n\n\nDiscussions, conclusions and recommendations\n\nA deterministic model is proposed to describe the transmission dynamics of coronavirus infection with early interventions. The study describes the basic qualitative properties of the model and carried out numerical simulations to confirm the qualitative results. The model is shown to have unique disease-free and endemic equilibria (see equation 2, theorem 1 and the proof). The disease-free equilibrium is locally asymptotically stable when R0<1 (see Figure 1). The endemic equilibrium is also locally asymptotically stable when R0≤1. The global stability of the disease-free and endemic equilibria are respectively established under the conditions; R0≤1 and R0>1.\n\nAnalysis of the responsiveness of the model parameters to marginal changes is also carried out to identify the most important factors to consider in the fight against the spread of the disease. The results show, in order of importance, that a marginal change in any of the following parameters will affect directly or inversely the reproduction number thereby affecting the transmission dynamics of the disease. These parameters are: the death rate μ, transmission probability β, recruitment rate Λ, rate at which exposed individuals join the infected class δ, early treatment rate τ1, rate of hospitalization of infected individuals θ and coronavirus induced death rate σ (see Table 2).\n\nWe observe from Table 2 that Λ, β and δ are directly proportional to R0 in order of importance. In other words, an increase (decrease) in any of these parameters will lead to an increase (decrease) in R0 as confirmed by Figure 3b on β and δ. The parameters that are however inversely proportional to R0 are μ, θ, τ1 and σ. An increase (decrease) in any of these parameters will lead to a decrease (increase) in R0 as confirmed by Figure 3a on τ1 and θ. This is also reflected in Figure 4 (a, b, c, d and e). Increasing early treatment reduces the infected population (see Figure 4b, c and d) and increases the non-infected population (see Figure 4a and e). This is also supported by Kim et al. [2020] and Strain et al. [2005] when they carried out independent studies into early treatment of infectious diseases.\n\nMany health care facilities are overstretched in terms of space, equipment and personnel because of the pandemic. This challenge can be handled by either providing more space, equipment and personnel, or by increasing the recovery rate of treated infected individuals. This study has confirmed that an increase in recovery rate reduces the hopitalized individuals and thereby reduces the pressure on health care facilities to take in more coronavirus and other patients (see Figure 6d).\n\nIt is assumed that the recovered gained permanent immunity because they develop antibodies that react and fight against initial infections. We also observe increases in the rate at which the exposed joins the infected (symptomatic) class (δ). When this happens the symptomatic are moved into hospitals for treatment and subsequently recovery. The effect is that the infected and recovered populations are increased but the susceptible population is reduced because of the immunity gained by the recovered (see Figure 5a, b, c, d and e).\n\nIt is also shown that as transmission probability increases the infected increase and the susceptible decrease (see Figure 7a, b, c and d).\n\nIt is recommended that:\n\n• early treatment of coronavirus should be considered. This can be effectively carried out when proper surveillance is enforced to identify asymptomatic individuals who are mostly at their early stage of infection. People should also be encouraged to use immune boosters to reduce the rate at which the exposed joins the infected while early treatment is enforced.\n\n• efforts should be made to reduce the rate of infection by insisting on people observing all the coronavirus protocols announced by World Health Organisation and other health institutions.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAuthor contributions\n\n\n\n• Christopher Saaha Bornaa: Conceptualization and algebriac analysis\n\n• Baba Seidu: Numerical analysis\n\n• Yakubu Ibrahim Seini: Proof reading, supervision and advisory role",
"appendix": "References\n\nAgusto FB, Teboh-Ewungkem MI, Gumel AB: Mathematical assessment of the effect of traditional beliefs and customs on the transmission dynamics of the 2014 ebola outbreaks. BMC Med. 2015; 13, 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsamoah JKK, Oduro FT, Bonyah E, et al.: Modelling of rabies transmission dynamics using optimal control analysis. J Applied Mathematics. 2017; 2017. Publisher Full Text\n\nAsamoah JKK, Bornaa CS, Seidu B, et al.: Mathematical analysis of the effects of controls on transmission dynamics of sars -cov-2. Alexandria Engineering J. 2020a. Reference Source\n\nAsamoah JKK, Owusu M, Oduro JF, et al.: Global stability and cost-effectiveness analysis of covid-19 considering the impact of the environment: using data from ghana. Chaos, Solitons and Fractals. 2020b; page 110103. Publisher Full Text\n\nBaloba EB, Seidu B, Bornaa CS: Mathematical analysis of the effects of controls on the transmission dynamics of anthrax in both animal and human populations. Computational Mathematical Methods Med. 2020; 022020. Publisher Full Text\n\nBornaa CS, Seini YI, Seidu B: Modelling zoonotic diseases with treatment in both human and animal populations. Commun. Math. Biol. Neurosci. 2017; 2017. Publisher Full Text\n\nBornaa CS, Seidu B, Daabo MI: Mathematical analysis of rabies infection. J Applied Mathematics. 2020; 17: 2020. Publisher Full Text\n\nBornaa CS, Seidu B, Makinde OD: Mathematical analysis of the impact of vaccination and poor sanitation on the dynamics of poliomyelitis. Int J Nonlinear Sciences Numerical Simulation. 2021; 70. Publisher Full Text\n\nCastillo-Chavez C, Blower S, Driessche P, et al.: Mathematical approaches for emerging and reemerging infectious diseases: models, methods, and theory. Springer; 2002.\n\nChitnis N, Hymanand J, Cushing J; Determining important parameters in the spread of malaria through the sensitivity analysis of a mathematical model. Bull. Math. Biol. 2008; 70: 1272–1296. PubMed Abstract | Publisher Full Text\n\nHethcote HW: The mathematics of infectious diseases. SIAM review. 2000; 42(4): 599–653.\n\nHu Z, Song C, Xu C, et al.: Clinical characteristics of 24 asymptomatic infections with covid-19 screened among close contacts in nanjing, china. Sci China life Sci. 2020; 63: 706–711. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nIvorra Benjamin ND, Ramos AM: A mathematical model to predict the risk of human diseases spread between countries—validation and application to the 2014–2015 ebola virus disease epidemic. Bull Math Biol. 2015; 77, 9. PubMed Abstract | Publisher Full Text\n\nKim P, Cushing JM, Xu C, et al.: Therapy for early covid-19-a critical need. JAMA. 2020. PubMed Abstract | Publisher Full Text\n\nLaSalle J: Stability theory for ordinary differential equations. J Differential Equations. 1968; 4. Publisher Full Text\n\nSeidu B, Bornaa CS, Makinde OD: An ebola model with hyper-susceptibility. Chaos, Solitons and Fractals. 2020; 138: 109938. Publisher Full Text\n\nStrain CM, Little SJ, et al.: Effect of treatment, during primary infection, on establishment and clearance of cellolar reservoirs od hiv-1. J Infect Dis. 2005; 191. PubMed Abstract | Publisher Full Text\n\nYang X, Chen L, Chen J: Permanence and positive periodic solution for the single-species nonautonomous delay diiffusive modelsl. Computers Mathematics Applications. 1996; 32: 116–312.\n\nZhisheng S, Van den Driessche P: Global stability of infectious disease models using lyapunov functions. SIAM J Applied Mathematics. 2012; 73. Publisher Full Text"
}
|
[
{
"id": "88778",
"date": "26 Jul 2021",
"name": "Mehmet Yavuz",
"expertise": [
"Reviewer Expertise Mathematical modelling in epidemiology",
"fractional calculus",
"applied mathematics",
"optimal control",
"bifurcation and chaos."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 should put proper punctuation at the end of all equations.\n\nIn numerical simulations, the authors need to explain where they have taken the parameter values from. Are they from the literature or estimated ones?\n\nWhat makes the proposed methods and COVID-19 model suitable for this unique task? What new development to the proposed model have the authors added (compared to the existing approaches)? These points should be clarified.\n\nWhat is the novelty of your work? There are some similar papers that have been investigated in epidemiology, especially COVID-19, although there are some minor differences in the structure of models. Please state it clearly.\n\nHave you employed any assumptions in your COVID-19 model and problem formulation? Please explain briefly.\n\nMore physical interpretations should be given. Please provide corresponding explanations of the figures in terms of their physical meanings and pointing out the novelty of the paper. How do figures support your scheme?\n\nThe authors should improve the introduction by including the recent development within the frame of the mentioned COVID-19 models. Also, their mathematical investigations and numerical simulations with the help of recently published papers should be considered by comparing their current model. Sensitivity analysis of the Reproduction number can be discussed deeply. In this connection, I suggest some interesting results:\n\nModeling and analysis of COVID-19 epidemics with treatment in fractional derivatives using real data from Pakistan1. A New Mathematical Modeling of the COVID-19 Pandemic Including the Vaccination Campaign. Open Journal of Modelling and Simulation 2. New Approaches to the Fractional Dynamics of Schistosomiasis Disease Model. Physica A: Statistical Mechanics and its Applications 3.\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? Partly\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
},
{
"id": "89506",
"date": "25 Aug 2021",
"name": "Ebenezer Bonyah",
"expertise": [
"Reviewer Expertise Mathematical Biology",
"Mathematical Modelling and Mathematics 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 authors appreciate that there are many mathematical models available on COVID-19.\n\nThe authors must provide the knowledge gap that this work is filling.\n\nThe authors must present anything new on the model formulated.\n\nThe authors must also provide a reason for using this numerical scheme for this study.\n\nFor the conclusions, I suggest for this to be in the past tense.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-518
|
https://f1000research.com/articles/10-820/v1
|
17 Aug 21
|
{
"type": "Research Article",
"title": "Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach",
"authors": [
"Amde Selassie Shifera",
"Christopher Pockrandt",
"Natalia Rincon",
"Yuchen Ge",
"Jennifer Lu",
"Ales Varabyou",
"Anne E. Jedlicka",
"Karen Sun",
"Alan L. Scott",
"Charles Eberhart",
"Jennifer E. Thorne",
"Steven L. Salzberg",
"Christopher Pockrandt",
"Natalia Rincon",
"Yuchen Ge",
"Jennifer Lu",
"Ales Varabyou",
"Anne E. Jedlicka",
"Karen Sun",
"Alan L. Scott",
"Charles Eberhart",
"Jennifer E. Thorne",
"Steven L. Salzberg"
],
"abstract": "Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. Methods: Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. Results: We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria (Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), two cases with fungi (Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. Conclusions: Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.",
"keywords": [
"sarcoidosis",
"ocular sarcoidosis",
"orbital sarcoidosis",
"metagenomics",
"next-generation sequencing",
"pathogen discovery",
"Campylobacter concisus",
"Neisseria elongate",
"Streptococcus salivarius",
"Pseudopropionibacterium propionicum",
"Paracoccus yee",
"Exophiala oligosperma",
"Lomentospora prolificans",
"Aspergillus versicolor",
"Mupapillomavirus 1"
],
"content": "Introduction\n\nSarcoidosis is a systemic inflammatory disease characterized by the formation of non-caseating granulomas in the affected tissues1. Although sarcoidosis can affect almost any organ in the human body, it most commonly affects the lungs, the skin and the ocular and periocular tissues. The frequency of ocular and periocular involvement in patients with sarcoidosis ranges between 25% and 60% depending on the particular population studied2. The manifestations of ocular and periocular sarcoidosis include uveitis, conjunctival granulomas, eyelid granulomas, orbital inflammation, dacryoadenitis, dacryocystitis, scleritis and optic neuropathy. Ocular and periocular sarcoidosis accounts for about 5% of patients seen in a uveitis practice and it results in blindness in at least one eye in approximately 10% of the affected patients2.\n\nIn spite of numerous investigations that have been carried out since the first case of sarcoidosis was reported in 1877 by Jonathan Hutchinson3, the etiology of sarcoidosis remains unknown. However, there is very strong evidence that supports the assertion that the pathogenesis of sarcoid granulomas involves an oligoclonal CD4 T cell-mediated immune response to a persistent antigen, most likely an exogenous antigen derived from microbial or inanimate sources4–6. Microbial sources of antigens that have been suspected of causing sarcoidosis include bacteria such as mycobacteria, Propionibacterium acnes, Tropheryma whipplei and Borrelia burgdorferi, fungi such as Coccidioides spp., and viruses such as Epstein-Barr virus, cytomegalovirus and hepatitis C virus4–10. It is possible that different antigens could be involved in different patients, resulting in a diverse pattern of organ involvement, natural history and clinical course. In addition to exposure to the requisite antigen, it is believed that the disease occurs only within the appropriate genetic background of the host5.\n\nThe availability of next-generation sequencing (NGS) technologies has opened vast opportunities for pathogen discovery in human disease11. We hypothesized that metagenomic sequencing using NGS would identify pathogen-derived microbial DNA within sarcoid granulomas. We conducted a metagenomics analysis on DNA extracted from archival tissue specimens of 16 cases of ocular and periocular sarcoidosis, and we detected possible microbial pathogens in eight of the cases. We anticipate that the identification of potential microbial etiologies of sarcoidosis may lead to large-scale metagenomics studies that can be validated by pathogen isolation followed by investigations to establish the pathogenic role of the suspected microorganisms in the causation of sarcoidosis.\n\n\nMethods\n\nThe Johns Hopkins University School of Medicine Institutional Review Board (IRB) approved this study (approval number IRB00126932), which was undertaken in accordance with the principles of the Declaration of Helsinki and in compliance with the Health Insurance Portability and Accountability Act. The study was categorized by the IRB as ‘Not Human Subjects Research’ and as such obtaining informed consent was not required.\n\nDemographic, clinical and histopathological data (from initial presentation to subsequent follow-ups) were retrospectively collected for each study subject by reviewing the electronic medical records of the subjects. For each subject, the data (including sex, age, race, diagnosis, and results of microbiological, histopathological and radiologic tests) were gathered in a de-identified manner before analysis was carried out.\n\nParaffin-embedded archival tissue specimens of subjects who had biopsies of ocular and periocular tissues at the Wilmer Eye Institute of Johns Hopkins Hospital during the period between February 2010 and February 2017, and that were positive for non-caseating granulomas, were included in the study. A total of 18 such specimens were identified: six specimens of orbital tissues, two specimens of eyelid tissues, two specimens of the lacrimal sac, five specimens of the conjunctiva, one specimen of the cornea and two specimens of the globe. In addition, a total of four archival tissue specimens (one from the conjunctiva and three from the lacrimal gland) that did not demonstrate non-caseating granulomas were included to be used as controls.\n\nFor each archival tissue specimen, 10 sections, each 10 µm thick, were cut from the paraffin blocks and used for DNA extraction. Two of the conjunctival specimens that were positive for non-caseating granulomas were excluded from the study due to poor quality of the DNA extracted from the specimens. Therefore, a total 16 positive specimens and four negative specimens were used.\n\nGenomic DNA was extracted from paraffin-embedded tissue sections using the QIAamp DNA FFPE tissue kit and deparaffinization solution according to the manufacturer’s (Catalog numbers 56404 and 19093, respectively, Qiagen, Valencia, CA, USA) recommended and supplementary protocols. Quality of DNA was assessed by Genomic ScreenTape analysis on a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA). The Quant-iT PicoGreen dsDNA reagent kit (Catalog number P7589, Invitrogen/ThermoFisher Scientific, Waltham, MA, USA) was used for quantitation of DNA samples, with fluorescent reads performed on a SpectraMax M2 plate reader (Molecular Devices, San Jose, CA, USA).\n\nLibraries were prepared from ten nanograms of DNA using the Ovation Ultralow V2 DNA-seq Library Preparation kit (Catalog number 0344, Tecan Genomics, Redwood City, CA, USA). The recommended protocol was followed with the exception of the initial fragmentation step. Fragmentation was performed enzymatically, instead of ultrasonically, using Celero fragmentation buffer and Celero fragmentation enzyme from the Celero PCR Workflow with Enzymatic Fragmentation kit (Catalog number 9363, Tecan Genomics). Fragmentation time was optimized to 10 minutes, and a modified purification was performed with AMPure XP beads (Catalog number A63881, Beckman Coulter, Brea, CA, USA). Library amplification was performed for 13 cycles based on the Manufacturer’s recommendation for starting input amount of DNA (10 ng), in an Applied Biosystems GeneAmp 9700 or Veriti thermal cycler (ThermoFisher Scientific). Cycling parameters were: 72°C for two minutes, 95°C for three minutes, (98°C 20 sec, 65°C 30 sec, 72°C 30 sec) for 13 cycles, 72°C for one minute, and a 4°C hold. Amplification primers and enzyme were part of the Ovation Ultralow V2 kit. Quality of purified libraries was assessed by D1000 ScreenTape analysis on a TapeStation 2200, with region analysis performed for sizing. Quantitation of libraries was performed by qPCR with the Kapa Library Quantitation kit for Illumina (Catalog number KK4824/07960140001, Roche, Basel, Switzerland) in an Applied Biosystems StepOne Plus Real Time PCR system (ThermoFisher Scientific). A six-point standard curve, with a concentration range of 20 pM to 0.0002 pM was run, as per the Kapa recommended protocol. Run parameters were an initial denaturation at 95°C for 5 minutes and 35 cycles (95°C 30 sec denaturation and 60°C 45 sec annealing/extension/data acquisition), followed by a ramp from 65°C to 95°C for melt curve analysis. qPCR results and sizing data were imported to the Kapa Library Quantitation Data Template for calculations of library concentrations and yields. Libraries were diluted to 10 nM, and an equimolar pool prepared. A final quality assessment of the library pool was performed by High Sensitivity DNA Lab Chip Analysis on a BioAnalyzer 2100 (Agilent Technologies), and a final quantity check was performed on a Qubit Flex Fluorometer using Qubit High Sensitivity DNA reagents and standards (Catalog number Q32854, Invitrogen/ThermoFisher Scientific).\n\nSequencing of the library pool was performed with a 300 cycle (2x150 bp) SP run on an Illumina NovaSeq6000 sequencer (Illumina, San Diego, CA, USA) at Johns Hopkins Genomics, Genetic Resources Core Facility, RRID:SCR_018669.\n\nFor each of the 20 metagenomics samples, we first removed all human sequences by aligning all paired reads to the GRCh38 human reference genome using Bowtie212 in very-sensitive mode. To ensure removal of all human sequences, we removed an entire read pair if either of the read mates aligned to the human reference.\n\nFor each patient, we generated two runs of 150-bp paired-end sequencing data. For simplicity, we concatenated the reads by merging the two runs from each patient. We then compared all patient samples against a KrakenUniq13 database consisting of 5,981 bacterial species (18,484 genomes), 295 archaeal species (374 genomes), 9,905 viral species (10,012 genomes), 250 eukaryotic pathogen (e.g. fungi, amoebas) species (388 genomes), the human GRCh38.p13 genome, and vector sequences. The total numbers of reads per sample, along with the numbers identified as microbial, are shown in Table 1.\n\nMicrobial reads include all reads identified as bacteria, fungi, other eukaryotic pathogens, or viruses. Samples 119, 120, 122, and 123 are controls.\n\nKrakenUniq13 classifies each read by breaking reads into overlapping k-mers, searching the database for the lowest common ancestor of each k-mer, and then assigning the overall read a taxon based on the k-mer taxon distribution. Unlike Kraken 114 and Kraken 215, KrakenUniq reports for every taxonomic classification - not only the read counts but also the number of distinct k-mers, giving extra confidence in classification. Hits with a low count of distinct k-mers are often false positives; e.g., due to low-complexity repetitive sequences in the genome of a pathogen.\n\nIn order to detect outlier read counts among the metagenomics samples, we used a modified Z-score calculation as defined by Iglewicz and Hoaglin16. As compared to a normal Z-score calculation which uses mean values that may be influenced by extreme outliers, this formula uses the median deviation and the sample median. The formula for the modified Z-score for sample i is as follows:\n\nModified Z-score_i = 0.6745*(X_i - X_median) / MAD\n\nwhere X_median is the median read count across all samples and MAD is the median absolute deviation. The median absolute deviation (MAD) is defined as the median of the absolute difference of the observation from the sample median:\n\nMAD = median(|X_i - X_median|)\n\nReads from species with a significant modified Z-score and a high distinct k-mer count were then extracted and aligned to the NCBI nucleotide database to verify whether they were true positives or whether they hit other species equally well or better, suggesting a false positive match.\n\nFor 7/9 candidate infectious microbes, we found small numbers of reads, ranging from 1–64, in one or more control samples. For 8/9 of these pathogens, we found small numbers of reads in other non-control samples. In order to clarify why these reads were present, we analyzed them to determine if they were either (a) computational false positives or (b) possible cross-contamination in the multiplexed sequencing experiment. In addition to counting reads, KrakenUniq counts the number of unique k-mers (k=31 in our experiments) found in each species in a sample13. Each 150-bp read may contain as many as 130 unique 31-mers, if the hit is a true positive and if each k-mer is distinct. For all of the candidate infectious agents, the number of unique k-mers per read was quite high, ranging from 50 to >100. If the unique kmer count for a read is low, the read may consist of low-complexity, repetitive sequence, suggesting that the match is a computational false positive. To check for this possibility, from each of the control samples that had reads matching a candidate infectious agent, we aligned those reads using BLAST17 against NCBI’s comprehensive “nr” nucleotide database. If the reads hit the genome of the candidate pathogen, that suggested cross-contamination in the sample. If the reads matched other genomes or did not match the genome of interest, that suggested they were false positives.\n\nThis evaluation found that small levels of cross-contamination explained the control sample matches for seven of the eight candidate pathogens identified in Table 3, as follows. (1) Kraken identified 0-4 reads as Campylobacter concisus in the control samples, and BLAST alignments confirmed that they matched C. concisus, suggesting a small amount of cross-contamination. (2) For Neisseria elongata, Kraken found 1-14 reads in the control samples, and all were confirmed by BLAST. (3) For Exophiala oligosperma, we found 1-2 reads in the controls and all were confirmed by BLAST. (4) For Streptococcus salivarius, we found 3-33 reads in the control samples, and we confirmed a random sample of them using BLAST. (5) We found 2-13 reads matching Pseudopropionibacterium propionicum in the control samples, and all were confirmed by BLAST. (6) We found 1-8 reads in the control samples matching Aspergillus versicolor and confirmed a random sample of them by BLAST. (7) We found 2-64 reads matching Paracoccus yeei in the control samples and all were confirmed by BLAST. (8) For Lomentospora prolificans, we found 0 reads in the control samples; however, Kraken identified 1-66 reads in the non-control samples. We searched a sample of these reads against “nr” using BLAST, and all aligned to different species while none had BLAST alignments to L. prolificans. Upon further inspection, all the reads had a very low number of unique k-mers. Thus, we determined that these reads were low complexity, repetitive sequences that yielded false positive matches.\n\n\nResults\n\nThe demographic and clinical data of the patients (16 cases and 4 controls) whose archival tissue specimens were used in the study are presented in Table 2. The cases ranged in age from 32 to 79 years while the controls ranged in age from 38 to 71 years. Among the cases, 13 were female and three were male, while among the controls three were female and one male. Seven of the cases were diagnosed to have systemic sarcoidosis while none of the controls were reported to have systemic sarcoidosis.\n\n*The rows with roman text represent the cases whereas the rows with italicized text represent the controls.\n\n#This patient also had sarcoidosis-associated panuveitis of the ipsilateral eye.\n\nFor each column, the value in bold text is significantly higher than any other value in that column.\n\nWe identified pathogens that were possibly associated with disease in eight of the 16 case samples (Table 3). For seven of the samples, a possible pathogen species was present at a much higher level than in any of the controls or the other clinical samples, and for one sample (sample 115), two possible pathogens were identified. For each of the eight samples and nine pathogens, the read counts for the pathogen were statistically higher than expected based on the distribution of read counts in all other samples. We measured this expectation using a modified z-score, which represents the number of standard deviations above the mean for the read count from the possible pathogen (see Methods). Below we briefly discuss each of the eight samples in which possible infectious agents were detected.\n\nSample 101. Sample 101 contained 179 read pairs from Campylobacter concisus, while no other sample had more than seven read pairs, which could be cross-contamination from the multiplexed sequencing run. The controls had 0-4 reads (Table 2). This is a highly significant finding, with a modified z-score of 119.\n\nSample 102: Sample 102 was notable for the presence of 49 read pairs from Mupapillomavirus 1, more commonly known as human papillomavirus type 1 (HPV 1). Strikingly, none of the other 19 samples had even a single read from this virus. We confirmed that all of the reads represented HPV 1, and that they covered ~3000 bp of this small (7811 bp) genome. Thus, the virus was clearly present in this sample, and this sample only.\n\nSample 107: Sample 107 contained 675 reads from Neisseria elongata. Most other case samples had very few reads from this bacterium, although sample 113 had 207 reads. The control samples had just 1-14 reads, suggesting that sample 107 had a clear excess from this species (modified z-score 37.2).\n\nSample 112: Sample 112 was noteworthy for having a strikingly large burden of sequence from the fungus Exophiala oligosperma, a known although somewhat unusual human pathogen18. E. oligosperma had a far higher count in sample 112 than in any other sample, with 11,965 read pairs, compared to just 0 to 14 reads in other samples, with the exception of sample 101 that had 65 reads. Alignment of the reads to the genome indicates that they cover approximately one million base pairs from the 38 megabase genome of this fungus, and thus they are (as expected) randomly dispersed throughout the genome.\n\nSample 113: Sample 113 contained 1,829 reads from Streptococcus salivarius, far more than were found in any other samples (modified z-score 175). Read counts in other samples ranged from 2 to 50, and the controls had 2 to 13.\n\nSample 114: Sample 114 contained 4,840 reads from Pseudopropionibacterium propionicum, a pathogen that is sometimes dismissed because it is mistaken for Propionibacterium acnes, a common skin bacterium19. Until 2016, the two bacterium were both placed in the genus Propionibacterium, at which point P. propionicum was re-classified into a distinct genus. Despite the similar name, P. propionicum causes very different types of infections. All other samples had fewer than 20 reads from this species, yielding a modified z-score of 465.\n\nSample 115: Sample 115 had 367 read pairs with near-perfect matches to the pathogenic fungus Lomentospora prolificans. Fewer than 10 reads from this fungus were found in other samples, except for sample 105 which had 66 reads. The small number of reads in other samples here (and in other cases) might represent cross-contamination between samples.\n\nSample 115: Sample 115 was the only sample with two candidate pathogens, both fungi. In addition to L. prolificans, sample 115 had 585 reads from Aspergillus versicolor. These reads are unambiguous matches to the genome, and all other samples had 20 or fewer matches to this fungus.\n\nSample 117: Sample 117 had 7,780 reads from Paracoccus yeei, a bacterial pathogen. Although P. yeei was detected in other samples, no other sample had more than 204 reads. Those might represent cross-contamination in the multiplexed sequencing run, given the far higher read count (modified z-score 402) in sample 117. Alignment to the genome demonstrated that the reads were well dispersed, covering 340 Kb of the 4.7 Mbp genome.\n\nHistopathological examination carried out as part of routine medical care of all the cases showed typical non-caseating granulomas. Representative histopathological images from three of the eight cases that were positive for microbial DNA are presented in Figure 1. Except for specimen 115, the seven other cases were negative on acid-fast and fungal stains at the time of initial histopathological evaluation. Specimen 115 did not undergo staining for acid-fast and fungi at the time of initial histopathological examination of the specimen (which was the same specimen used in our study) that was obtained from the patient during a corneal transplant procedure. However, this case underwent another corneal transplant procedure eight months after the initial transplant and the specimen obtained at the time, while still showing non-caseating granulomas, was negative on acid-fast and fungal stains.\n\nLight microscopy revealed non-caseating granulomatous inflammation in the orbit (A, B) and conjunctiva (C). Original magnifications 100x (A), 200x (B), 400x (C). A was from sample 107; B was from sample 101; C was from sample 114. These images were selected for illustrative purposes and the images were all obtained by the diagnostic pathology laboratory at the Johns Hopkins Hospital as part of routine medical care. For histopathological examination, briefly, paraffin sections 5 µm thick were cut and stained with hematoxylin and eosin using standard protocols by the pathology laboratory.\n\n\nDiscussion\n\nIn this study we conducted a metagenomics analysis of DNA extracted from archival tissue specimens that were obtained from 16 cases with ocular or periocular sarcoidosis and identified DNA evidence of a possible microbial pathogen in eight of the cases. The microbial agents identified from the tissue specimens were five species of bacteria (Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), three species of fungi (Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one species of virus (Mupapillomavirus 1).\n\nThe case that was positive for Campylobacter concisus DNA had orbital and pulmonary sarcoidosis. C. concisus is a Gram-negative bacterium that colonizes the oral cavity of humans20,21. Currently, humans are the only known hosts of this bacterium20,21. A few studies have found an association between C. concisus and Barrett’s esophagus22,23. In addition, recent studies have also demonstrated association between Crohn’s disease and C. concisus, which could translocate from the oral cavity to the intestine24,25. It is plausible that C. concisus could be aspirated from the oral cavity to the lungs, and then also potentially to distant organs such as the orbit, where it could incite an inflammatory process.\n\nThe case that was positive for Neisseria elongata DNA had orbital sarcoidosis with no systemic sarcoidosis reported. N. elongata is a Gram-negative bacterium that is part of the normal flora of the oral cavity26. There are a number of case reports of infective endocarditis associated with colonization by N. elongata26–29. In addition, the bacterium has been implicated in some cases of osteomyelitis29,30.\n\nThe case in which Streptococcus salivarius DNA was detected had conjunctival sarcoidosis without reported evidence of systemic sarcoidosis. S. salivarius is a Gram-positive bacterium which is part of the normal flora of the oral cavity31. It establishes itself in the human oral cavity within a few hours after birth and persists as a predominant inhabitant of the oral cavity32. The bacterium has been associated with invasive infections including meningitis31, bacteremia33 and prosthetic joint infection34. Interestingly, S. salivarius has also been associated with exogenous endophthalmitis following keratoplasty with a contaminated donor cornea35 and after an intravitreal injection36.\n\nPseudopropionibacterium propionicum (formerly known as Propionibacterium propionicum, Arachnia propionica and Actinomyces propionicus) DNA was detected in a case that had conjunctival sarcoidosis without reported systemic sarcoidosis. P. propionicum is a Gram-positive bacterium that is part of the human oral flora37. It has been associated with human infectious diseases that resemble actinomycosis. There are case reports of the bacterium being associated with lacrimal canaliculitis, cervicofacial infections38,39, tympanomastoiditis40, pulmonary and thoracic infections19,41,42, osteomyelitis43 and brain abscess44. Infection by P. propionicum causes chronic granulomatous inflammation characterized by abscesses, draining sinuses and fibrosis19,45.\n\nParacoccus yeei DNA was detected in a patient who had sarcoidosis that involved the iris, ciliary body, choroid and retina; this case did have a reported evidence of cutaneous sarcoidosis. P. yeei is a Gram-negative bacterium that is found naturally in soil and brine46. In a study involving 1321 patients with idiopathic uveitis, Drancourt et al. detected P. yeei in one patient by conducting 16S rDNA sequencing on an intraocular fluid specimen47. In another, study P. yeei was cultured from the aqueous humor of a patient who had developed corneal graft rejection48. In addition, P. yeei has been associated with peritonitis in a patient undergoing peritoneal dialysis49 and with cutaneous infection followed by bacteremia in a patient with heart failure50.\n\nThe case in which Exophiala oligosperma DNA was detected had conjunctival sarcoidosis with no reported systemic sarcoidosis. E. oligosperma is a dimorphic fungus that has been associated with cutaneous and subcutaneous lesions18 and olecranon bursitis51. Exophilia species have been isolated from the skin, cutaneous tissues, the heart, the lungs, bone and the central nervous system51–54. Interestingly, a member of the genus Exophiala (E. jeanselmei) has been associated with keratitis55 and another member (E. dermatitidis) with endophthalmitis56.\n\nThe case in which DNA belonging to each of Lomentospora prolificans and Aspergillus versicolor was simultaneously detected had corneal sarcoidosis with reported pulmonary sarcoidosis; in addition, the case had sarcoidosis-associated panuveitis of the affected eye. L. prolificans is an anamorphic fungus that has been associated with localized bone and joint infections in the immunocompetent host and with disseminated disease (involving the lungs, the ears, the eyes and the central nervous system) in the immunocompromised host57,58. A. versicolor is a filamentous fungus. It has been associated with invasive pulmonary aspergillosis59, onychomycosis60 and endogenous endophthalmitis61.\n\nThe case that was positive for Mupapillomavirus 1 had orbital sarcoidosis that involved the extraocular muscle tissues with no systemic sarcoidosis reported. Mupapillomavirus 1 is a double-stranded DNA virus that belongs to the virus family Papillomaviridae. It has been isolated from plantar warts62 and from punctate keratotic lesions of the foot63. Interestingly, the virus has also been detected, using a PCR method, in the lesions of cutaneous sarcoidosis in a patient who also had pulmonary sarcoidosis64. In addition, other human papillomaviruses have been associated with ocular diseases, including pterygium and ocular surface squamous neoplasia65.\n\nIn this study, we have identified nine different microorganisms in eight cases of ocular and periocular sarcoidosis. It is not known at this time if any of these microorganisms play any role in the causation of sarcoidosis. The microbial agents could gain access to the ocular and periocular tissues directly from the environment (especially after trauma or surgery) or could reach this tissues via hematogenous spread after initial colonization of distant tissues such as the lungs, the skin and the subcutaneous tissues. It is interesting to note that four of the five bacterial species that were identified by our study are also part of the human oral microbiome. In those cases, the oral cavity could be the source of the microorganisms that involved the ocular and periocular tissues.\n\nOne perplexing finding of our study is that none of the nine microorganisms were detected in more than one case. A possible explanation for this observation is that sarcoidosis is an etiologically heterogenous disease. In support of this argument, it is important to note that sarcoidosis, in addition to being associated with a number of microbial agents, has also been linked to a number of inanimate sources of antigens, including tattoo ink, aluminum, zirconium, talc, and insecticides5,6.\n\nAnother limitation of our study is that potential RNA viruses could not be detected due to the nature of the assay. The relatively small sample size and the fact that paraffin-embedded archival tissue specimens were used are also additional shortcomings. Future studies using a metagenomics approach on a much larger sample size and employing fresh tissue specimens from a variety of sources are recommended.\n\n\nConclusions\n\nIn this study, using a metagenomics approach, we identified nine potential microbial agents in tissue specimens of eight cases of ocular and periocular sarcoidosis. The role of these microorganisms in the causation of sarcoidosis is not clear at this time. Our study has limitations due to the relatively small sample size and due to the fact that metagenomics analysis was carried out on archival tissue specimens. Large-scale metagenomics studies using fresh tissue specimens are needed to provide a better understanding of the potential role of microbial agents in the causation of sarcoidosis. The results of such studies could lead to improved means for the diagnosis and treatment of sarcoidosis.\n\n\nData availability\n\nNCBI BioProject: Metagenomics sequencing of infectious microbes from ocular sarcoidosis tissue specimens. Accession number PRJNA745199; https://identifiers.org/NCBI/bioproject:PRJNA745199.",
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(formerly CDC group EO-2), a novel bacterial species associated with human infection. J Clin Microbiol. 2003; 41(3): 1289–94. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDrancourt M, Berger P, Terrada C, et al.: High prevalence of fastidious bacteria in 1520 cases of uveitis of unknown etiology. Medicine (Baltimore). 2008; 87(3): 167–76. PubMed Abstract | Publisher Full Text\n\nKanis MJ, Oosterheert JJ, Lin S, et al.: Corneal graft rejection complicated by Paracoccus yeei infection in a patient who had undergone a penetrating keratoplasty. J Clin Microbiol. 2010; 48(1): 323–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArias MA, Clark J: Paracoccus yeei as a cause of peritoneal dialysis peritonitis in the United Kingdom. IDCases. 2019; 15: e00486. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFunke G, Frodl R, Sommer H: First comprehensively documented case of Paracoccus yeei infection in a human. J Clin Microbiol. 2004; 42(7): 3366–8. 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}
|
[
{
"id": "138258",
"date": "06 Jun 2022",
"name": "Lynn M. Hassman",
"expertise": [
"Reviewer Expertise ocular immunology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nShifera et al. present a well written analysis of microbial DNA in 16 cases previously diagnosed as ocular or periocular sarcoidosis based on the gold standard histopathologic demonstration of non-caseating granulomas without demonstrable pathogens. They apply next-generation sequencing (NGS )and metagenomic analysis to 16 archival specimens from cases diagnosed as sarcoidosis along with 4 control samples. Based on significant enrichment in specific microbial sequences, they identified 8/16 cases and 0/4 controls with a likely microbial association, including one case in which 2 organisms were detected. Notably, none of the cases were positive for the same microbial sequence enrichment. Each case is presented in the manuscript with a succinct and informative description of the associated microorganism.\nIn light of the advancement in pathogen detection afforded by NGS, this study calls into question the diagnosis of sarcoidosis in some of their cases, a diagnosis which requires the absence of detectable pathogens. This is particularly salient in the presented case with corneal sarcoidosis which required 2 corneal transplants, in which DNA from 2 fungal organisms were detected. This case reads suspiciously like infectious keratitis, a more common diagnosis than sarcoid keratitis.\nOn the other hand, the presence of microbial DNA is not absolute evidence for a causal infection and caution must be applied in presuming an infectious etiology. Consistent with this, a prevailing theory in the etiology of sarcoidosis is that it represents an aberrant immunologic reaction to antigenic remnants of a prior infection, rather than to an active, ongoing infection.\nIn the future, NGS, combined with positive response to appropriate therapy, may improve diagnosis of infectious causes of ocular and periocular inflammation, potentially shrinking the number of cases deemed “sarcoidosis”.\nThis study is well-written and informative and its data demonstrate the utility of NGS for identifying either potential microbial triggers of sarcoidosis or potential infectious causes of granulomatous ocular and periocular inflammation. The only criticism is the discussion reads as a suggestion that infection may be causal in sarcoidosis. If this is the author’s position, it should be cited with supporting literature. Otherwise, minor revision to discuss the uncertainty that above cases might represent actual infection vs an immunologic response to a prior infection (i.e. sarcoidosis) is warranted.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "141758",
"date": "27 Sep 2022",
"name": "Eric B Suhler",
"expertise": [
"Reviewer Expertise Uveitis",
"clinical ocular immunology",
"clinical trials"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is scientifically sound and proposes a provocative and potentially highly fruitful area of future research into the etiopathogenesis and potential novel treatment of sarcoidosis. Sarcoidosis, while often appropriately presented as an etiologic diagnosis in and of itself, is in fact an idiopathic diagnosis with typical etiologic and histopathologic findings related to presumed exposure to an unknown inciting and possibly infectious antigen. The authors followed this current understanding and applied modern microbiologic techniques to attempt to ascertain more specifically what etiologic agents might be the culprit inciting organisms and found numerous candidates, suggesting that phenotypic sarcoidosis may be triggered by multiple inciting organisms, and laying the groundwork for future prospective studies on specific causative agents, which in the future might lay the groundwork for novel and more effective therapeutics.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-820
|
https://f1000research.com/articles/8-1529/v1
|
29 Aug 19
|
{
"type": "Research Article",
"title": "Prevalence of malaria and quantification of cytokine levels during infection in East Nile locality, Khartoum State: a cross-sectional study",
"authors": [
"Hwida Barkat",
"Ahmed Bakheet Abd Alla",
"Ahmed Galander",
"Tagwa Salah",
"Tayseer Elfaki",
"Ali Nasir",
"Hwida Barkat",
"Ahmed Galander",
"Tagwa Salah",
"Tayseer Elfaki",
"Ali Nasir"
],
"abstract": "Background: The cytokines interferon gamma (IFN-γ), interleukin-10 (IL-10) and tumor necrosis factor-α (TNF- α) play an important role in malaria infection. The aim of this study was to determine the prevalence of malaria and to evaluate cytokine responses to malaria infection in patients from the East Nile locality of Khartoum State. Methods: This study was carried out from May to July 2018 in the East Nile Locality, Khartoum State. Blood samples were collected from 384 randomly selected patients for blood film analysis. Of these, 39 were selected for cytokine level analysis (10 control and 29 patient samples), determined using enzyme-linked immunosorbent assays. Results: The malaria prevalence rate among 384 patients was 18.5%. Plasmodium falciparum was the most prevalent (13%), while the prevalence of Plasmodium vivax was 4.6%. The rate of mixed infection was 0.8%. There was a higher prevalence rate (22.7%) in males than females (15.6%). However, we found no significant correlation between cytokine levels and parasitemia in the study group. Nevertheless, our study demonstrated a significant correlation between cytokine levels and recurrent infections. Conclusions: Together, our data show that malaria remains a public health problem in East Nile locality with a high prevalence. Additionally, cytokine levels were found to be correlated with recurrent malaria infection.",
"keywords": [
"cytokines",
"IL – 10",
"TNF-α",
"IFN-γ",
"recurrent",
"malaria",
"Plasmodium"
],
"content": "Introduction\n\nMalaria is a mosquito-borne disease that affects humans and animals. This condition is caused by a protozoan parasite of the genus Plasmodium. Malaria symptoms include fever and headache, which result from parasite invasion of red blood cells. In severe cases, malaria infection may progress to coma or death (Elmardi et al., 2011). There are five Plasmodium species that are known to cause disease in humans (P. falciparum, P. vivax, P. ovale, P. malariae, and the recently described P. knowlesi). The species that causes the most severe cases is P. falciparum. Malaria control efforts in Sudan began in 1904, when Dr. A. Balfour succeeded in eradicating malaria from Khartoum (Malik et al., 2006). Determination of the correct prevalence of malaria is essential in implementing effective control strategies to curb its dissemination (Malik et al., 2006).\n\nImmunity to Plasmodium develops slowly and protection against Plasmodium occurs later than protection against malaria symptoms. The immune responses will not be same for the liver and blood stages because Plasmodium expresses various antigens at the liver and blood stages (Langhorne, 2005). Cytokines may assume a significant role in protection and pathology in malaria. The early effective inflammatory reaction is regulated by IFN-γ, IL-12. TNF- α appears to be crucial for parasitemia control in malaria infection (Artavanis-Tsakonas et al., 2003). However, pro-inflammatory cytokines (TNF- α, IFN-γ, IL-1 and IL-6) were associated with severe malaria (Malaguarnera & Musumeci, 2002). The high production of proinflammatory cytokines may increase cytoadherence of parasitized red blood cells to the endothelium through upregulation of adhesion molecules in P. falciparum infections (Day et al., 1999).\n\nThe expression of cytokines (pro- and anti-inflammatory) are said to be involved in malaria pathogenesis. Severe malaria has been associated with low serum levels of IL-12 and low IL-10 to TNF- α serum concentration ratios in a few studies of childhood malaria in holoendemic areas.\n\nIn order to explore the effect of the immune response to malaria and the development of clinical immunity, this study aimed to measure and determine the prevalence of malaria and quantify cytokine levels in patients with malaria infection in the East Nile locality.\n\n\nMethods\n\nThis cross-sectional study was carried out in the East Nile locality, which is located in the eastern part of Khartoum State, Sudan. This study was conducted in different pre-urban areas during the period from 1st May to 23rd of July 2018.\n\nThe study population included participants of all ages and genders from a population admitted to Elbanjadeed Hospital, Aldebaba Medical Health Center, Eid Babekir Medical Health Center, Helat Koko Medical Health Center and Omdom Medical Health Center. In total, 384 participants were asked to participate in this study, all of whom were admitted for malaria diagnosis. Participants were selected using quota sampling and all patients admitted for malaria diagnosis were eligible to be included in the study. The age groups were categorized as follows: less than 10 years, 11–49 years and over 50 years old. After participants signed an informed consent form for participation in the study, a questionnaire was used by expert laboratory technician to collect demographic data (information about age, sex, residence and occupation) and medical history of chronic disease (renal disease, heart disease and diabetes mellitus or other chronic disease) from patients enrolled in the study.\n\nIn total, 384 samples were collected from patients admitted for malaria infection at hospitals and health centers. The sample size was calculated on the following formula (Daniel, 1999):\n\n\n\nwhere N = sample size, Z = statistic for a level of confidence (1.96), P = prevalence in study area (50%) and d = precision (5%).\n\nFrom each patient, thick and thin blood films were prepared using finger prick blood samples taken as part of the routine diagnosis of infection with Plasmodium species. Thin films were fixed with methanol and slides were placed face down on a drying rack for five minutes to allow the methanol to fix. Thick and thin blood films were stained with Giemsa stain at a concentration of 10% for 10 minutes. The stain was flushed from the slides by adding drops of buffered water until all the stain has been washed away. Where the blood film analysis was positive for malaria, 5 ml of venous blood was collected from each patient into a sterile container. For cytokine analysis, 5ml of venous blood was also collected from 10 participants who tested negative for malaria and agreed to participate further in the study. These participants were selected using stratified random sampling, with two participants being randomly selected from each of the five health centers. Following collection, blood samples were centrifugated at 3000 rpm for 10 minutes. After centrifugation, the serum was separated and transferred to another labeled sterile container and stored in refrigerator at 4oC until use.\n\nAfter the films dried, they were examined microscopically by experienced personal to determine the parasite stages (ring, trophozoite, gametocyte and schizont), using the thin blood film to identify the species of Plasmodium and the thick film to classify parasitemia as follows:\n\n+: 1–10 parasites per 100 thick film fields\n\n+ +: 11–100 parasites per 100 thick film fields\n\n+ + +: 1–10 parasites per one thick film field\n\n+ + + +: more than 10 parasites per one thick film field\n\nFor cytokine analysis, 29 of the patient serum samples were selected using simple stratified sampling, with five positive samples randomly selected from each health center and nine randomly selected from the hospital. Cytokine analysis was not performed for all samples due to financial restrictions. The stored serum was brought to the laboratory and was allowed to thaw. Serum concentrations of IFN-y, IL-10, TNF-α were determined using an enzyme-linked immunosorbent assay (ELISA) according to manufacturer’s instructions (BioLegend’s ELISA MAX™ Deluxe Sets, catalog numbers 430104, 430604, and 340204 for IFN-y, IL-10, and TNF-α, respectively) for the patient samples and 10 control samples.\n\nBriefly, 100µL of diluted capture antibody solution was added to each well and the sealed plate was incubated overnight between 2–8°C. The plates were washed four times and then blocked by adding 200µL assay diluents to each well, then were sealed and incubated for one hour with shaking on a palate shaker at 500 rpm with a 0.3cm circular orbit. The plates were washed four times and then 100μl diluted standards and samples were added to each well. The plate was sealed and incubated at room temperature for two hours with shaking. The plate was washed four times, then 100µL diluted detection antibody solution was added to each well. Plates were sealed and incubated at room temperature for one hour with shaking. The plate was washed four times, then 100μl diluted avidin–HRP solution was added to each well. The plate sealed and was incubated at room temperature for 30 minutes with shaking. The plate was washed five times and then soaked for 30 seconds to one minute per wash. Then, 100µL fresh TMB substrate solution was added to each well and incubated in the dark for 20 minutes. Finally, 100 µL of stop solution was added to each well and the absorbance was read with the SPECTROstar Nano Microplate Reader at 540 nm and 570 nm within 15 minutes.\n\nData were analyzed using SPSS version-20. The Chi-squared test was performed to determine statistical significance and a P-value of less than 0.05 was considered statistically significant.\n\nEthical clearance for this study was obtained from Committee of Scientific Research Deanship, Sudan University of Science and Technology, ethical approval number (DSR – IEC – 12 – 07). Written informed consent for participation and publication of the data was obtained from all participants included in this study or for children, from their guardian.\n\n\nResults\n\nA total of 384 patients were enrolled in this study, of which 154 were male and 230 were female. Their ages were grouped into three categories: less than 10 years old (134), 11 – 49 years old (198) and more than 50 years old (52).\n\nFirst, we sought to determine the prevalence of malaria in our study population. To this end, we collected blood samples from our patients and examined them using blood films. Out of 384 blood samples collected from different pre-urban areas (medical centers and hospitals) in the East Nile locality during the period from May to July 2018 (pre- malaria season), 71 (18.5%) were found to be positive and 313 (81.5 %) were negative for malaria (Table 1) (Abd Alla & Brakat, 2019). Moreover, we observed a higher prevalence of malaria among males (22.7%) compared to females (15.6%) in our study population (Table 2). In addition, analysis of the prevalence among different age groups revealed that highest prevalence rate was in the under 10 age group (20.1%), followed by the 11–49 age group with a prevalence of 19.7%, while the lowest prevalence rate was reported among the over 50 age group (2%) (Table 3).\n\nNext, we determined the species distribution of Plasmodium species in our study population. We observed that P. falciparum had the highest prevalence rate (13%), followed by P. vivax (4.6%). However, mixed infection by P. falciparum and P. vivax had the lowest prevalence rate (0.8%). We failed to detect any positive results for P. malariae or P. ovale infection in our study population (Table 4).\n\nNext, we determined the distribution of severe malaria in the studied population. Our data showed that most (58%) of the study population had a low parasite count (mild parasitemia), while 13% had a moderate parasitemia (++). We detected no cases that exhibited severe parasitemia (+++ and ++++) (Table 5) and no statistically significant association between age group and parasitemia (Table 6).\n\nCytokines may play a role in protection and pathology in malaria. Thus, we investigated the cytokine profile in 29 patients and 10 controls from our study population. In particular, we investigated serum levels of IFNγ, TNF-α, and IL-10 with malaria infection in the study population. Interestingly, mean serum levels of IFNγ were significantly higher in malaria-infected individuals compared to non-infected individuals (P value = 0.026). However, TNF-α serum levels were comparable between patients and non-infected individuals (P value = 0. 646). Mean serum levels of IL-10 were higher in patients compared to non-infected individuals, although this difference was not statistically significant (P value = 0.071) (Table 7).\n\nNext, we sought to determine whether there is a correlation between the cytokine profiles of individuals enrolled in our study and severity of malaria and/or recurrent infection. However, we found no correlation between levels of IFNγ, TNF-α, or IL-10 and level of parasitemia (Table 8). Intriguingly, levels of TNF-α and IL-10 were significantly higher in patients who suffered from recurrent malaria infection compared to those who did not (Table 9). However, we failed to detect a significant correlation between levels of IFNγ and recurrent malaria infection (Table 9).\n\n\nDiscussion\n\nThe findings of our study revealed a prevalence rate of malaria of 18.5%. This rate was greater than the rate reported in Khartoum by El Mekki et al. (2012), who reported the prevalence of malaria in 5% and 11% in Dar Al Salam Camp and Jabal Awlia Camp, respectively. El Sayed et al. (2000) reported that Khartoum, which was formerly malaria free, can be considered as a hypoendemic or mesoendemic area in which malaria is unstable and epidemic outbreaks are common; our results agree with their findings.\n\nOur study show that Falciparum malaria is the most prevalent and constitutes about 13% of all infections, benign tertian Vivax malaria has prevalence of 4.6%, and the lowest prevalence rate of 0.8% is observed for mixed infection (P. falciparum and P. vivax). However, we observed no cases of P. malariae and P. ovale infection. Moreover, males had higher prevalence rate (22.7%) of malaria infection than females (15.6%). Our study findings agree with a study in Khartoum by Abdalla et al. (2007), who reported that the overall prevalence of malaria was 28.2 % and was higher in males than in females.\n\nThe highest prevalence rate (53.8%) of moderate parasitemia was in the under 10 years age group. Although children are more susceptible to malaria infection due to a slow developing immune system, a high prevalence rate (34.5%) of mild parasitemia was reported among the 11–49 years age group. A lower prevalence rate of 2% and mild parasitemia 12.1% was reported among the over 50 age group. This finding was closer to the finding of Igwe et al. (2014) in Nigeria, who reported that the highest prevalence of asymptomatic malaria parasitemia (87.5%) was found in parturient women who were ≤19 years, while the lowest prevalence (68.2%) occurred in those who were 40–49 years old. In the present study we observed that age group was not significantly associated with parasitemia. This is in agreement with a study done by El Khalifa et al. (2008), who found no significant difference in parasitemia among those aged five years and above.\n\nIn this study, serum levels IFN-γ, TNF- α and IL-10 were measured in healthy controls and in patients with P. falciparum and P. vivax infection and IFN-γ was found to be significantly higher in patients than in non-infected individuals. This finding is in line with a study in Poland by Wroczynska et al. (2005), who reported that the mean serum level of IFN-γ was found to be significantly higher in severe and uncomplicated malaria groups compared to the controls. Also, another study done by Favre et al. (1997) reported that these findings are consistent with a requirement for an early production of IFN-γ to mount resistance against infection. Interestingly, in this study, a significant correlation between IL-10 with gender and age was found. This association between initial IL-10 levels and parasite densities agreed in part with the findings of Hugosson et al. (2004), who reported similar findings during patient treatment, indicating that IL-10 levels may play a role in clearance of parasites during treatment. In addition, they also suggest that there are age-related differences in immunity and the development of partial clinical tolerance.\n\nThe present study reported no association between parasite density and levels of IFNγ, TNF-α and IL-10. These findings are in line with study done by Jason et al. (2001) in which serum IL-10 levels had statistically significant association with level of parasitemia. Furthermore, our data agrees with a study by Nnaemaka et al. (2009), who found no significant correlation between IL-10, IL-12 and IFNγ in asymptomatic individuals with parasitemia; however, Wroczynska et al. (2005) found that IL-10 and IL-12 were associated with malaria. In this study, there was significantly increased production of IL-10 and TNF-α in patients with recurrent malaria. This finding was in agreement with a study done by Edward et al. (2008), who reported that the high levels of IL-10 observed during malarial episodes may be beneficial, acting to reduce the inflammatory response. However, they may also be detrimental and decrease antiparasitic cellular immune responses. This is suggested by our data, with significant levels of TNF- α found in patients with recurrent malaria infection. This is in line with Medzhitov et al. (2012), who reported that these observations are predictable, with the possibility that recurrent malaria may drive the host towards a disease tolerant state, so as to diminish the negative effects of disease-related pathology. In subjects who are routinely infected by malaria, the pro-inflammatory response may be immediately controlled by regulatory mechanisms. This impact might be particularly exaggerated in this study area, where transmission is particularly extreme.\n\n\nData availability\n\nFigshare: hoda datta.sav. https://doi.org/10.6084/m9.figshare.8986178.v2 (Abd Alla & Brakat, 2019)\n\nThis project contains the following underlying data:\n\n- hoda datta.sav (demographic, behavioral and medical data for each participant and results of the microscopic examination)\n\n- samle and control.sav (cytokine levels for 39 patient and control samples, determined using ELISA)\n\n- Data dictionary_FL.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Grant information\n\nThe author(s) declared that there were no grants were involved in supporting this work.\n\n\nAcknowledgements\n\nWe would like to express our immense gratitude and appreciation to the Deanship of Scientific Research-Sudan University of Science and Technology, who supported this project by providing space in which to carry out the cytokine analysis performed in this study.\n\n\nReferences\n\nAbd Alla A, Brakat HE: hoda datta.sav. 2019. http://www.doi.org/10.6084/m9.figshare.8986178.v1\n\nAbdalla SI, Malik EM, Ali KM: The burden of malaria in Sudan: incidence, mortality and disability--adjusted life--years. Malar J. 2007; 6(1): 97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArtavanis-Tsakonas K, Tongren JE, Riley EM: The war between the malaria parasite and the immune system: immunity, immunoregulation and immunopathology. Clin Exp Immunol. 2003; 133(2): 145–52. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDaniel WW: Biostatistics: A Foundation for analysis in the health sciences. 7th ed, R Wiley. New York. 1999. Reference Source\n\nDay NP, Hien TT, Schollaardt T, et al.: The prognostic and pathophysiologic role of pro- and antiinflammatory cytokines in severe malaria. J Infect Dis. 1999; 180(4): 1288–97. PubMed Abstract | Publisher Full Text\n\nEdward RK, Atis M, Michal F, et al.: Maternal peripheral blood level of IL-10 as a marker for inflammatory placental malaria. Malar J. 2008; 7(1): 26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl Khalifa SM, Mustafa IO, Wais M, et al.: Malaria control in an urban area: a success story from Khartoum, 1995-2004. East Mediterr Health J. 2008; 14(1): 206–215. PubMed Abstract\n\nElmardi KA, Noor AM, Githinji S, et al.: Self-reported fever, treatment actions and malaria infection prevalence in the northern states of Sudan. Malar J. 2011; 10(1): 128. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl Mekki MA, Aburas NA, Alghaithy AA, et al.: Prevalence and Molecular Identification of Malaria Parasite in Displaced Camps in Khartoum State, Sudan. 2012; 4(1): 7–12. Publisher Full Text\n\nEl Sayed BB, Arnot DE, Mukhtar MM, et al.: A study of the urban malaria transmission problem in Khartoum. Acta Trop. 2000; 75(2): 163–71. PubMed Abstract | Publisher Full Text\n\nFavre N, Ryffel B, Bordmann G, et al.: The course of Plasmodium chabaudi chabaudi infections in interferon-gamma receptor deficient mice. Parasite Immunol. 1997; 19(8): 375–83. PubMed Abstract | Publisher Full Text\n\nHugosson E, Montgomery SM, Premji Z, et al.: Higher IL-10 levels are associated with less effective clearance of Plasmodium falciparum parasites. Parasite Immunol. 2004; 26(3): 111–7. PubMed Abstract | Publisher Full Text\n\nIgwe NM, Joannes UO, Chukwuma OB, et al.: Prevalence and parasite density of asymptomatic malaria parasitemia among unbooked paturients at Abakaliki, Nigeria. Journal of Basic and Clinical Reproductive Sciences. 2014; 3(1): 44–8. Reference Source\n\nJason J, Archibald LK, Nwanyanwu OC, et al.: Cytokines and malaria parasitemia. Clin Immunol. 2001; 100(2): 208–18. PubMed Abstract | Publisher Full Text\n\nLanghorne J: Immunology and immune pathogenesis of malaria. National institute for medical research, the Ridgeway, MiLLHiLL, London, NW7 1AA, uk. 2005. Publisher Full Text\n\nMalaguarnera L, Musumeci S: The immune response to Plasmodium falciparum malaria. Lancet Infect Dis. 2002; 2(8): 472–8. PubMed Abstract | Publisher Full Text\n\nMalik EM, Hanafi K, Ali SH, et al.: Treatment-seeking behaviour for malaria in children under five years of age: implication for home management in rural areas with high seasonal transmission in Sudan. Malar J. 2006; 5(1): 60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMedzhitov R, Schneider DS, Soares MP: Disease tolerance as a defense strategy. Science. 2012; 335(6071): 936–41. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNnaemeka C, Okafor CM, IdowuAyede Y, et al.: Cytokine profiles and antibody responses to Plasmodium falciparum malaria infection in individuals living in Ibadan, southwest Nigeria. Afr Health Sci. 2009; 9(2): 66–74. PubMed Abstract | Free Full Text\n\nWroczyńska A, Nahorski W, Bąkowska A, et al.: Cytokines and clinical manifestations of malaria in adults with severe and uncomplicated disease. Int Marit Health. 2005; 56(1–4): 103–14. PubMed Abstract"
}
|
[
{
"id": "58145",
"date": "16 Jan 2020",
"name": "Yaowapa Maneerat",
"expertise": [
"Reviewer Expertise Immunopathology in malaria."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAs per my knowledge, there have been several studies in roles of cytokine profiles in human and animal malaria. This study aimed to determine important cytokines in malaria. These included IFN-γ, IL-12. TNF- α. They used rather appropriate sample size. However, as follows, it was found some points are unclear and should be clarified.\n\nThe conclusion in the abstract is not clear. The authors did not indicate any cytokines.\n\nThe rationale and the benefit of study is not clear.\n\nThe author did not show the difference in any cytokine levels between P. falciparum and P. vivax infected patients.\n\nIt seems that there are too many tables. Is it possible to merge Table 1 and 2; 3 and 6?\n\nCorrelation between parasitemia and cytokines in Table 8 is not reliable. Sample size (n=4) is too small for determining correlation.\n\nThe authors did not mentioned about detail of patients in ELISA results. Why sample size was 10 control and 29 patients?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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? No",
"responses": []
},
{
"id": "66205",
"date": "03 Jul 2020",
"name": "Rusliza Basi",
"expertise": [
"Reviewer Expertise Immunotherapeutic target for malaria infection."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt was mentioned that patients serum samples were selected randomly for cytokines analysis. How does this random selection carry out? Does it take into consideration the age of patients since they are categorized according to age at the beginning? There would be differences in cytokine release profile between child, adult and elderly as the level of immune response between the three groups towards invading organisms would be different. So how does the selection carry out among the three groups of patients?\n\nThe symbol for gamma for IFN must be presented properly with the right symbol… not “y”.\n\nWhat is the age profile or category of the 29 patients in whom the cytokine profile was carried out? It would be interesting to see if the cytokines release is influenced by age.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/8-1529
|
https://f1000research.com/articles/10-153/v1
|
26 Feb 21
|
{
"type": "Research Article",
"title": "Regional disparities in postnatal care among mothers aged 15-49 years old in Indonesia",
"authors": [
"Mochammad Nur Cahyono",
"Ferry Efendi",
"Harmayetty Harmayetty",
"Qorinah Estiningtyas Sakilah Adnani",
"Hsiao Ying Hung",
"Mochammad Nur Cahyono",
"Harmayetty Harmayetty",
"Qorinah Estiningtyas Sakilah Adnani",
"Hsiao Ying Hung"
],
"abstract": "Background: In Indonesia, maternal mortality remains high, significantly 61.59% occur in the postnatal period. Postnatal care (PNC) provision is a critical intervention between six hours and 42 days after childbirth and is the primary strategy to reduce maternal mortality rates. However, underutilization of PNC in Indonesia still remains high, and limited studies have shown the regional disparities of PNC in Indonesia. Methods: This study aims to explore the gaps between regions in PNC service for mothers who have had live births during the last five years in Indonesia. This study was a secondary data analysis study using the Indonesian Demographic and Health Survey (IDHS) in 2017. A total of 13,901 mothers aged 15-49 years having had live births within five years were included. Chi-squared test and binary logistic regression were performed to determine regional disparities in PNC. Results: Results indicated that the prevalence of PNC service utilization among mothers aged 15-49 years was 70.94%. However, regional gaps in the utilization of PNC service were indicated. Mothers in the Middle of Indonesia have used PNC services 2.54 times compared to mothers in the East of Indonesia (OR = 2.54; 95% CI = 1.77-3.65, p<0.001). Apart from the region, other variables have a positive relationship with PNC service, including wealth quintile, accessibility health facilities, age of children, childbirth order, mother's education, maternal occupation, husband's age, and husband's education. Conclusion: Structured policies are needed to reduce gaps in areas with low service utilization. Developing innovative strategies to address PNC inequality in maternal services to improve maternal health is expected.",
"keywords": [
"postnatal care",
"regional disparities",
"reduced inequalities"
],
"content": "Introduction\n\nMaternal morbidity and mortality are a serious global health challenge. In 2019, the World Health Organization (WHO) revealed that 94% of maternal mortality occurred in low and middle-income countries, of which Indonesia is one (World Health Organization, 2019; World Health Organization et al., 2015). During 2000 and 2017, the maternal mortality ratio plunged by about 38% worldwide. Even with this decline, Sub-Saharan Africa and Southern Asia accounted for approximately 86% of maternal deaths worldwide. Southern Asia alone accounted for nearly one-fifth (58,000), which demonstrated the struggle to improve maternal health (World Health Organization, 2019; World Health Organization et al., 2015). In the Indonesia context, the government determined a target to reach an important goal of reducing maternal mortality rate to 102 per 100,000 live births in 2015 (Bappenas, 2015; Ministry of Health Republic of Indonesia, 2018). Despite the significant efforts to expand maternal health programmes, recent evidence showed that Indonesia was off-track to reach the Millenium Development Goals (MDGs) target by 2015. In 2015, maternal mortality deaths in Indonesia were three times higher than the MDGs target (Ministry of Health Republic of Indonesia, 2018; UNICEF & World Health Organization, 2015; World Health Organization et al., 2015). Hence, reducing maternal mortality ratio to less than 70 per 100,000 by 2030 as one of the Sustainable Development Goals (SDGs) target could be a critical challenge for Indonesia (UNICEF & World Health Organization, 2015; United Nations, 2017; World Health Organization, 2012).\n\nMost maternal mortality deaths are preventable or treatable if skilled healthcare, such as midwives, is provided during the postnatal period. Critical interventions during the postnatal period must be delivered to prevent maternal mortality deaths (Lawn et al., 2016; World Health Organization et al., 2015). In the Indonesian setting, the cause of maternal mortality is predominantly due to postpartum haemorrhage, followed by indirect causes, such as heart disease, severe anaemia, malaria, HIV/ AIDS and hepatitis. Many factors have been linked to interventions of postpartum haemorrhage which cause emergency cases, and skilled health care required to respond effectively to emergencies (Adisasmita et al., 2015; Mahmood et al., 2018). However, PNC remains a critical intervention to reduce maternal deaths in Indonesia. A new health programme called EMAS (Expanding Maternal and Neonatal Survival), was implemented by the Indonesian government in 2012, focused on improving maternal health care. The programme aimed at ensuring that every woman has access to quality maternal healthcare, including childbirth assistance by skilled health personnel in healthcare facilities (a target of 2018 strategic plan: 82%), four visits of Antenatal care (ANC) (78% ), PNC, and providing ANC (87%). However, the national data revealed that utilization of PNC among 34 provinces in Indonesia remain varied and was considered lower compared to the childbirth assistance by skilled health personnel coverage. Socioeconomic, geographical, and demographic factors influence the underutilization of PNC. Current systematic reviews show that levels of education, poverty, and limitations of access to PNC services are common issues in low-and middle-income countries linked to inequities in the use of PNC services (Langlois et al., 2015).\n\nIn an Indonesia context, the national data in 2018 revealed that the average percentage of PNC visits for the first time in Indonesia was 93.3%. The highest percentage of visits occurred in Yogyakarta (99.6%) and the lowest percentage of visits was in Papua (56.3%). However, there were regional gaps in PNC visits across the provinces in Indonesia. Also, PNC utilization in rural areas was lower than urban areas in Indonesia (Kementerian Kesehatan Republik Indonesia, 2018; Ministry of Health Republic of Indonesia, 2018; Probandari et al., 2017). It is worth noting that 61.59 % of maternal mortality rates occurred during the postnatal period in Indonesia. Additionally, evidence shows that the quality of PNC is lower in most districts and cities among the Eastern Region in Indonesia. PNC must be performed a minimum of three times: within the first six hours to the third day after the delivery, from the fourth day to the 28th after the delivery and the 29th day to the 42nd day after childbirth. The standards of PNC including examination for vital signs; the apex of the uterus; lochia and other per vagina fluids; breasts and counselling for exclusive breastfeeding; provision of communication, information about and education of PNC, and family planning (Ministry of Health Republic of Indonesia, 2018; Probandari et al., 2017).\n\nSeveral studies show that regional disparities in PNC occur in several countries. In Ethiopia, there were differences in each region and variations at regional levels at the utilization of PNC among women (Sisay et al., 2019). PNC service in Zambia was also reported to experience regional disparities (Jacobs et al., 2017). In the same vein, in Bangladesh, disparities in the utilization of maternal health services were also reported (Raheem et al., 2019). However, research focused on regional disparities on PNC among mothers aged 15–49 years old in Indonesia are not well investigated. This study was conducted to analyze the gap between regions in PNC service utilization among mothers aged 15 – 49 years old who have had live births during the last five years in Indonesia. This study is significant because it can be a source of information and a reference regarding regional disparities in the utilization of PNC services in Indonesia. This research could complete a bigger picture for consideration in resolving disparities maternal services in Indonesia.\n\n\nMethods\n\nThis study analyzed and reported unit data from the 2017 Indonesian Demographic Data Survey (IDHS) collected by the Inner City Fund (ICF). This study is part of the International Demographic and Health Survey (DHS) program. In this study, unit data consist of women aged 15–49 years old having had live births in the last five years preceding the survey.\n\nThe purpose of the cross-sectional study of the IDHS conducted by the ICF from July 24 to September 30, 2017 was to offer up-to-date projections of basic demographic and health indicators. The IDHS study demonstrates a broad overview of population problems in Indonesia.\n\nWe utilized the data conducted by the national and provincial representatives. This cross-sectional study represents 1,970 census blocks urban and rural areas in Indonesia. The census block obtained 59,100 female respondents aged 15–49 years old. The survey employed a two-stage stratified cluster sampling method. The first stage was the selection of several census blocks by systematic sampling proportional size. In the second stage, 25 ordinary households were selected with systematic sampling from the listing. In this study, a sample of 13,901 women aged 15–49 years from 34 provinces in Indonesia was analyzed. The inclusion criteria were taken from IDHS that included all women aged 15–49 years who had given birth in the last five years. The exclusion criteria were whether the variables incomplete or not available.\n\nEthical review boards approved ethical clearance for the Inner City Fund OCR Macro (number 45 CFR 46) and the national board review from the Ministry of Health of Republic Indonesia.\n\nBefore the survey, an informed consent was obtained from the respondents based on voluntary participation.\n\nThe dependent variable of this study was PNC visits. According to the recommendation of the Ministry of Health Republic of Indonesia, PNC must be performed at minimum three times: at the first six hours to the third day after the delivery, on the fourth day to the 28th after the delivery and the 29th day to the 42nd day after childbirth (Ministry of Health Republic of Indonesia, 2018). This data was based on the mother’s perception of PNC utilization during the postnatal period. Independent variables analyzed in this study were the related geographic and socioeconomic factors, including a region of residence, the place of residence, wealth quintile, health insurance, access to health facility, age, gender, birth rank, education, and occupation.\n\nThe residence region was grouped as six regions, namely Sumatera, Jawa, Bali & Nusa Tenggara, Kalimantan, Sulawesi, Maluku & Papua, and of which were also categorized as West Indonesia, Middle Indonesia and East Indonesia. The place of residence was determined as rural and urban areas. The wealth quintile of households was set into five categories: poorest, poorer, middle, richer, and richest. The wealth quintile of households was scored based on wealth criteria (DHSProgram, 2016). Health insurance was divided into two categories, namely yes and no. Access to the health facility was categorized into two, namely difficult and not. Children’s age was divided into five categories: less than one month, one month, two months, three months, four months. The gender of the child, namely female and male. Birth rank was categorized as first child, second, third, fourth and so on. Mother’s age divided into six categories: 15–24, 25–29, 30–34, 35–39, 40–49, and 45–49, while husband’s age divided into seven categories: 11–20, 21–30, 31–40, 41–50, 51–60, 61–70, 71–80. Mother’s and husbands’ education levels were grouped into no education, primary, secondary, and higher education. Mother’s and husband’s occupation was divided into two categories: not working and working.\n\nData were analyzed using STATA version 16.0. The descriptive statistics method was also utilized for showing what kinds of data. Due to variables, the chi-square test was performed to determine variables correlated to the PNC utilization. Binary logistic regression was utilized to determine disparity in this study. Measurement of associations among variables was expressed as Odds Ratio (OR) and 95% Confidence Interval (CI). Significant variables were tested with a p-value of 0.05 and 95% CI, which are considered the disparity in PNC among mothers aged 15–49 years in Indonesia.\n\n\nResults\n\nA total of 13,901 women aged 15–49 years old with live births in the last five years preceding the survey were interviewed. Table 1 shows the bivariate analysis that there were ten categories among some variables associated with the utilization of PNC visits (p-value < 0.05). These variables include geographic factors, region, socio-economy (wealth quintile and access to the health facility), children (age of child and birth rank), mother factors (age, education and occupation), husband factors (age, education, and occupation). Residence, socioeconomic (health insurance ownership), child gender, mother’s age and husband’s occupation did not show associations with the utilization of PNC visits among mothers aged 15–49 years old in Indonesia (Table 1). More detail results can be found in Table 1.\n\n*p<0.05; **p<0.01;***p<0.001\n\nTable 2 shows that the least distribution of respondents is in the East of Indonesia. Nearly half of participants who live in the East of Indonesia did not use the PNC services. More than half of participants who live in the East of Indonesia was classified as lowest. Interestingly, most participants who live in the East of Indonesia stated that there was no problem with access to the health facility. More detail characteristics of participants can be found in Table 2.\n\nTable 3 reveals that nearly half of participants who live in Sumatera, Kalimantan, Maluku and Papua did not use the PNC service. The highest number of participants classified as lowest was found in Maluku & Papua. For health insurance ownership, more participants who live in Kalimantan did not have health insurance. The highest number participants having four and more children per household were found in Maluku & Papua (Table 3).\n\nIn multivariate analysis, the participants who live in the Middle of Indonesia utilized PNC services 2.54 times more than the participants who live in the West of Indonesia (OR = 2.54; 95% CI = 1.77-3.65). The participants who live in the East of Indonesia had 0.71 fewer odds than participants in Indonesia’s West (OR = 0.71; 95% CI = 0.52-0.96). The participants who live in Java were 1.46 times more likely to use PNC services (OR = 1.46; 95% CI = 1.26-1.69) compared to participants living in Sulawesi (OR = 0.53; 95% CI = 0.35-0.80). (Table 4). Details of the results of a multivariate analysis shown in Table 4.\n\n*p<0.05; **p<0.01; ***p<0.001.\n\nTable 5 reveals the middle category women based on wealth index had PNC service’s utilization increased by 1.25 greater odds (OR = 1.25; 95% CI = 1.07-1.47) more than the richer category mothers (OR = 1.23; 95% CI = 1.04-1.45). Participants who thought that access to the health facility was not a problem had an odds ratio of 1.29 greater than participants who considered access to the health facility to be a major problem in using PNC service (OR = 1.29; 95% CI = 1.10-1.51). Mothers having children aged three months had used PNC service 1.43 times (OR = 1.43; 95% CI = 1.23-1.66) more than mothers with children aged four months (OR = 1.30; 95% CI = 1.12-1.51). Mothers who had a second child had utilized PNC service 0.88 times (OR = 0.88; 95% CI = 0.78-0.99) more than mothers who had a third child (OR = 0.86; 95% CI = 0.74-0.99). Mothers who had higher education had 2.11 times the chance to utilize PNC visits (OR = 2.11; 95% CI = 1.24-3.59) compared to those with lower level education (OR = 1.80; 95% CI = 1.09-2.98). Mothers with husband’s aged 41–50 had a higher chance of utilization PNC visits (OR = 2.18; 95% CI = 1.31-3.63) compared to mothers with husband’s aged 31–40 (OR = 2.07; 95% CI = 1.26-3.40). Details of the results of a multivariate analysis shown in Table 5.\n\n*p<0.05; **p<0.01; ***p<0.001.\n\n\nDiscussion\n\nThis study aimed to examine the gap across the region in Indonesia for PNC utilization among mothers aged 15–49 years old using the 2017 IDHS data sets. PNC has been the primary strategy to improve maternal health outcomes to reduce the high maternal mortality deaths in Indonesia. Therefore, assessing the regional disparities in PNC may provide evidence for the government to resolve discrepancies in maternal services in Indonesia. This study demonstrated that the prevalence of PNC service utilization among mothers aged 15–49 years was 70.94%. This finding was higher than other research in Sub-Saharan Africa, and Ethiopia with Abebo & Tesfaye (2018) and Tessema et al. (2020), respectively finding that 47.9% and 52.48% of women had used PNC service. An intertwined complex factor, such as the health system, maternal health policies, and socio-cultural variations across countries, may hinder women’s use of the PNC service.\n\nThe findings in this study revealed the geographic influence on mothers for utilization of PNC service. Mothers who settled in the Middle of Indonesia had increased odds of using PNC service, while those which lived in the East of Indonesia had decreased odds. This result is congruent with previous research carried out in Ethiopia (Sisay et al., 2019). In Ethiopia, the geographic factor is correlated to the utilization of PNC service due to the region’s level of development and location. Evidence in Indonesia shows that the socio-economic development, such as industrial, housing, public transportation, road facilities and health facilities in the East of Indonesia, lagged compared to the West of Indonesia (Ministry of Health Republic of Indonesia, 2018; Soewondo et al., 2019; Suparmi et al., 2018). Therefore, it is a call of action to provide equality in developing human resources and infrastructure to reduce the possibility of gaps.\n\nAdditionally, mothers who live in Java are 1.46 times more likely to use PNC services than mothers who live in Sulawesi where they are 0.53 less likely to utilize PNC services. Consistent with previous studies performed in Indonesia, Java has dominance development compared to other islands because this island is the centre of the Indonesian government (Laksono et al., 2020). The Java island oriented and centred development model has harmed maternal health outcomes in Indonesia (Bappenas, 2018). Natural resources, human resources and facilities must be equal throughout Indonesia, so the gap between islands could be minimized.\n\nThis study revealed that the wealth index was significantly linked to PNC service utilization among mothers aged 15–49 years old in Indonesia. Mothers from the middle households based on the wealth index had PNC service’s utilization increased by 1.25 greater odds (OR = 1.25; 95% CI = 1.07-1.47) more than the richer mothers (OR = 1.23; 95% CI = 1.04-1.45). Interestingly, this result was not consistent with that of research done in Pakistan, Ethiopia, and Tanzania, where mothers from the richer wealth quintile were significantly associated with the utilization of PNC services (Berhe et al., 2019; Mohan et al., 2017; Yunus et al., 2013). However, in this study we have found that, statistically, the odds ratio was quite similar between middle and richer households. Additionally, the previous study in other parts of Ethiopia demonstrated that sociodemographic factors, such as income, did not correlate with the use of PNC services (Angore et al., 2018). Mothers from richer households were more likely to access the PNC services. Ownerships of consumer goods at home, such as motorcycles and cars, may increase the risk at ease transportation, making them have no strain to access the health facility.\n\nThe present study showed that access to the health facility was correlated to PNC service in Indonesia. With mothers who thought that access to the health facility was not a problem, they had an odds ratio of 1.29 greater in using PNC service than mothers who considered access to the health facility difficult. Previous research conducted in Malawi has found a significant association between the health facility and the utilization of PNC services. Other Ethiopia studies have demonstrated that physical accessibility plays an essential variable in health service utilization (Kim et al., 2019; Tarekegn et al., 2014). Access to the health facility is related to the costs incurred, which is influenced by having transportation to the health facility, which is considered expensive. Long and shorter distances, better roads, and better public transportation may increase access to the health facility, primarily in Indonesia, with its massive gaps in development across the country (Bappenas, 2018).\n\nIn this study, mothers having children aged three months increased the likelihood to use PNC services about 1.43 times (OR = 1.43; 95% CI = 1.23-1.66) more than mothers with children aged four months (OR = 1.30; 95% CI = 1.12-1.51). A similar study in Nepal showed that PNC service utilization in the early postnatal period was most likely due to the motherhood transition period (Sanjel et al., 2019). The possible reason could be that mothers with fewer children, and younger children, may want information and petrified of complications during the postnatal period. In the Indonesia setting, the first neonatal examination (KN1) is carried out at 6–48 hours after baby is born, which is at the same time for the first PNC visit (KF1). The second neonatal examination (KN2) is carried out between 3–7 days with the second PNC visit (KF2). The third neonatal examination (KN3) occurs alongside the third PNC visit (KF3), which is between 8–28 days after birth (Ministry of Health Republic of Indonesia, 2018).\n\nAlso, mothers who have second child had a 0.88 times likelihood to utilize PNC service (OR = 0.88; 95% CI = 0.78-0.99) than mothers having a third child (OR = 0.86; 95% CI = 0.74-0.99). This is congruent with previous studies conducted in Ethiopia and India, which showed that the higher the child’s birth order, the lower the utilization of PNC services (Ali & Chauhan, 2020; Sisay et al., 2019). A possible reason could be that mothers who had more children were more likely experienced in motherhood and had appropriate knowledge from previous maternal experiences and childcare, hence restraining PNC service.\n\nThis study revealed that mothers who hold higher education qualifications have 2.11 times the chance of utilizing PNC visits (OR = 2.11; 95% CI = 1.24-3.59) compared to those with lower level education (OR = 1.80; 95% CI = 1.09-2.98). The finding is similar to a study conducted in Ethiopia, which revealed that a mother’s education was significant to PNC utilization (Tarekegn et al., 2014). The possible reason could be that educated women have a greater opportunity to be informed and are more aware of seeking advice and treatment from skilled healthcare personnel than uneducated women.\n\nThis study demonstrated that the husband’s age was significantly linked to the utilization of PNC among mothers aged 15–49 years in Indonesia. Mothers who have husbands aged 41–50 have a higher chance of utilizing PNC visits than mothers who have husbands aged 31–40. These findings were in line with another study in India that showed that the husband’s age was associated with PNC’s wives’ service (Jungari & Paswan, 2019). Husband’s autonomy and power in decision-making regarding wive’s needs, including their health care needs, remained persistent. Husband’s age may be linked to the level of maturity and primary controller, which exacerbates their wives' access to the health service (Jungari & Paswan, 2019; Sekine & Carter, 2019).\n\nTo the best of our knowledge, this is the first study to examine the gaps across the region in utilization PNC service among mothers aged 15–49 years old in Indonesia, which is one of a country in Southeast Asia that contribute to the global burden of maternal mortality rates in the world. The strengths of our study that we utilized the national and provincial data representatives, which internationally standardized. However, we also note some limitations. The IDHS data analyzed in this study was collected using the cross-sectional method and mother’s recall preceding survey prone to the possibility bias information.\n\n\nConclusion\n\nThis study reveals the gap across the region for PNC utilization among mothers aged 15–49 years old in Indonesia. This study’s findings provide evidence to complete the bigger picture for the government to resolve discrepancies in maternal services in Indonesia. Structured policies are needed to reduce gaps in areas with low service utilization. Developing innovative strategies to address inequality in maternal services to improve maternal health is inescapable. Future research should explore the interregional gaps and factors that cause maternal health service utilization by using a different platform.\n\n\nData availability\n\nData used in this study is available online from the Indonesian 2017 Demographic and Health Survey (DHS) website under the DHS VII recode column. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.",
"appendix": "References\n\nAbebo TA, Tesfaye DJ: Postnatal care utilization and associated factors among women of reproductive age Group in Halaba Kulito Town, Southern Ethiopia. Arch Public Health. 2018; 76: 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAdisasmita A, Smith CV, El-Mohandes AAE, et al.: Maternal characteristics and clinical diagnoses influence obstetrical outcomes in Indonesia. Matern Child Health J. 2015; 19(7): 1624–1633. PubMed Abstract | Publisher Full Text\n\nAli B, Chauhan S: Inequalities in the utilisation of maternal health care in rural India: Evidences from national family health survey III & IV. BMC Public Health. 2020; 20(1): 369. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAngore BN, Tufa EA, Bisetegen FS: Determinants of postnatal care utilization in urban community among women in Debre Birhan Town, Northern Shewa, Ethiopia. J Health Popul Nutr. 2018; 37(1): 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBappenas: Laporan pencapaian tujuan pembangunan milenium di Indonesia 2014. Jakarta, Indonesia: Badan Perencanaan Pembangunan Nasional. 2015.\n\nBappenas: Prakarsa pemerintah daerah dalam upaya pengurangan kesenjangan wilayah dan pembangunan daerah. Jakarta, Indonesia: Bappenas. 2018. Reference Source\n\nBerhe A, Bayray A, Berhe Y, et al.: Determinants of postnatal care utilization in Tigray, Northern Ethiopia: A community based cross-sectional study. PLoS One. 2019; 14(8): e0221161. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDHSProgram: Wealth Index. 2016. Reference Source\n\nJacobs C, Moshabela M, Maswenyeho S, et al.: Predictors of antenatal care, skilled birth attendance, and postnatal care utilization among the remote and poorest rural communities of Zambia: a multilevel analysis. Front Public Health. 2017; 5: 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJungari S, Paswan B: What he knows about her and how it affects her? Husband’s knowledge of pregnancy complications and maternal health care utilization among tribal population in Maharashtra, India. BMC Pregnancy Childbirth. 2019; 19(1): 70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKementerian Kesehatan Republik Indonesia: Laporan nasional riset kesehatan dasar: Jakarta. 2018.\n\nKim ET, Singh K, Speizer IS, et al.: Availability of health facilities and utilization of maternal and newborn postnatal care in rural Malawi. BMC Pregnancy Childbirth. 2019; 19(1): 503. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaksono AD, Rukmini R, Wulandari RD: Regional disparities in antenatal care utilization in Indonesia. PLoS One. 2020; 15(2): e0224006. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLanglois EV, Miszkurka M, Zunzunegui MV, et al.: Inequities in postnatal care in low-and middle-income countries: a systematic review and meta-analysis. Bull World Health Organ. 2015; 93(4): 259–270G. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLawn JE, Blencowe H, Waiswa P, et al.: Stillbirths: rates, risk factors, and acceleration towards 2030. Lancet. 2016; 387(10018): 587–603. PubMed Abstract | Publisher Full Text\n\nMahmood MA, Mufidah I, Scroggs S, et al.: Root-cause analysis of persistently high maternal mortality in a rural district of Indonesia: Role of clinical care quality and health services organizational factors. BioMed research international. 2018; 2018(3673265): 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMinistry of Health Republic of Indonesia: Indonesia health profile Jakarta. Indonesia: Ministry of Health Republic of Indonesia. 2018.\n\nMohan D, LeFevre AE, George A, et al.: Analysis of dropout across the continuum of maternal health care in Tanzania: findings from a cross-sectional household survey. Health Policy Plan. 2017; 32(6): 791–799. PubMed Abstract | Publisher Full Text\n\nProbandari A, Arcita A, Kothijah K, et al.: Barriers to utilization of postnatal care at village level in Klaten district, central Java Province, Indonesia. BMC Health Serv Res. 2017; 17(1): 541. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRaheem E, Khan JR, Hossain MS: Regional disparities in maternal and child health indicators: Cluster analysis of districts in Bangladesh. PLoS One. 2019; 14(2): e0210697. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSanjel K, Onta SR, Amatya A, et al.: Patterns and determinants of essential neonatal care utilization among underprivileged ethnic groups in Midwest Nepal: a mixed method study. BMC Pregnancy Childbirth. 2019; 19(1): 310. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSekine K, Carter DJ: The effect of child marriage on the utilization of maternal health care in Nepal: A cross-sectional analysis of Demographic and Health Survey 2016. PLoS One. 2019; 14(9): e0222643. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSisay MM, Geremew TT, Demlie YW, et al.: Spatial patterns and determinants of postnatal care use in Ethiopia: findings from the 2016 demographic and health survey. BMJ Open. 2019; 9(6): e025066. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSoewondo P, Johar M, Pujisubekti R, et al.: Inspecting primary healthcare centers in remote areas: Facilities, activities, and finances. Jurnal Administrasi Kesehatan Indonesia. 2019; 7(1): 89–98. Publisher Full Text\n\nSuparmi, Kusumawardani N, Nambiar D, et al.: Subnational regional inequality in the public health development index in Indonesia. Glob Health Action. 2018; 11(sup1): 1500133. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTarekegn SM, Lieberman LS, Giedraitis V: Determinants of maternal health service utilization in Ethiopia: analysis of the 2011 Ethiopian Demographic and Health Survey. BMC Pregnancy Childbirth. 2014; 14(1): 161. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTessema ZT, Yazachew L, Tesema GA, et al.: Determinants of postnatal care utilization in sub-Saharan Africa: a meta and multilevel analysis of data from 36 sub-Saharan countries. Ital J Pediatr. 2020; 46(1): 175. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUNICEF and World Health Organization: A decade of tracking progress for maternal, newborn and child survival the 2015 report. Geneva, Switzerland. 2015. Reference Source\n\nUnited Nations: Sustainable Development Goals 17 goals to transform our world. 2017. Reference Source\n\nWorld Health Organization: Coutdown to 2015 Maternal, Newborn & Child Survival. 2012. Reference Source\n\nWorld Health Organization: Maternal mortality. 2019. Reference Source\n\nWorld Health Organization, UNICEF, UNFPA, et al.: Trends in maternal mortality: 1990 to 2015 Estimates by WHO, UNICEF, UNFPA, World Bank Group and the United Nations Population Division. 2015. Reference Source\n\nYunus A, Iqbal S, Munawar R, et al.: Determinants of postnatal care services utilization in Pakistan-insights from Pakistan demographic and health survey (PDHS) 2006-07. Middle East J Sci Res. 2013; 18(10): 1440–1447. Reference Source"
}
|
[
{
"id": "80365",
"date": "16 Mar 2021",
"name": "Asmaa Salah Eldin Mohamed Saleh",
"expertise": [
"Reviewer Expertise Community health nursing",
"maternal and children health nursing",
"geriatric health nursing",
"health promotion",
"health education",
"occupational health nursing",
"public health nursing",
"primary health nursing",
"rehabilitation 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\nHello, best greeting - It is my pleasure to review this article, thanks to the editors and authors.\nI found this article was written in good condition by following the scientific rules for writing and I found nothing to be critic on it except just a few notes that do not affect the article structure; like authors mention Java and Jawa in entire the article, I suggest unifying the term mentioned in the article.\nIn the conclusion section, the authors mentioned that “Structured policies are needed to reduce gaps in areas with low service utilization. Developing innovative strategies to address PNC inequality in maternal services to improve maternal health is expected”. It would be preferred to have clearly applicable recommendations which serve as the solution for the article hypothesis.\nThe references in the article must be written in chronologically way in the same pattern for all.\nTable 3: Socio-demographic characteristic of participants PNC in Indonesia based on region (n=13,901). The total sum of (No) use of PNC is not right (4039) it is 4040, you need to review it.\nMany thanks, with my best wishes.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "7011",
"date": "16 Aug 2021",
"name": "Ferry Efendi",
"role": "Author Response",
"response": "We thank the reviewer for the thoughtful review of our manuscript. The term mentioned in the article, which is Java, has been complete and corrected. Thank you for your suggestions. We have revised as follows: The results suggest the need for national policy focuses on service equality, accessible and reliable implementation to improve postnatal care utilization among mothers to achieve the maximum results for the Indonesian Universal Health Coverage plan. The reference list has been completed and corrected. We appreciate the reviewer drawing our attention to this error, which has been corrected in our resubmission (4040)."
}
]
},
{
"id": "89395",
"date": "29 Jul 2021",
"name": "Kusrini S. Kadar",
"expertise": [
"Reviewer Expertise Community health",
"health education",
"health promotion",
"nursing workforce"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very interesting study providing information of the utilization of PNC services in Indonesia. The authors have described the gaps across the region clearly. We can see which regions in Indonesia utilized more PNC service as well as other factors contributing to this utilization.\n\nAs this study using secondary data from Indonesian DHS in 2017, this situation might have changed now, perhaps it is good to add in the title the year of the survey.\n\nIn the method section, it is not very clear whether the authors explain the method used by the IDHS or the method for this study. The information provided in this section hinders the possibility of others to replicate this study. Need more detailed information, step-by-step of what the authors did in this method section1.\nIn the variable, for example, the authors categorized the mothers' age into six groups however there is no reference of this categorizing whether using WHO definition or else. Need to provide more information regarding this section.\nStatistical analysis is already clear and can be replicated. The description of the result also has been clear.\nIn the discussion part, the authors' explanation is very repetitive. Every paragraph has a similar pattern where it started from the finding, comparing with previous study and additional explanation. Although this pattern can be accepted, however somehow make this part very boring. The authors tend to start the statement with: this study inline with.... the result congruent with...consistent with previous study... If it's possible to change the pattern in every paragraph not only the word that is used.\nLastly, there are some words that can be changed such as husband with spouse.\n\nTerm for explaining regions in Indonesia can be changed (follow the time zone of Indonesia):\n\n\"West of Indonesia\" with Western part/regions of Indonesia/Western Indonesia. \"Middle of Indonesia\" with Central part/regions of Indonesia/Central Indonesia. \"East of Indonesia\" with Eastern part/regions of Indonesia/Eastern Indonesia.\nFor language clarity, I encourage the authors to use an English language editing service to produce more clear sentences and paragraphs.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7012",
"date": "16 Aug 2021",
"name": "Ferry Efendi",
"role": "Author Response",
"response": "1. We appreciate the reviewer’s positive feedback and recommendations. We have added in the title the year of the survey as suggested. It would now read “Regional disparities in postnatal care among mothers aged 15-49 years old: An analysis of the Indonesian Demographic and Health Survey 2017”. 2. Thank you for your feedback. The sentence have been revised as follow: This study was a secondary data analysis using the most recent data from the 2017 Indonesian Demographic Data Survey (IDHS) collected by the Inner City Fund (ICF). This study is part of the International Demographic and Health Survey (DHS) program. We clarify that in the data availability section the information required for other researchers to replicate this study. Data used in this study is available online from the Indonesian 2017 Demographic and Health Survey (DHS) website under the DHS VII recode column. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm. While the guide for using datasets for analysis is available at https://dhsprogram.com/data/Using-DataSets-for-Analysis.cfm. Other researchers will be able to access the data set in the same way as the authors and the authors do not have special access rights that others do not have. Further, we clarify that unlike other secondary data, DHS secondary data is structured and well organized to produce high-quality data. We have added more information on methods section for the purpose of replicability. Authors categorized the mothers' age into six groups based on the reference from DHS report, we have added the information on the methods section. 3. We appreciate the reviewer’s positive feedback and recommendations. The discussion has been revised according to the reviewer suggestion. The sentence have been revised as follows: for example: Among the geographic groups analyzed in this study, mothers who settled in the Middle of Indonesia had increased odds of using PNC service, while those who lived in the East of Indonesia had decreased odds. Similarly, in Ethiopia. Other paragraphs: However, earlier research is done in Pakistan, Ethiopia, and Tanzania, revealed where mothers from the richer wealth quintile were significantly associated with the utilization of PNC services… Other Ethiopia studies have demonstrated that physical accessibility plays an essential variable in health service utilization… In this study, mothers having children aged three months increased the likelihood to use PNC services about 1.43 times (OR = 1.43; 95% CI = 1.23-1.66) more than mothers with children aged four months (OR = 1.30; 95% CI = 1.12-1.51). A similar study in Nepal showed that PNC service utilization in the early postnatal period was most likely due to the motherhood transition period. 4. We appreciate the reviewer drawing our attention to check words, which has been corrected in our resubmission with “spouse” and term for explaining regions in Indonesia as suggested (Western Indonesia, Central Indonesia and Eastern Indonesia). 5. The professional English language editing service has been utilized to clarify sentences."
}
]
}
] | 1
|
https://f1000research.com/articles/10-153
|
https://f1000research.com/articles/10-190/v1
|
08 Mar 21
|
{
"type": "Research Article",
"title": "Non-commercial pharmaceutical R&D: what do neglected diseases suggest about costs and efficiency?",
"authors": [
"Marcela Vieira",
"Ryan Kimmitt",
"Suerie Moon",
"Ryan Kimmitt",
"Suerie Moon"
],
"abstract": "Background: The past two decades have witnessed significant growth in non-commercial research and development (R&D) initiatives, particularly for neglected diseases, but there is limited understanding of the ways in which they compare with traditional commercial R&D. This study analyses costs, timeframes, and attrition rates of non-commercial R&D across multiple initiatives and how they compare to commercial R&D using the Portfolio-to-Impact (P2I) model as parameter of comparison. Methods: This is a mixed-method, observational, descriptive and analytic study. We contacted 48 non-commercial R&D initiatives and received quantitative data from 8 organizations on 83 candidate products, and qualitative data through 14 interviews from 12 organizations. Results: The quantitative data suggested that non-commercial R&D for new chemical entities is largely in line with P2I averages regarding total costs and timeframes, with variation by phase. The qualitative data identified more reasons why non-commercial R&D costs would be lower than commercial R&D, timeframes would be longer and attrition rates would be equivalent or higher, though the magnitude of effect is not known. The overall emerging hypothesis is that direct costs of non-commercial R&D are expected to be equivalent or somewhat lower than commercial, timeframes are expected to be equivalent or somewhat longer and attrition rates would be equivalent. Conclusions: The study found that non-commercial R&D differs in many significant ways from commercial R&D. However, it is possible that the sum of these differences cancelled each other out such that total costs, timeframes and attrition rates were largely in line with P2I averages. Given the nascent area, with almost no prior literature focusing on costs, timeframes or attrition rates of non-commercial R&D initiatives, we see the merits of this study as generating hypotheses for further testing against a larger sample of quantitative data, and for understanding reasons underlying any significant differences between non-commercial and commercial initiatives.",
"keywords": [
"research and development",
"product development",
"non-commercial R&D",
"commercial R&D",
"neglected diseases"
],
"content": "Introduction\n\nThe costs, timeframes and attrition rates of biomedical research and development (R&D) has long been of interest to scholars, practitioners and policymakers alike. These questions have recently gained increased salience in light of concerns about the potentially declining productivity of commercial R&D; missing technologies such as products for neglected diseases of poverty, antibiotics or outbreak-prone pathogens; and the high and rising prices of medicines such as those for cancers or rare diseases. Improved understanding of the biomedical R&D process is essential to address these societal challenges.\n\nRelatedly, the question has arisen as to whether different approaches to organizing, financing or incentivizing R&D – sometimes referred to as “alternate” or “new” business models of R&D – can address some of the shortcomings of the traditional approach. One area where there has been significant experimentation in alternate business models is neglected diseases (ND) that predominantly affect people in low- and middle-income countries (LMICs). In addition to (usually early-stage) research taking place in academic or public institutes, later-stage product development for NDs has received increased funding and attention through the creation of about two dozen product development partnerships (PDPs)1. With at least two decades of significant non-commercial R&D efforts behind us, primarily focused on the NDs, it is an opportune moment to examine more closely how they compare to traditional commercial R&D on costs and efficiency. Several studies of specific non-commercial R&D initiatives have been published2–7, but we did not find any research examining costs, timeframes or attrition rates across more than one initiative.\n\nThis study sought to contribute to the knowledge base by gathering evidence on the costs, timeframes and attrition rates of “non-commercial” R&D initiatives and analyse how they compared to estimates of commercial R&D. “Non-commercial” R&D is defined as undertaken primarily with a not-for-profit purpose. Often, the lead organizations of such initiatives are academic or governmental in nature, or non-profit PDPs. For-profit firms frequently play a collaborating role by providing access to compound libraries, technical expertise, and/or products for use in testing, among other in-kind contributions. However, these initiatives are not part of the firm’s core commercial portfolio or strategy, as they are not expected to generate significant (if any) market returns. Therefore “non-commercial” should not be interpreted as excluding the private sector. Furthermore, we prefer to use the broader term “non-commercial” rather than “non-profit” as in some cases a developer may earn profit or revenue on a product as a way to offset costs.\n\nThe Portfolio-to-Impact (P2I) tool was used as a parameter of comparison in the study. P2I is a modelling tool initially developed by TDR (Special Programme for Research and Training in Tropical Diseases) co-sponsored by the United Nations Children’s Fund (UNICEF), the United Nations Development Programme (UNDP), the World Bank and World Health Organization (WHO), to estimate funding needs to accelerate health product development from late stage preclinical study to phase III clinical trials, and to model potential product launches over time. A description of the tool is available elsewhere8. This study was undertaken as part of a TDR-led consortium of organizations that conducted further analysis of the P2I model throughout 2019.\n\n\nMethods\n\nThe study was designed to collect: 1) quantitative data from non-commercial R&D initiatives on costs, timeframes and attrition rates, and 2) qualitative data from non-commercial R&D initiatives and/or experts on such initiatives to explain existing costs, timeframes and attrition rates and reasons why these might or might not differ from commercial R&D. Data was collected between June and September 2019. Participants were given the opportunity to review and comment on a first draft of the research report but were not allowed to withdraw their data (a copy of the consent form is available with the full research report as extended data; Annex 4, pp. 91–949). All data has been aggregated and anonymized.\n\nThe study population was selected using the database of pipeline technologies for neglected diseases developed by Duke University and Policy Cures Research10. The database does not include all non-commercial R&D initiatives – for example, it excludes biodefense projects that are largely publicly-funded – but it is the most comprehensive database of which we are aware focusing on R&D for neglected diseases, which is by nature largely non-commercial. We used a version of the spreadsheet “Candidates in the pipeline for neglected diseases, as of August 31, 2017” sent to us by the authors, which included a categorization of the organizations by developer type. We selected all not-for-profit organizations that were directly involved in conducting R&D, which included product development partnerships (PDPs), academic and research institutions and public research institutes and other public sector organizations. There were a total of 443 candidate products and 285 organizations that fit this initial criterion. All 16 PDPs were included given their organizational focus on non-commercial R&D, and the list of PDPs was complemented by other studies1,11. In addition to PDPs, we included organizations that had at least one product that had reached Phase 3. Another 32 organizations were included after this second selection, and three additional organizations were included through snowball sampling. The final list of organizations is available in the full research report (extended data; Annex 1, pp. 77–789). We contacted each organization by email, with the initial request addressed to the organization’s most senior executive (e.g. Chief Executive Officer, Executive Director, Managing Director) to ensure leadership was aware of and agreed to our interview request, as recommended by the ethical review process. In specific cases, where we had reason to know another employee would be relevant to or aware of our research project, we copied other individuals on the initial email. The senior executive often delegated the interview to one or more staff, such as the lead staff person responsible for R&D, finance, policy and/or external relations.\n\nWe developed a questionnaire using MS Excel to collect quantitative data from the organizations in our sample on the costs, timeframes, and attrition rates for a given organization or project (extended data; Annex 2, pp. 79–899). We also included quantitative data on costs, timeframes or attrition rates published in reports or articles prior to the start of this study from four organizations4–7. For timeframes, we consulted data available on the organizations’ websites and in the clinical trials database ClinicalTrials.gov.\n\nWe created a quantitative dataset in Excel combining data provided by respondents with publicly available information pertaining to the costs, timeframes, and attrition rates of non-commercial R&D initiatives. Data was anonymized and combined by product archetype. Due to the limitations of our dataset, we limited our analysis to only two P2I archetypes: simple and complex new chemical entities (NCE-Simple, NCE-Complex)12. Only one organization provided information about diagnostics and two about vaccines (one only included aggregated totals for one product), and we excluded these from the analysis as it would be impossible to protect the anonymity of the organizations.\n\nSeveral assumptions were made to standardize the data and allow comparison (see detailed methodology in extended data; pp. 31–329). For costs, we assumed that money was spent at a steady rate across the time period of each phase. For data in currencies other than USD, a yearly exchange rate from the year in which the cost was incurred was used to make the conversion into USD. Totals were calculated in 2017 dollars to facilitate comparison with P2I model figures. Inflation and deflation adjustments used the standard consumer price index.\n\nFor timeframes, we calculated total time spent in development as the sum of time spent in Pre-clinical, Phase 1, 2 and 3. Phase 1a and 1b trials were counted as phase 1. Phase 2a, 2b, and 2c trials were counted as phase 2, as were phase 2/3 tests. Phase 3a and 3b are both counted as phase 3. An average of time per trial for each phase was taken to estimate the amount of time required for a given clinical phase. For some data points, early stage testing was aggregated for multiple drug candidates and total time spent in a phase was divided by the number of candidates. Many candidates have multiple trials in each phase and the average of all trials was used.\n\nA list of questions for semi-structured interviews was developed to collect the qualitative data (extended data; Annex 3, p. 909). The questions were not pilot tested. Most interviews lasted about one hour and were either conducted in person in Geneva or using videoconferencing software and were recorded upon agreement of the participant. Interviews were held with individuals with a high degree of familiarity about product development from the organizations included in the study. Interviews were held by the three authors (MV- MPH, researcher, female; RK – researcher, male; SM – PhD., director of research, female) and no one else was present besides the participants and the researchers.\n\nTranscription or notes from the interviews were analysed and coded using NVivo 12. Interviews were coded by MV based on themes derived from the data, and reviewed by SM. A description of the coding tree is not available. Interviews were anonymized both at individual and organization level and each was given a number (PO - participant organization) for quotation identification. Given the small sample size, data saturation was not reached.\n\nWe used parameters from the Portfolio-to-Impact (P2I) tool v2, which was initially developed by TDR8 and updated by Duke University and Policy Cures Research10. The P2I Model is based on assumptions of costs, timeframes and attrition rates. Assumptions on development costs at each phase were based on clinical trial costs from Parexel’s R&D cost sourcebook, derived from historical data on health product development of more than 25,000 candidates for all diseases, and further refined and validated by interviews. The underlying data used to construct those assumptions is not publicly available and it was not possible to disaggregate costs, timeframes or attrition rates by commercial vs non-commercial developer. Given that non-commercial R&D (in particular, non-commercial late-stage product development) is both relatively recent and small in scale, we assume that the vast majority of the data used to construct the P2I averages comes from commercial R&D. We compared our quantitative data to P2I averages, and our qualitative data compared non-commercial with commercial R&D.\n\nWe conducted a literature review on costs, timeframes and attrition rates of biomedical R&D to compare other estimates with those of the P2I Model (available at the Knowledge Portal on Innovation and Access to Medicines). There is a wide range of estimates, most focusing on the development of new chemical entities (NCEs) by pharmaceutical companies (commercial R&D). P2I averages are at the low end of the range of cost estimates available for commercial R&D13–16, are somewhat higher for phase 1, lower for phase 2 and within the same range for phase 3 timeframes14,17–19 and success rates are lower for complex NCEs and in the same range for simple NCEs17,18,20–23. In comparison to the few estimates available for non-commercial R&D initiatives4,24, the P2I Model assumptions estimate lower success rates in all clinical development phases, while preclinical is higher. A more detailed literature review is available in the full research report.\n\n\nResults\n\nWe contacted a total of 48 organizations: 23 did not respond, 12 declined and 13 participated in some way (not all participating organizations provided both quantitative and qualitative data) - a participation rate of 27%. In total, we obtained quantitative data regarding 8 organizations and 83 products - 37 drug candidates (13 NCEs, 8 repurposed drugs and 16 not specified), as well as 19 vaccine and 27 diagnostic candidates. Qualitative data was obtained from 14 interviews with 20 individuals from 12 organizations; out of those, 18 individuals provided their perspective based on projects conducted within their own organizations and two were experts with knowledge of a range of organizations.\n\nQuantitative data on non-commercial R&D costs were largely in line with the P2I model estimates, with some variation by phase. For simple NCEs, total costs for non-commercial R&D were 13% higher than the P2I estimates (51.87 million USD for non-commercial vs 45.84 million USD for P2I) (Figure 1). The largest differences were in pre-clinical and phase 1 – where the costs in our sample were more than double the P2I model estimates. Conversely, phase 2 and 3 trials were less expensive for simple NCEs in our data, but by a small margin. The sample size is too small for statistical significance or to generalize to non-commercial R&D more broadly; rather, the findings merely suggest a hypothesis that overall costs to develop simple NCEs are similar between non-commercial R&D initiatives and P2I averages.\n\nThe figure compares the development costs collected from the organizations in the study and the averages in the P2I Model for the archetype “new chemical entities – simple”. The comparison is made for different stages of development preclinical, phase 1, phase 2 and phase 3 and total costs. Data shows higher costs for collected data at preclinical, phase 1 and total, and lower costs at phase 2 and phase 3. Collected data for preclinical is based on 4 data points (n=4), for phase 1 n=3, for phase 2 n=3 and for phase 3 n=2.\n\nFor complex NCEs, total costs were similar to the P2I model, 8% lower (53.98 million USD for non-commercial vs 58.93 million USD in P2I) (Figure 2). In contrast with simple NCEs, for complex NCEs non-commercial preclinical and phase 1 costs were lower than the P2I model. Notably, phase 2 costs were much higher in our dataset (12.65 million USD vs 6.39 million USD in P2I). This could be in part because of the high proportion of phase 2/3 trials in the dataset, as well as the ratio of phase 2b to 2a tests being higher than the P2I data. Phase 3 costs were substantially lower than the P2I estimates, which may be explained by the fact that many pivotal trials were in phase 2. The opportunity to forgo phase 3 testing would drive up phase 2 costs while lowering phase 3 costs. The proportion of pivotal phase 2 tests may be different between P2I and our dataset. As with simple NCEs, the findings merely suggest a hypothesis that should be tested against a larger dataset – that overall costs to develop complex NCEs are similar between non-commercial R&D initiatives and P2I averages.\n\nThe figure compares the development costs collected from the organizations in the study and the averages in the P2I Model for the archetype “new chemical entities – complex”. The comparison is made for different stages of development preclinical, phase 1, phase 2 and phase 3 and total costs. Data shows lower costs for collected data at preclinical, phase 1, phase 3 and total, and higher costs at phase 2. Collected data for preclinical is based on 8 data points (n=8), for phase 1 n=6, for phase 2 n=4 and for phase 3 n=4.\n\nTo assess how sensitive our results were to coding by archetypes (i.e. characterizing a product as “simple” or “complex” NCEs), we combined our data from both categories and found that total costs (48.9m USD) lay between P2I’s NCE-simple and NCE-complex estimates (45.8m-59.9m USD) (Figure 3). This sensitivity analysis suggests that total non-commercial costs are largely in line with P2I parameters, even if there are some differences in coding of archetypes.\n\nThe figure compares the development costs collected from the organizations in the study combining the archetypes “new chemical entities – simple” and “new chemical entities – complex” combined and the averages in the P2I Model for the archetypes “drug repurposed complex”, “new chemical entities – simple” and “new chemical entities – complex”. The comparison is made for different stages of development preclinical, phase 1, phase 2 and phase 3 and total costs.\n\nThe qualitative data identified 12 factors that drove costs up or down in the different phases of product development within non-commercial R&D initiatives9 (Table 1). Most responses focused on the clinical stages of development rather than pre-clinical or earlier. Three factors pushed costs upward, and five factors pushed costs downward for non-commercial R&D in comparison with commercial. Four factors were categorized as indeterminate as they would affect both non-commercial and commercial R&D in the same way. The table below presents a summary of the factors influencing costs. A description of the factors and sample quotes are available in the full research report.\n\nThe table lists the factors influencing costs for non-commercial research and development (R&D) in relation to commercial R&D. Factors are classified in three columns: “costs pushed upward”, “indeterminate” and “costs pushed downward”. There are three factors listed for pushing costs upwards, four factors as indeterminate and five factors pushing costs downward.\n\nThere were more factors that would push costs for non-commercial R&D down vis-à-vis commercial models. However, as the qualitative data does not tell us about the magnitude of the effects, no firm conclusions can be drawn on whether non-commercial R&D would generally cost the same, less or more than commercial R&D.\n\nThe quantitative data showed that for simple NCEs, timeframes between non-commercial R&D and P2I averages were roughly similar. Non-commercial R&D had shorter preclinical times (1.65 years vs 2.49 years in P2I), and longer phase 1 times (2.61 vs 1.80 years in P2I). Non-commercial R&D also had much shorter phase 2 times (1.75 vs 3.38 years in P2I), while phase 3 times were slightly higher (3.67 vs 3.18 years in P2I). Overall, our dataset suggested modestly faster timeframes for non-commercial simple NCE development, taking 9.67 years vs. 10.85 years in the P2I model (Figure 4).\n\nThe figure compares the development times collected from the organizations in the study and the averages in the P2I Model for the archetype “new chemical entities – simple”. The comparison is made for different stages of development preclinical, phase 1, phase 2 and phase 3 and total costs. Data shows shorter times for collected data at preclinical, phase 2 and total, and longer times at phase 1 and phase 3. Collected data for preclinical is based on 2 data points (n=2), for phase 1 n=3, for phase 2 n=3 and for phase 3 n=2.\n\nFor complex NCEs, non-commercial pre-clinical testing was much shorter (1.00 vs 2.87 years in P2I), phase 1 testing slightly shorter (1.67 vs 1.93 years in P2I), phase 2 longer (4.25 vs 3.51 years in P2I), and phase 3 longer (4.0 vs 2.8 years in P2I) (Figure 5). Overall, non-commercial development time was nearly identical, at 10.92 compared to 11.11 years for the P2I model. Possible explanations for these differences could be a result of the ratio of phase 2a to phase 2b tests included in phase 2. The P2I model does not suggest what proportion of its phase 2 tests are 2a compared to 2b, but for our data set, there were many phase 2b tests, which may have increased the amount of time in this phase. Pre-clinical time may have been shorter due to our decision to divide the time in this stage of development among multiple candidates, as that is how some data was shared with us. It is unclear how many preclinical studies in the P2I dataset would have been calculated in this way.\n\nThe figure compares the development times collected from the organizations in the study and the averages in the P2I Model for the archetype “new chemical entities – complex”. The comparison is made for different stages of development preclinical, phase 1, phase 2 and phase 3 and total costs. Data shows shorter times for collected data at preclinical, phase 1 and total, and longer times at phase 2 and phase 3. Collected data for preclinical is based on 1 data point (n=1), for phase 1 n=6, for phase 2 n=4 and for phase 3 n=1.\n\nThe qualitative data identified 12 factors influencing timeframes for non-commercial R&D (Table 2). As with costs, the identified factors were categorized by their potential to push timeframes up or down for non-commercial R&D in comparison to commercial R&D. Seven factors were likely to lengthen timeframes for non-commercial R&D, no factors were likely to shorten timeframes and five factors were categorized as indeterminate. The table below presents a summary of the factors influencing timeframes. A longer description of the factors and sample quotes are available in the full research report9.\n\nThe table lists the factors influencing timeframes for non-commercial research and development (R&D) in relation to commercial R&D. Factors are classified in three columns: “timeframes longer”, “indeterminate” and “timeframes shorter”. There are seven factors listed for longer timeframes, five factors as indeterminate and no factors for shorter timeframes.\n\nThere were a number of factors that would lengthen timeframes for non-commercial R&D vis-à-vis commercial models, or that were indeterminate (Table 2). Notably, in none of the interviews did a respondent argue that non-commercial R&D would move faster. As the qualitative data does not tell us about the magnitude of the effect, no firm conclusions can be drawn on whether non-commercial R&D would take generally the same amount of time or more than commercial R&D.\n\nThe quantitative data on attrition rates was the most difficult to obtain, and there did not appear to be a standard methodology nor practice of calculating such rates within participating organizations. As all non-commercial initiatives in our sample had relatively small portfolios (compared to large commercial firms), attrition rates might not be meaningful. We judged that the data we received could not be aggregated across organizations, nor was it adequate for hypothesis generation. Further research is needed in this area.\n\nInterviewees were also asked about the main factors that drive attrition rates up or down in the different phases of product development. This question generated a wide range of responses, and different organizations took quite different approaches to conceptualizing – let alone calculating – attrition rates. There was also reasonable disagreement as to whether or when a higher attrition rate is undesirable. Some interviewees argued that it is beneficial for an organization to “fail early and fail fast” – that is, to have a high(er) attrition rate in pre-clinical or Phase 1. Too low of an attrition rate could also suggest an organization is not taking enough risk, particularly in the earlier and lower-cost phases of R&D.\n\nThe qualitative data identified nine factors influencing attrition rates for non-commercial R&D (Table 3). As with costs and timeframes, the identified factors were categorized as likely to drive attrition rates higher or lower for non-commercial R&D in comparison to commercial R&D. Three factors were identified as pushing attrition rates higher for non-commercial R&D, one factor as pushing attrition rates lower and five factors were categorized as indeterminate. The table below presents a summary of the factors influencing attrition rates. A longer description of the factors and sample quotes are available in the full research report9.\n\nThe table lists the factors influencing attrition rates for non-commercial research and development (R&D) in relation to commercial R&D. Factors are classified in three columns: “attrition rate higher”, “indeterminate” and “attrition rate lower”. There are three factors listed for higher attrition rates, five factors as indeterminate and one factor for lower attrition rates.\n\nThere were more factors that would raise attrition rates for non-commercial R&D vis-à-vis commercial models, than would lower them, but most of the factors raised by respondents were indeterminate. As the qualitative data does not tell us about the magnitude of the effect, no firm conclusions can be drawn on whether non-commercial R&D would be characterized by higher, lower or equivalent attrition rates as commercial R&D.\n\n\nDiscussion\n\nThe quantitative and qualitative data combined paint a complex, if grainy, picture. Keeping in mind the very small sample of quantitative data, the following hypotheses emerge from the analysis.\n\nRegarding costs, the quantitative data suggest that non-commercial R&D total costs are about the same overall as P2I averages for NCEs. It should be noted that in comparison to other estimates available in the literature for commercial R&D, P2I averages are on the low end of the spectrum. The qualitative data identified many more reasons why non-commercial costs would be lower than commercial R&D, but did not shed light on the magnitude of the effects. The overall emerging hypothesis is that total direct costs of non-commercial R&D are expected to be equivalent or somewhat lower than commercial. Indirect costs for commercial R&D are expected to be higher due to higher overhead and capitalization costs.\n\nRegarding timeframes, the quantitative data suggest that non-commercial R&D timeframes would be slightly shorter for simple NCEs and equivalent for complex NCEs in comparison to P2I averages. Yet the qualitative data identified many more reasons why non-commercial timeframes would be longer than commercial; the data did not shed light on the magnitude of the effects. The overall emerging hypothesis is that timeframes of non-commercial R&D are expected to be equivalent or somewhat longer than commercial.\n\nRegarding attrition rates, the quantitative data was not adequate for analysis. The qualitative data uncovered more reasons why attrition rates might be higher in non-commercial R&D, but also provided a number of reasons why they might be lower or there might be no difference. Again, the magnitude of the effects is not quantified. The overall very tentative hypothesis that emerges is that attrition rates for non-commercial R&D would be equivalent to commercial R&D.\n\nThe study found that non-commercial R&D might differ in many significant ways from its commercial counterparts. However, it is possible that the sum of these differences cancels each other out such that total costs, timeframes and attrition rates would be largely equivalent to commercial R&D. If non-commercial R&D is characterized by equivalent or lower costs, equivalent or longer timeframes, and equivalent attrition rates to commercial R&D, the final expected direct costs and quantity of products resulting from a pipeline of non-commercially developed candidate technologies would be equivalent to those resulting from commercial R&D. In other words, the estimated parameters of the P2I v2.0 model are supported by this analysis, keeping in mind the differences between P2I averages and other estimates available in the literature for commercial R&D.\n\nThat said, this study identified a number of significant differences between non-commercial and commercial R&D. The many variables that affect cost, timeframes and attrition rates also highlight that caution is merited when comparing any single trial, product or organization against average benchmarks, as there are many legitimate reasons for departure from the mean. Therefore, the P2I model may need to be modified when applied more narrowly. While differences may get averaged out when the model is applied to a pipeline of nearly 450 candidates across a broad range of diseases (the intended use of the P2I model), they may be magnified in the narrower context of a single disease, technology type, or organization.\n\nFinally, we re-emphasize that the small size and heterogeneity of the dataset means that these are tentative conclusions. Further quantitative research is needed to test these hypotheses against larger datasets. And further qualitative research is needed to deepen our understanding of the strengths and weaknesses of non-commercial R&D initiatives, and how well they function as alternatives to the traditional commercial model, especially beyond neglected diseases where commercial interests are higher.\n\n\nConclusions\n\nThis was an observational, descriptive and analytic study of non-commercial R&D initiatives. The main limitations of the study were the small non-random sample size and the short period of time in which the study was conducted, which can partially explain the limited amount of quantitative data received. We also recognize that respondents may have had incentives to report costs, timeframes or attrition rates that were favourable to their organizations. Although we sought to check quantitative data against publicly available sources, in general very little relevant data was in the public domain or it was only available at a high level of aggregation. As a result, we have sought to be cautious in drawing inferences from the data.\n\nGiven the nascent nature of the area, with almost no prior literature focusing on costs, timeframes or attrition rates of non-commercial R&D initiatives, we see the merits of this study as generating hypotheses for further testing against a larger sample of quantitative data, and for providing intuition regarding reasons underlying any significant differences between non-commercial and commercial initiatives. The emerging hypothesis is that non-commercial R&D is comparable to commercial initiatives in efficiency, as indicated by direct costs, timeframes and attrition rates.\n\nIt is also important to highlight that many non-commercial R&D initiatives arose because the commercial model did not meet important global public health needs. This study did not compare the patient, population-level, equity or health system benefits offered by the products emerging from non-commercial vs commercial initiatives – only the costs, timeframes and attrition rates to develop those products. A fuller comparison could take both into account.\n\nFor future research, it may be useful both to expand the dataset on NCEs and also dedicate special attention to improving our understanding of non-commercial vaccine and diagnostics R&D, recalling that we excluded vaccines and diagnostics from our quantitative analysis due to very limited data, and were only able to examine a small sample for simple and complex NCEs.\n\nFinally, in future research it would be useful to interview a broader range of stakeholders. Our interviews focused on practitioners with direct knowledge of non-commercial R&D initiatives involved in product development for neglected diseases, usually employees of the initiatives themselves. A more thorough picture is likely to emerge through interviews with additional non-commercial initiatives, and a broader range of their partners and funders.\n\n\nData availability\n\nZenodo: Quantitative data: costs and timeframes_ non-commercial pharmaceutical R&D. https://doi.org/10.5281/zenodo.451970912.\n\nThis project contains the following underlying data:\n\n- Quantitative data_costs.csv\n\n- Quantitative data_timeframes.csv\n\n- README_quantitativedata_coststimeframes.txt\n\nThe qualitative data is confidential to protect participant confidentiality as required by the Ethics Review Committee given the small number of organizations active in the field. Selected quotes from the interviews are available in the full research report at the Graduate Institute Institutional Repository at https://repository.graduateinstitute.ch/record/2988349.\n\nThe Graduate Institute Geneva Institutional Repository: Do costs, timeframes and attrition rates differ between non-commercial and commercial biomedical R&D ? A study of neglected diseases R&D and the P2I model. https://repository.graduateinstitute.ch/record/2988349.\n\nThis report contains the following extended data:\n\n- Consent form (Annex 4, pp. 91–94)\n\n- The final list of organizations (Annex 1, pp. 77–78)\n\n- Questionnaire for quantitative data (Annex 2, pp. 79–89)\n\n- Assumptions made to standardize the data and allow comparison (pp. 31–32)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthors contributions\n\nMarcela Vieira - Conceptualization, Funding Acquisition, Methodology, Investigation, Data Collection, Data Curation, Formal Analysis, Writing – Original Draft Preparation\n\nRyan Kimmitt - Investigation, Data Collection, Data Curation, Visualization, Formal Analysis, Writing – Review & Editing\n\nSuerie Moon - Conceptualization, Funding Acquisition, Methodology, Investigation, Data Collection, Formal Analysis, Supervision, Validation, Project Administration, Writing – Review & Editing",
"appendix": "Acknowledgements\n\nWe thank Temmy Sunyoto, post-doctoral researcher at the Global Health Centre, for revision and comments that greatly improved the manuscript.\n\n\nReferences\n\nMunoz V, Visentin F, Foray D, et al.: Can medical products be developed on a non-profit basis? Exploring product development partnerships for neglected diseases. Sci Public Policy. 2015; 42(3): 315–38. Publisher Full Text\n\nDNDi: An Innovative Approach to R&D for Neglected Patients: Ten Years of Experience and Lessons Learned by DNDi. Drugs for Neglected Diseases Initiative; 2014. Reference Source\n\nDNDi: 15 years of needs-driven innovation for access: Key lessons, challenges, and opportunities for the future. Drugs for Neglected Diseases Initiative; 2019. Reference Source\n\nBurrows JN, Duparc S, Gutteridge WE, et al.: New developments in anti-malarial target candidate and product profiles. Malar J. 2017; 16(1): 26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOdevall L, Hong D, Digilio L, et al.: The Euvichol story - Development and licensure of a safe, effective and affordable oral cholera vaccine through global public private partnerships. Vaccine. 2018; 36(45): 6606–6614. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpeich B, von Niederhäusern B, Blum CA, et al.: Retrospective assessment of resource use and costs in two investigator-initiated randomized trials exemplified a comprehensive cost item list. J Clin Epidemiol. 2018; 96: 73–83. PubMed Abstract | Publisher Full Text\n\nGunn A, Bandara S, Yamey G, et al.: Pipeline analysis of a vaccine candidate portfolio for diseases of poverty using the Portfolio-To-Impact modelling tool. F1000Res. 2019; 8: 1066. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTerry RF, Yamey G, Miyazaki-Krause R, et al.: Funding global health product R&D: the Portfolio-To-Impact Model (P2I), a new tool for modelling the impact of different research portfolios. Gates Open Res. 2018; 2: 24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoon S, Vieira M, Kimmitt RWR: Do costs, timeframes and attrition rates differ between non-commercial and commercial biomedical R&D? A study of neglected diseases R&D and the P2I model. Global Health Centre Working Paper; No. 22/2020. Geneva, Graduate Institute of International and Development Studies, Global Health Centre. 2020. Reference Source\n\nYoung R, Bekele T, Gunn A, et al.: Developing new health technologies for neglected diseases: a pipeline portfolio review and cost model. Gates Open Res. 2018; 2: 23. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPolicy Cures Research: G-Finder 2018. Neglected Disease Research and Development: Reaching new heights. Policy Cures Research; 2019. Reference Source\n\nVieira MCF, Kimmitt R, Moon S: Quantitative data: costs and timeframes_ non-commercial pharmaceutical R&D (Version V.1) [Dataset]. Zenodo. 2021. http://www.doi.org/10.5281/zenodo.4519709\n\nMestre-Ferrandiz J, Sussex J, Towse A: The R and D cost of a new medicine. Office of Health Economics; 2012. Reference Source\n\nDiMasi JA, Grabowski HG, Hansen RW: Innovation in the pharmaceutical industry: New estimates of R&D costs. J Health Econ. 2016; 47: 20–33. PubMed Abstract | Publisher Full Text\n\nSertkaya A, Birkenbach A, Berlind A, et al.: Examination of clinical trial costs and barriers for drug development. 2014. Reference Source\n\nJayasundara K, Hollis A, Krahn M, et al.: Estimating the clinical cost of drug development for orphan versus non-orphan drugs. Orphanet J Rare Dis. 2019; 14(1): 12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbrantes-Metz RM, Adams C, Metz AD: Pharmaceutical Development Phases: A Duration Analysis. SSRN Electron J. 2004. Publisher Full Text\n\nWong J: Data Protection for Biologics - Should the Data Exclusivity Period Be Increased to 12 Years? UNSWLJ Student Series No. 16-07; 2016. Reference Source\n\nMartin L, Hutchens M, Hawkins C: Clinical trial cycle times continue to increase despite industry efforts. Nat Rev Drug Discov. 2017; 16(3): 157. PubMed Abstract | Publisher Full Text\n\nKola I, Landis J: Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov. 2004; 3(8): 711–6. PubMed Abstract | Publisher Full Text\n\nHay M, Thomas DW, Craighead JL, et al.: Clinical development success rates for investigational drugs. Nat Biotechnol. 2014; 32(1): 40–51. PubMed Abstract | Publisher Full Text\n\nSmietana K, Siatkowski M, Møller M: Trends in clinical success rates. Nat Rev Drug Discov. 2016; 15(6): 379–80. PubMed Abstract | Publisher Full Text\n\nBIO - Biotechnology Innovation Organization, Biomedtracker, Amplion: Clinical Development Success Rates 2006-2015. 2016. Reference Source\n\nNwaka S, Ridley RG: Virtual drug discovery and development for neglected diseases through public-private partnerships. Nat Rev Drug Discov. 2003; 2(11): 919–28. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "81104",
"date": "29 Mar 2021",
"name": "Dzintars Gotham",
"expertise": [
"Reviewer Expertise Pharmaceutical policy",
"health economics",
"global health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor and authors,\nThank you for the opportunity to review this interesting, well-designed, and important study. I suggest accepting with minor changes (treated in F1000Research as ‘approved with reservations'). My comments are mostly about interpretation/reporting rather than methodology.\nWith kind regards,\nDzintars\n***\nAbstract: Methods: not clear if it is 8+14 or 8 included in 14.\nResults: ‘more reasons’- more than what? Oxford comma before “and attrition” could help readability.\nConclusions: Suggest to start this with the headline finding: quantitatively costs and timeline were similar from survey and the P2I model. Currently drafting states attrition rates were also similar but this does not seem to be reflected in the text.\nIntroduction: First sentence should be, “have long been”.\nSome sources should be cited for the points in first paragraph regard declining productivity, e.g:\nWieseler B, McGauran N, Kaiser T. New drugs: where did we go wrong and what can we do better? BMJ 2019; l4340.\n\nWorld Health Organization, World Intellectual Property Organization, World Trade Organization. Promoting Access to Medical Technologies and Innovation: Intersections between public health, intellectual property and trade. 2nd Edition. 2020 https://www.wto.org/english/res_e/booksp_e/who-wipo-wto_2020_e.pdf.\nFor the general reader, one or two more sentences explaining what NDs are would be useful, and that there has historically been next to zero private sector investment due to no prospect of return on investment. The same for the concept of PDPs.\nI would suggest the term ‘development time’ could be clearer than the term ‘timeframe’.\nMethods: Para 1 – please delete ‘existing’ (what does this mean?).\n‘simple’ and ‘complex’ NCEs are not standard concepts – please add a sentence explaining (or just a verbatim quote of how Terry/Yamey et al. defined them: Simple - Validated target or mechanism of action, Complex – Novel target or mechanism of action without understanding of disease pathogenesis). This could otherwise be misunderstood: in other contexts, there are ‘complex non-biologics’ (e.g. glatiramer), or, separately, the FDA concept of a ‘complex API’.\nResults: In general: It would be helpful to have one more table, to summarize the quantitative findings all in one place (in addition to the useful bar charts that compare individual metrics).\nThe qualitative data provide an interesting outline of the beliefs held by non-commercial drug developers regarding the comparison of their R&D process to commercial process. However, the comparison of ‘number of factors’ seems very tenuous. I would suggest to delete, “There were more factors that would push costs for non-commercial R&D down vis-à-vis commercial models.” as the authors acknowledge the number of ‘factors’ is meaningless in the following sentence. The following sentence ‘no firm conclusions can be drawn’ is also fairly self-evident and so would suggest the whole paragraph is deleted. The same for the analogous paragraphs in the following two sub-headings under the qualitative results (timeframes and attrition rates).\nTimeframes: First sentence, please reword as “…timeframes were roughly similar between…”.\nAttrition rates: “As all non-commercial initiatives in our sample had relatively small portfolios (compared to large commercial firms), attrition rates might not be meaningful. […] data we received could not be aggregated across organizations, nor was it adequate for hypothesis generation.”\nPlease provide a bit more details on your reasoning for not aggregating and not reporting the responses you received, and why you believe small portfolios would make rates not meaningful. Not intuitively clear to me.\nDiscussion: “The overall very tentative hypothesis that emerges is that attrition rates for non-commercial R&D would be equivalent to commercial R&D.” I do not see any basis for this statement from the findings of the study, even with the ‘very tentative’ caveat.\nDevelopment costs are hugely below what is reported by private industry – why? Also interesting to note that – my impression without looking up precise figures – development times are fairly similar to what industry reports, while costs are much lower. That makes intuitive sense as there is an inherent minimum development time needed for trials to see drug effects etc., while costs can be more labile and may be misreported.\n\nAlso, development costs seem substantially lower than DNDi report – why? (Drugs for Neglected Diseases initiative (DNDi) (2019), 15 Years of Needs-Driven Innovation for Access: Key Lessons, Challenges, and Opportunities for the Future, Geneva: DNDi.)\nYou mention PDPs often develop products starting with a candidate compound ‘donated’ by private industry. Is it possible to sub-set which drugs came from a for-profit compound library and which didn’t?\nIt would be worth touching upon, in the Discussion, why (whether?) it was necessary to keep respondent data anonymised and aggregated. Why do non-profits keep these data secret? Was it apparent to the authors, from preliminary discussions or from past experience, that non-profits would be unwilling to share data unless anonymised and aggregated? If so, interesting to the reader and valuable to future researchers to state this, I think.\nThe quantitative part of the study effectively ends up being a validation exercise for the P2I model. That is valuable and interesting, but could be discussed a bit more in Background and Discussion – e.g. pointing out that P2I has not been previously externally validated (to my knowledge?) and the implications of the validation provided by this study, i.e. that P2I can indeed be used to plan ND R&D project funding.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7003",
"date": "16 Aug 2021",
"name": "Marcela Vieira",
"role": "Author Response",
"response": "We thank you for your valuable comments and suggestions. We have amended the text to incorporate the changes and provide a point-by-point response to your comments below. Abstract: 1) Methods: not clear if it is 8+14 or 8 included in 14. Response: We thank you for pointing this out, and clarify that 8 is the number of organizations that submitted quantitative data, and 12 is the number of organizations that were interviewed for collection of the qualitative data (through 14 interviews). They might or might not be the same. For ease of comprehension, we decided to change the abstract to mention only the total number of organizations that participated in the study and left the detailed information in the “results” section. 2) Results: ‘more reasons’- more than what? Oxford comma before “and attrition” could help readability. Response: Thank you, we added a comma before “and attrition” for improved readability. 3) Conclusions: Suggest to start this with the headline finding: quantitatively costs and timeline were similar from survey and the P2I model. Currently drafting states attrition rates were also similar but this does not seem to be reflected in the text. Response: Thank you for the suggestion, we changed the conclusions about attrition rate, and specified that the quantitative data suggested that costs and timelines are largely in line with commercial averages. Introduction: 4) First sentence should be, “have long been”. Response: Thank you, we changed it accordingly. 5) Some sources should be cited for the points in first paragraph regard declining productivity, e.g: Wieseler B, McGauran N, Kaiser T. New drugs: where did we go wrong and what can we do better? BMJ 2019; l4340. World Health Organization, World Intellectual Property Organization, World Trade Organization. Promoting Access to Medical Technologies and Innovation: Intersections between public health, intellectual property and trade. 2nd Edition. 2020 https://www.wto.org/english/res_e/booksp_e/who-wipo-wto_2020_e.pdf. Response: We thank you for the suggestions, however we believe that the first article focuses on another topic regarding the quality and benefits of new approved drugs, which is not a topic we discuss in our paper. We added the second reference in the introduction. 6) For the general reader, one or two more sentences explaining what NDs are would be useful, and that there has historically been next to zero private sector investment due to no prospect of return on investment. The same for the concept of PDPs. Response: We agree and added one sentence further explaining neglected diseases and another on PDPs. 7) I would suggest the term ‘development time’ could be clearer than the term ‘timeframe’. Response: We thank you for the suggestion, and changed “timeframe” to “timeline” throughout the paper. Methods: 8) Para 1 – please delete ‘existing’ (what does this mean?). Response: Thank you for pointing this out, we deleted ‘existing’. 9) ‘simple’ and ‘complex’ NCEs are not standard concepts – please add a sentence explaining (or just a verbatim quote of how Terry/Yamey et al. defined them: Simple - Validated target or mechanism of action, Complex – Novel target or mechanism of action without understanding of disease pathogenesis). This could otherwise be misunderstood: in other contexts, there are ‘complex non-biologics’ (e.g. glatiramer), or, separately, the FDA concept of a ‘complex API’. Response: We thank you for the comment and have added the definitions as suggested. Results: 10) In general: It would be helpful to have one more table, to summarize the quantitative findings all in one place (in addition to the useful bar charts that compare individual metrics). Response: Thank you for suggesting, we added a table summarizing the quantitative findings (new Table 5). 11) The qualitative data provide an interesting outline of the beliefs held by non-commercial drug developers regarding the comparison of their R&D process to commercial process. However, the comparison of ‘number of factors’ seems very tenuous. I would suggest to delete, “There were more factors that would push costs for non-commercial R&D down vis-à-vis commercial models.” as the authors acknowledge the number of ‘factors’ is meaningless in the following sentence. The following sentence ‘no firm conclusions can be drawn’ is also fairly self-evident and so would suggest the whole paragraph is deleted. The same for the analogous paragraphs in the following two sub-headings under the qualitative results (timeframes and attrition rates). Response: We thank you for the valuable comment, however, as we are trying to develop intuition for hypotheses generation, we decided to keep the sentence stating the number of factors that were identified in one direction or the other, with the recognition that the magnitude of the effect of each factor is not known (as already stated). We believe that counting the number of factors that might differentiate commercial and non-commercial R&D is relevant for the discussion in the paper, and that we have accurately stated the limitations. We have, however, deleted ‘firm’ before conclusions, to state more forthrightly that no conclusions can be drawn. 12) Timeframes: First sentence, please reword as “…timeframes were roughly similar between…”. Response: Reworded. 13) Attrition rates: “As all non-commercial initiatives in our sample had relatively small portfolios (compared to large commercial firms), attrition rates might not be meaningful. […] data we received could not be aggregated across organizations, nor was it adequate for hypothesis generation.” Please provide a bit more details on your reasoning for not aggregating and not reporting the responses you received, and why you believe small portfolios would make rates not meaningful. Not intuitively clear to me. Response: We changed the text to better clarify why the data could not be aggregated (it was not reported by all organizations, and it was not calculated consistently across those that did) and better explain the small portfolio effect (one or two failures lead to large swings in failure rates). Discussion: 14) “The overall very tentative hypothesis that emerges is that attrition rates for non-commercial R&D would be equivalent to commercial R&D.” I do not see any basis for this statement from the findings of the study, even with the ‘very tentative’ caveat. Response: We modified the discussion and conclusion regarding attrition rates to state that the data does not allow for hypothesis generation. 15) Development costs are hugely below what is reported by private industry – why? Also interesting to note that – my impression without looking up precise figures – development times are fairly similar to what industry reports, while costs are much lower. That makes intuitive sense as there is an inherent minimum development time needed for trials to see drug effects etc., while costs can be more labile and may be misreported. Response: Thank you for your comment, we added more information about the parameter of comparison, further explaining that P2I averages are in line with other estimates for commercial R&D but there are a couple of estimates that are much higher (and added a table illustrating the range of estimates for costs - new Table 1). However, explaining the reasons why these estimates are so much higher is beyond the scope of the paper. 16) Also, development costs seem substantially lower than DNDi report – why? (Drugs for Neglected Diseases initiative (DNDi) (2019), 15 Years of Needs-Driven Innovation for Access: Key Lessons, Challenges, and Opportunities for the Future, Geneva: DNDi.) Response: We added the DNDi report in the table illustrating the range of estimates for R&D costs (mentioned above). Explaining the reasons why the estimates differ among each other is beyond the scope of the paper. However, it is only preclinical costs in P2I that are lower than DNDi figures. DNDi costs for Phase I is in-between P2I NCE Simple and Complex and DNDi figures for Phase II and III combined are lower than P2I averages. We also flag in the conclusions the DNDi estimate for cost to bring one successful product to market, including cost of failures -- but this is a different figure from the per candidate/per phase numbers that P2I uses and that we report in the new Table 1. 17) You mention PDPs often develop products starting with a candidate compound ‘donated’ by private industry. Is it possible to sub-set which drugs came from a for-profit compound library and which didn’t? Response: The quantitative data received does not allow for this disaggregation and the information about the origin of the compound was not provided. 18) It would be worth touching upon, in the Discussion, why (whether?) it was necessary to keep respondent data anonymised and aggregated. Why do non-profits keep these data secret? Was it apparent to the authors, from preliminary discussions or from past experience, that non-profits would be unwilling to share data unless anonymised and aggregated? If so, interesting to the reader and valuable to future researchers to state this, I think. Response: As stated under “data availability”, the data was aggregated and anonymised to protect participant confidentiality as required by the Ethics Review Committee given the small number of organizations active in the field. Participant organizations were not asked if they would be willing to share their data openly, and we believe that this discussion falls beyond the scope of the paper. 19) The quantitative part of the study effectively ends up being a validation exercise for the P2I model. That is valuable and interesting, but could be discussed a bit more in Background and Discussion – e.g. pointing out that P2I has not been previously externally validated (to my knowledge?) and the implications of the validation provided by this study, i.e. that P2I can indeed be used to plan ND R&D project funding. Response: Upon reflection, we have revised the paper to emphasize that we cannot draw any conclusions regarding attrition rates. Given the lack of data suitable for analysis regarding attrition rates, we have also amended our conclusions; our data does validate P2I estimates regarding costs and timelines, but does not validate the full P2I Model in terms of predictions for a portfolio of non-commercial R&D projects given the absence of attrition rate data. We added this in the discussion and conclusion sections. As we already discussed in the paper, the P2I model may need to be modified when applied more narrowly to smaller and more specialized portfolios in the context of a single disease, technology type, or organization. Also, as mentioned in the introduction, our study was conducted as part of a TDR-led consortium of organizations that conducted further analysis of the P2I model throughout 2019. The other studies applied the P2I Model to their specific organizations and can be helpful for this discussion."
}
]
},
{
"id": "82089",
"date": "06 Apr 2021",
"name": "Claudia Vaca González",
"expertise": [
"Reviewer Expertise Pharmacoepidemiology",
"regulatory issues and access-to- medicines public policy-making processes."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 really valuable, well conducted and useful study. The report is well written and clear.\nBellow some comments to improve the discussion and conclusions:\nThe study aims to generate hypotheses about the main differences between noncommercial and commercial initiatives. The overall emerging hypothesis is that timeframes of non-commercial R&D are expected to be equivalent or somewhat longer than commercial, but the authors do not comment any other factors that could impact this hypothesis, in order to conduct further studies, i.e.:\n- The size of the portfolio: a very reduced noncommercial portfolio that could become harder efforts to conduct the clinical studies in opposite with the commercial initiatives where the extended portfolio may leverage the efficiency.\n- The fulfillment of regulatory requirements: the commercial initiatives usually have an in-house or outsourcing regulatory and market access department to fulfill (and anticipate) any regulatory requirement. Is it the same in noncommercial initiatives? could these differences impact the total cost and the frame time of R&D?\n\nThere is not any critical appraisal of the used P2I model. Is it comprehensive at all? Is there any relevant factor that wasn't included or missed? How much of the missed information is intrinsic related to the model complexity? Is it possible to become the model easier to fulfill?\n- I would not be worried about the size of the sample, more deeply qualitative data coming from experts and staffers could be rich on bring some other key factors to the table in order to understand the differences and similarities of noncommercial and commercial initiatives. Having that data, some researchers could rethink the models as P2I to make it easier to fulfill. I mean, to try to do the reverse investigation beginning at the end and go to the beginning.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7004",
"date": "16 Aug 2021",
"name": "Marcela Vieira",
"role": "Author Response",
"response": "We thank you for your valuable comments and suggestions. We have amended the text to incorporate the changes and provide a point-by-point response to your comments below. 1) The study aims to generate hypotheses about the main differences between noncommercial and commercial initiatives. The overall emerging hypothesis is that timeframes of non-commercial R&D are expected to be equivalent or somewhat longer than commercial, but the authors do not comment any other factors that could impact this hypothesis, in order to conduct further studies, i.e.: - The size of the portfolio: a very reduced noncommercial portfolio that could become harder efforts to conduct the clinical studies in opposite with the commercial initiatives where the extended portfolio may leverage the efficiency. - The fulfillment of regulatory requirements: the commercial initiatives usually have an in-house or outsourcing regulatory and market access department to fulfill (and anticipate) any regulatory requirement. Is it the same in noncommercial initiatives? could these differences impact the total cost and the frame time of R&D? Response: Thank you for your comments. The full research report (included as underlying data) provides more information about each of the factors mentioned in the interviews, including portfolio size, size of the organization and regulatory expertise. The full research report also includes selected quotes to better illustrate each point and how they might affect costs, timeframes and attrition rates. However, we chose to exclude these more detailed discussions from the article-length version of the study, in order to report the results in a more concise manner. 2) There is not any critical appraisal of the used P2I model. Is it comprehensive at all? Is there any relevant factor that wasn't included or missed? How much of the missed information is intrinsic related to the model complexity? Is it possible to become the model easier to fulfill? I would not be worried about the size of the sample, more deeply qualitative data coming from experts and staffers could be rich on bring some other key factors to the table in order to understand the differences and similarities of noncommercial and commercial initiatives. Having that data, some researchers could rethink the models as P2I to make it easier to fulfill. I mean, to try to do the reverse investigation beginning at the end and go to the beginning. Response: Thank you for raising this discussion. The literature review and the quantitative and qualitative data collected under this study indicates that the underlying assumptions in the P2I Model for costs and timelines are in line with other estimates available in the literature and roughly similar to the data collected for non-commercial R&D. We believe that the qualitative data -- reported in more detail in the full research report -- does provide useful additional context regarding how the P2I model may be applied and interpreted, and would refer readers there. The data collected regarding attrition rates was not suitable for analysis and therefore the application of the full P2I model could not be validated. As discussed in the paper, the P2I Model may need to be modified when applied more narrowly to smaller and more specialized portfolios in the context of a single disease, technology type, or organization. Also, as mentioned in the introduction, our study was conducted as part of a TDR-led consortium of organizations that conducted further analysis of the P2I model throughout 2019. The other studies applied the P2I Model to their specific organizations and can be helpful for this discussion. That said, we believe that the Model is a useful tool and fairly easy to use as it requires only that the user inputs information about their average costs, timeframes and attrition rates (which can be modified according to the organization’s own figures). However, our study was not directly intended to suggest changes to the P2I Model and we believe that this discussion falls beyond the scope of the paper."
}
]
},
{
"id": "82091",
"date": "19 Apr 2021",
"name": "Lia Hasenclever",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is of interest because there is a lot of controversy about R&D costs, and it brings new evidence. However, it does contain some inaccuracies. The most serious of these is the use of the term non-commercial. The use of this term is unusual, the most correct would be to use non-profit institutions. Furthermore, what the author calls offset costs, in fact, are indirect costs and not profits. I suggest using the conventional term It would be interesting to add a definition of what the author understands for each of the adopted comparison parameters: costs, timeframes and attrition rates (p….). This would make reading easier and reach a wider audience.\n\nIs the work 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": "7005",
"date": "16 Aug 2021",
"name": "Marcela Vieira",
"role": "Author Response",
"response": "We thank you for your valuable comments and suggestions. We have amended the text to incorporate the changes and provide a point-by-point response to your comments below. 1) The article is of interest because there is a lot of controversy about R&D costs, and it brings new evidence. However, it does contain some inaccuracies. The most serious of these is the use of the term non-commercial. The use of this term is unusual, the most correct would be to use non-profit institutions. Furthermore, what the author calls offset costs, in fact, are indirect costs and not profits.I suggest using the conventional term. Response: We thank you for your suggestion. However, as explained in the introduction, we prefer to use the term non-commercial, instead of non-profit, as some organizations might earn profit, but that is not their main purpose for conducting product development. The term “profit” is used as the difference between the amount earned in revenues and the amount spent to bring a product to market. We removed the part on “offset costs” and rephrased the sentence for clarification. 2) It would be interesting to add a definition of what the author understands for each of the adopted comparison parameters: costs, timeframes and attrition rates (p….). This would make reading easier and reach a wider audience. Response: We added a definition of each of the terms."
}
]
}
] | 1
|
https://f1000research.com/articles/10-190
|
https://f1000research.com/articles/9-1051/v1
|
26 Aug 20
|
{
"type": "Correspondence",
"title": "Evidence for side effects of cannabidiol (CBD) products and their non-conformity on the European food market – response to the European Industrial Hemp Association",
"authors": [
"Dirk W. Lachenmeier",
"Stephan G. Walch",
"Stephan G. Walch"
],
"abstract": "An interesting and valuable discussion has arisen from our recent article (Lachenmeier et al., 2020) and we are pleased to have the opportunity to expand on the various points we made. Equally important, we wish to correct several important misunderstandings that were made by Kruse and Beitzke (2020) on behalf of the European Industrial Hemp Association (EIHA) that possibly contributed to their concerns about the validity of our data, toxicological assessment and conclusions regarding regulatory status of cannabidiol (CBD) products. First and foremost, our study did only assess the risk of psychotropic Δ9-tetrahydrocannabinol (THC) without inclusion of non-psychotropic Δ9-tetrahydrocannabinolic acid (THCA). Secondly, as this article will discuss in more detail, there is ample evidence for side effects of CBD products, not only in paediatric patients, but also in adult users of over-the-counter CBD products (including inadvertent “high” effects). Thirdly, the exposure and risk assessment was conducted using up-to-date guidelines according to the European Food Safety Authority (EFSA) and the German Federal Institute for Risk Assessment (BfR). And finally, the current legal situation in the European Union, without approval of any hemp extract-containing product according to the Novel Food regulation, actually allows blanket statements that all such products are illegal on the market, and this indeed would imply a general ban on the use and marketing of such products as food or food ingredients until such an approval has been granted. We hope that this reassures the F1000Research readership regarding the validity of our results and conclusions. We are pleased, though, that the EIHA has acknowledged the fact that there are non-compliant CBD products available, but according to our data these are a substantial fraction of the market.",
"keywords": [
"Tetrahydrocannabinol",
"cannabidiol",
"Cannabis sativa",
"hemp",
"food supplements",
"risk assessment",
"drug effects"
],
"content": "Introduction\n\nWe actually agree with a main premise of the European Industrial Hemp Association (EIHA)’s comments; namely, that legal compliance and safety for both producers and consumers of cannabidiol (CBD) products must be ensured1. If this can be achieved by their suggestion of a mandatory industry self-regulated approach1 rather than by our suggestion of strict regulations2,3 is another question. In light of the experience with industry self-regulations in other fields, this suggestion remains highly doubtful4,5; it especially appears not well-thought-out how a self-regulation may be mandatory and how this demand can be enforced. Otherwise, we had previously suggested the necessity for a common regulatory approach regarding hemp food products on a European level, such as enforceable maximum levels for Δ9-tetrahydrocannabinol (Δ9-THC)6. To even increase the legal void by the assessment of hemp extract-based food products as non-foods within the international and national narcotic regulations7 is clearly not helpful.\n\nApart from these issues, which are political rather than scientific, the main finding presented in our study is that the levels of psychoactive Δ9-THC in many CBD products on the market exceed acceptable thresholds of toxicity. Furthermore, hemp extract-based CBD products were assessed as unapproved novel foods. For both reasons, the marketing of such products is illegal according to European Union (EU) food laws2 (if we assume that the products are foods and not narcotics). The disputation provided by EIHA to refute our assessment is based on claims rather than facts and we therefore take this chance to corroborate our assessment by further data published since the last revision of our paper in January 2020.\n\nLet us now consider each criticism of the EIHA1 in detail:\n\n\nSide effects of CBD products\n\nThe literature regarding side effects of CBD was considerably expanded since the writing of our article, so that besides the anecdotal reports and paediatric studies already mentioned, several case reports8–10, a survey9, a meta-analysis of clinical trials11 and a post marketing safety assessment of a full spectrum hemp extract12 became available. Specifically the survey9 reports observations of side effects including “feeling high”, an effect likely to be explained by Δ9-THC contamination rather than by CBD. Similarly, effects of “a little high”, brief periods of mild intoxication, were described following ingestion of several brands of CBD products in Virginia, USA10. The post marketing safety assessment showed gastrointestinal effects as most commonly reported side effect12. We have included this information into a new version (version 3; v313) of our article2 to strengthen our arguments. Besides the mentioned human evidence, experimental research in vivo and in vitro resulted in concerns about hepatotoxicity14, teratogenicity15, and gut inflammation16.\n\nThe arguments of EIHA in refuting any side effects of CBD products are not convincing not only from a pharmacological standpoint, but it is also rather unscientific to refute side effects on the basis that the responsible authority in the UK has not been made aware of any safety incident till now1. First, due to the very short time of public use of CBD, only acute toxic events would currently appear, while chronic toxic events, such as liver toxicity, may take years to develop. Second, there is currently no system of nutrivigilance implemented in the UK or most other EU member states, so that there is no formal registration of such cases.\n\n\n“THC” definition and estimation of daily dose of products\n\nUnfortunately, a misunderstanding regarding our definition of Δ9-THC has apparently occurred at EIHA. From the methods section and our definition of the abbreviation of THC as Δ9-tetrahydrocannabinol, it should be clear that we only include the psychotropic Δ9-THC and not the non-psychotropic Δ9-tetrahydrocannabinolic acid (THCA) in our risk assessment. In deviation of the suggested practice to implement the German guidance values for total THC (i.e. the sum of Δ9-THC and THCA)17, we only have compared the psychotropic Δ9-THC with the guidance values. This practice is clearly in favour of the food business operator (FBO) because – as the EIHA correctly states – a major part of total THC may be comprised by THCA1. We have updated our article to clarify this issue on several instances and to avoid future misunderstandings13.\n\nRegarding the exposure assessment, we confirm to have conducted an estimation of the daily intake in those instances, where a maximum recommended daily dose was missing in the labelling. This is in accordance with the requirements of Art. 14 of Regulation (EC) No. 178/2002 laying down the general principles and requirements of food law18, which specifies that the information provided to the consumer must be considered in determining whether any food is unsafe. As we will elaborate further in the following, our exposure estimations are both practical and realistic from the standpoint of consumer health protection.\n\nThe authors consider 8 g of tea product consumption per day as an absolutely common and realistic scenario, e.g. comparable to consuming 1 teapot (for example 8 g infused in 1 L of water). The German Federal Institute for Risk Assessment (BfR) even suggests a slightly higher amount of 2 g / 200 mL infusion (10 g/L) and suggests that the actual acute consumption quantities for herbal tea as an analogon for hemp tea are in the order of 1.3 litres (P95)19. Regarding the question of carry-over of THC into the infusion, the BfR has recently reviewed the evidence including the study cited by EIHA20 and another study by our group21. The BfR concluded: “The BfR is of the opinion that the assumption of 100% carryover is justified, as experimental data on the carryover point to high fluctuations”19. Therefore, we currently fail to see the evidence to change our exposure assessment for tea. Perhaps the EIHA can submit their unpublished test reports (see footnote 10 in Kruse & Beitzke1) to the BfR for re-evaluation of their opinion, or even preferably make them publicly available in the form of a dataset for their article1.\n\nFinally, the allegation of the EIHA that we “ignored or overruled” the recommended daily dose on the label or the brewing instruction of the FBO1 is untrue, as we certainly used this information when available (see dataset22).\n\nAccording to the labelling, the syrup is intended to be used to prepare a beverage in 1:10 dilution with water. According to the BfR recommendation for tea, we assumed the use of 130 ml syrup to prepare 1.3 L of final beverage. The consumption of this amount of alcohol-free beverage is certainly not excessive nor is our assumption arbitrary or results-oriented. We would like to explicitly reject this unscientific and unfounded accusation of the EIHA1 that the CVUA Karlsruhe or its employees’ work is results-oriented, in the sense that we exaggerate the risk of hemp products aiming to prohibit them from the market. On the contrary, the CVUA Karlsruhe works in its expert activities completely independent from any interests and our highest goal is the protection of the consumer from health damage.\n\nThere appears to be a misunderstanding about what is a “shot”. A shot is a form of concentrated beverage to be consumed as such and it is not a food supplement. The flask contains a single whole portion of the “shot” intended by the manufacturer to be consumed at once (e.g. compare “shots” of energy drinks). The “shot” is therefore clearly a “ready-to-eat” product, which is covered by the German guidance values.\n\nRegarding the evaluation of so-called CBD oils, which are typically constituted of full spectrum hemp extracts mixed into edible oils to achieve CBD concentrations in the range 5–15% being sold as food supplements, the allegation of EIHA that we dismiss the many cases in which the dosage or recommended daily intake was provided correctly by the respective manufacturers1, must be clearly rebutted. As can be seen in our dataset22, as well as in Table 2 of our article2, we have consistently and unambiguously used the labelled dosage of the manufacturers for the comparison with the toxicological thresholds. Naturally, for the products where no dosage had been labelled, exposure had to be estimated similar to the estimation for the beverages discussed above.\n\nThe product under specific scrutiny of EIHA is a special case as it was only labelled as “CBD oil” with no labelling suggesting it to be a “food supplement”. Therefore, the discussion regarding what consumers might expect from food supplements is not helpful. We believe that consumption of 10 ml (about 1 tablespoon) of an oil that is not labelled as “supplement” or with any other warning labels, is not an exaggerated or unrealistic scenario in all objectivity. It must also be considered that the THC content in this product was so high, that the consumption of 1/10 of the amount (i.e. 1 mL) would also exceed the lowest observed adverse effect level (LOAEL) and therefore lead to the same outcome. Nonetheless, we have clarified footnote 2 in Table 2 in the v3 of our article13 expanding the explanation of our exposure assessment in this case. It must be noted, however, that even if we would exclude this clearly exceptional and outlying product from our sample collective, all results and conclusions of our article are still valid. We are also surprised that the EIHA takes offence in our activities and responsibilities as part of governmental food control in Germany, while the problem clearly lies with FBOs that mislabel and misrepresent their products. Furthermore, for each of the products in Table 2 of our article2, detailed expert opinions were produced for the responsible food control authorities that had initially submitted the samples to our institute. In some cases, our expert opinions have become part of court proceedings and the courts have confirmed the risk assessment of the CVUA Karlsruhe, as well as the risk management measures of the authorities in all cases known to date23–25.\n\n\nMitigation of THC effects by interaction with CBD?\n\nThe allegation of EIHA that we have dismissed the interaction between THC and CBD1, in the sense that CBD would mitigate the effects of THC, can be clearly rebutted. First and foremost, the underlying risk assessment in our expert opinions is based on the opinion of the Panel on Contaminants in the Food Chain of the European Food Safety Authority (EFSA)26, which has considered interaction effects. However, EFSA concluded the information is controversial and not consistently antagonistic26. This is consistent with more recent research of Solowij et al.27 that the effects of Δ9-THC may even be enhanced by low-dose CBD (e.g., as found in food supplements) and may be particularly prominent in infrequent cannabis users. Positive findings regarding antagonistic effects (e.g. Pisanti et al.28 cited by EIHA) were typically found for much higher dosing regimens, i.e. aiming to mitigate the adverse effects of THC in hashish and marihuana, while another study with smoked cannabis did not detect such an effect29.\n\nWe strongly believe, in line with EFSA, that the current scientific evidence does not allow for considering cumulative effects in low dose CBD oils and hemp extracts. The applicability of the acute reference dose (ARfD) of 1 μg Δ9-THC per kg body weight – without considering interactions by CBD – was recently re-confirmed by EFSA30.\n\nAs the EIHA mentioned this argument, we have decided to include a short rationale into the v3 of our article13 for reasons of completeness. Otherwise, our article is not a basic toxicological research article about the rationale for risk assessment but an applied research article, which has based the risk assessment on the guidelines of the responsible risk assessment authorities BfR19 and EFSA26,30. Therefore, we would invite EIHA to correspond directly with these institutions, when they believe there is scientific evidence or new data that might change the available assessments. Currently, we see no such data. It should be noted that the EIHA has unsuccessfully tried lobbying the risk assessment bodies into providing more “reasonable” guidance values for THC (e.g., see Banas et al.31), and we believe that a comment on our scientific article is not the right place to continue this effort.\n\n\nIllegality of all hemp products containing isolated CBD or hemp extracts\n\nWhile the regulatory status is not part of our chemical and toxicological research, we thank the EIHA for pointing out this issue, as there is a potential misunderstanding of the lobbyist regarding the most up-to-date regulations and decisions of EU and national legislators as well as of the courts, which is evidenced by the outdated references cited by EIHA1.\n\nWe also thank the EIHA1 for the re-iteration of our conclusion that “basically all available CBD products based on hemp extract marketed as food or food supplement within the EU are therefore illegally sold”. We still stand by this conclusion.\n\nIt is certainly true that case-by-case decisions have to be conducted in official food control, and of course we have exactly done this for each product, which was submitted to our laboratory for evaluation. However, the situation of hemp-extracts is a particular one, because of its regulatory status as unapproved novel food. This status allows for such a blanket statement, that each single product that contains hemp extract as ingredient can be judged as illegally placed on the market. It should be noted that this assessment is independent of the amount of hemp extract or its concentration of CBD. Regarding the THC levels found, which are widely variable, a case by case decision has to be made in any case, which spans from unsuspicious levels below the German guidance levels up to exceedance of the LOAEL dose, which we judge as a serious risk in consideration of Art. 14 of Regulation (EC) No. 178/200218.\n\nThe EIHA1 is also correct in considering the EU Novel Food Catalogue, which leads to this “blanket” assessment of hemp extracts as being novel, as legally not binding and that it is only an indicator for court decisions. What the EIHA, however, fails to mention is the fact that there are a number of court decisions that have actually endorsed the suggestions of the novel food catalogue and have confirmed the actions of the authorities in prohibiting the placing of the respective CBD product on the market24,25,32–38. To our knowledge, there currently is no court ruling, that might have endorsed the EIHA opinion.\n\nFurthermore, the court rulings have also disproved the claims of the EIHA about the burden of proof for determining the novelty of a food. The opinion of EIHA1 in this regard is based on outdated, incomplete evidence. In their decision about the marketability of a CBD product, the administrative court of the German Federal State Baden-Württemberg ruled that the food business operator has the burden of proof25. This is in accordance with Article 4(1) of Regulation (EU) No 2015/2283, which states that the food business operator shall verify that foods which he or she has placed on the market in the EU, fall within the scope of this Regulation or not39. Also outside the CBD field, the burden of proof has been imposed on the FBOs in several court rulings confirming Art. 4(1) of Regulation (EU) No 2015/2283 (see review of court rulings in Meyer et al.40). For a more detailed assessment of CBD court rulings see our recent review41.\n\nFinally, we cannot follow the arguments of the EIHA1 that European Court of Justice decisions regarding pharmacological effects might be relevant or that the novelty of a product is connected with an associated abstract health risk. The novelty of a product purely depends on the fact that it was not used for human consumption to a significant degree within the EU before 15 May 199739. The novelty does not depend on potential pharmacological effects or health risks of the product.\n\nThe German Federal Office of Consumer Protection and Food Safety (BVL) recently published a statement that the classification of food containing CBD in the press release of EIHA of March 3, 2020, is not correct42. The BVL states that for extracts of Cannabis sativa L. and derived products containing cannabinoids (e.g. CBD) a significant history of consumption in the EU has still not been demonstrated by the economic operators, nor by the EIHA or any other association42. For this reason, they are still considered EU-wide as novel foods42.\n\nIn conclusion, we believe that the responsible authority can currently make conclusions on the non-marketability of CBD products based on a lack of novel food approval, and additionally based on the lack of safety when THC thresholds are exceeded. We must stress here that the responsible local authority’s tasks clearly include the enforcement of the Novel Food Regulation39 as well of the food safety rules18. This is practiced all over Europe and evidenced by the numerous alerts found in the EU’s Rapid Alert System for Food and Feed (RASFF)43.\n\n\nJudgement about food producers of CBD products\n\nSince the publication of our article2, a number of studies have confirmed our analytical results. Food control authorities in Europe have reported various offences of FBOs selling CBD products against the European food law. More than 150 notifications regarding CBD as unauthorised novel food ingredient and/or unauthorised THC in CBD products were shared in the RASFF. In Belgium, about half of 213 products seized from CBD shops exceeded a threshold of 0.2% THC+THC-A and large discrepancies were observed between labelled and measured CBD concentration44. The Food Safety Authority of Ireland (FSAI) reported that from 38 tested CBD products, 37% exceeded the safe limit of THC dosage set by EFSA (1 µg/kg body weight/day), 34% were classified as novel food lacking approval, 36% were food supplements lacking the necessary notification of the competent authority, 92% were tested to contain differences between analytical and declared CBD content of more than 10%, and finally 50% contained misleading claims such as unauthorised health claims or medicinal claims45. An analysis of over-the-counter CBD products from the UK found that only 38% of 29 products were within 10% of advertised CBD content and 55% had measurable levels of THC or cannabinol46. Similarly, only 3 out of 25 cannabidiol products from the State of Mississippi (USA) were within 20% of label claim, and 3 exceeded 0.3% THC47. Similar studies from Italy48, the Netherlands49, and the USA50 are available.\n\nIn consideration of these consistent reports worldwide, we actually cannot find a better wording than our original statement: “In our opinion the systematically high Δ9-THC content of CBD products is clearly a “scandal” on the food market. Obviously, the manufacturers have – deliberately or in complete ignorance of the legal situation – placed unsafe and unapproved products on the market and thus exposed the consumer to an actually avoidable risk.”\n\nWe fully stand by this conclusion and have even expanded our judgement of the CBD industry in a recent editorial, which concluded that the illegal market of CBD products may provide a strong rationale for the necessity of a paradigm shift towards pre-marketing approval in regulating food supplements3.\n\nThe following arguments of EIHA1, starting with obsolete letters of the EU commission (written at a time when hemp extracts were not available on the market, highlighting their irrelevance to the current situation) and some disconnected information about novel food status, without providing any evidence at all besides unsubstantiated claims, cannot plausibly refute our conclusions. Instead, we have provided ample evidence – based on EFSA criteria26 – that a substantial number of CBD products on the market is not safe (69% of samples above ARfD of EFSA) and all samples (100%) were judged on a case-by-case basis as unapproved novel foods. Additionally, all samples (100%) were non-compliant with mandatory labelling rules and/or used unapproved health claims2. We feel that this is ample proof for our statement above, which is based on facts.\n\nThe CVUA Karlsruhe as part of the food control system in the EU also clearly wishes to reject the allegation of EIHA1 that the institute conducts “discrimination”, “undifferentiated action” and “arbitrariness”. We have assessed all products sent to our institute for evaluation in a transparent and consistent fashion (the criteria for evaluation were published in 201951), conducted our toxicological and regulatory assessment on a case-by-case basis2, and even allowed public scrutiny by publishing our full dataset22.\n\nRegarding the concerns of EIHA to defend the reputable hemp industry against “free riders”, “black sheep” or “cowboys”, we can ensure them that food control includes this segment of the market as well, e.g. by conducting sampling of online stores. Otherwise, the EIHA has the possibility to take their own steps against such practices on the basis of the national laws against unfair commercial practices (e.g. in Germany “Gesetz gegen den unlauteren Wettbewerb (UWG)”).\n\nThe closing remarks of EIHA1 in this section appear ill-considered. First, it is commendable that EIHA wants to ensure compliance with the law and consumer safety. But how can this solely be achieved by an industry standard? And how can an industry standard be made mandatory for all FBOs? Perhaps on a voluntary basis for the members of EIHA, but clearly not for the whole industry, and not for the “free riders”, “black sheep” or “cowboys”. As stated before, we would certainly agree with an improved legal basis for hemp food products similar to other vertical regulations in the food sector, such as the EU spirit drinks regulation. However, we fail to see how this can be achieved as an industry standard.\n\nRegarding the lack of communication between EIHA and public authorities, we recall a technical discussion at our institute at the end of 2018 and are also aware that the EIHA was invited to present their evidence at the “Working Group Novel Food” in Brussels52.\n\nFinally, we congratulate the EIHA for the decision to facilitate novel food applications by conducting extensive toxicology studies.\n\n\nJudgement of the hemp industry in the food sector\n\nThe quote \"Currently CBD users must be aware that they may be ‘participating in one of the largest uncontrolled clinical trials in history’” of Pál Pacher included in a Newsweek article53 is in our opinion very fitting to the reality of the market. First, Pál Pacher is clearly an authority regarding cannabis research (e.g., Refs.54–57). Second, the comment is regarding CBD and not regarding THC, and we currently cannot see a substantial difference between CBD content of food or nutritional supplements on the markets in the USA and Europe. Along with the lack of labelling detected in our study and the suggestions of many manufacturers to “gradually increase the dosage”, pharmacologically active CBD dosages similar to prescription medications may be easily reached by commercial over-the-counter CBD products on the market in Europe. As noted above, no nutrivigilance is typically conducted and no safety assessment has been conducted for the products, because the manufacturers put them on the market before achieving novel food approval.\n\n\nProposal of a legal ban on hemp extracts\n\nWe wonder why our statement “For cannabis-derived products, such as CBD, the problem is aggravated by conflicting regulations in the narcotic, medicinal, and food law areas. For example, hemp extract based products of similar composition could be treated as illegal narcotics, prescription-based medicinal products, or novel foods” is criticized by the EIHA1, when they actually provide supporting evidence with their examples of melatonin or garlic that certain substances could fall into either legal realm depending on labelling sometimes even when the concentration is similar (e.g., also compare sage tea58 or Ginkgo biloba extract59).\n\nOur statement also has been validated by the recent potential suggestion of the European Commission (according to press information7) to consider hemp extracts as narcotic, and hence remove them from the possibility to be marketed as food or food supplement. As detailed elsewhere3,41, we believe that it would be disproportional to regulate CBD products as narcotic drug according to the principle of \"ultima ratio\" in criminal law. In closing, we would therefore like to note that we actually have suggested a regulated legalization of CBD products. Therefore, we question how or why the EIHA is interpreting this as the proposal of a “ban”.\n\n\nConclusions\n\nWe hope our response informs the F1000Research readership about the most recent evidence regarding the toxicological and regulatory evaluation of CBD products. We believe that the Correspondence article of the EIHA1 has made many unsubstantiated claims and is unable to discredit our scientific work that was based on a validated and externally accredited analytical method2 with fully transparent criteria for risk assessment based on BfR19 and EFSA26.\n\nWe hope that the promised extensive toxicological studies and quality standards of EIHA will include the following research questions:\n\nThe deviation of the content of commercial CBD preparations from the labelling consistently found in studies worldwide (see above) could partially derive from instability of CBD during storage60. Research regarding stabilization of CBD appears necessary to ensure CBD stability during shelf-life.\n\nAs a degradation of CBD is expected even in material from synthetic origin61, the degradation products must be identified and toxicologically assessed.\n\nAvoidance of THC contamination and adherence to food standards for THC.\n\nToxicological assessment of CBD as food ingredient aiming to identify acceptable daily intakes without risk for the consumer or pharmacological effects. Currently, there is no consensus of what constitutes a safe CBD dose, with recommendations ranging from as low as 4 mg/day62 over 17.5 mg/day to 60 mg/day63.\n\nInteractions between different compounds such as antagonistic or enhancing effects of the cannabinoid mixture contained in hemp extracts.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.",
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ECLI:DE:OVGNI: 2019: 1212: 13ME320.19.00; 2019.\n\nVG Freiburg: Beschluss vom 21. Oktober 2019 - 10 K 2840/19. 2019.\n\nVGH Baden-Württemberg: Beschluss vom 16. Oktober 2019 - 9 S 535/19. 2019.\n\nEFSA Panel on Contaminants in the Food Chain (CONTAM): Scientific opinion on the risks for human health related to the presence of tetrahydrocannabinol (THC) in milk and other food of animal origin. EFSA J. 2015; 13(6): 4141. Publisher Full Text\n\nSolowij N, Broyd S, Greenwood LM, et al.: A randomised controlled trial of vaporised Δ9-tetrahydrocannabinol and cannabidiol alone and in combination in frequent and infrequent cannabis users: acute intoxication effects. Eur Arch Psychiatry Clin Neurosci. 2019; 269(1): 17–35. PubMed Abstract | Publisher Full Text\n\nPisanti S, Malfitano AM, Ciaglia E, et al.: Cannabidiol: State of the art and new challenges for therapeutic applications. Pharmacol Ther. 2017; 175: 133–50. PubMed Abstract | Publisher Full Text\n\nHaney M, Malcolm RJ, Babalonis S, et al.: Oral cannabidiol does not alter the subjective, reinforcing or cardiovascular effects of smoked cannabis. Neuropsychopharmacology. 2016; 41(8); 1974–82. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEuropean Food Safety Authority (EFSA)Arcella D, Cascio C, et al.: Acute human exposure assessment to tetrahydrocannabinol (Δ9-THC). EFSA J. 2020; 18(1): e05953. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBanas B, Beitzke B, Carus M, et al.: Reasonable guidance values for THC (Tetrahydrocannabinol) in food products. Position paper of the European Industrial Hemp Association (EIHA). Hürth, Germany: European Industrial Hemp Association (EIHA); 2017. Reference Source\n\nVG Düsseldorf: Beschluss vom 27. September 2019 - 16 L 2333/19. 2019. Reference Source\n\nVG Cottbus: Beschluss vom 08.01.2020 - 3 L 230/19. ECLI:DE:VGCOTTB:2020:0108.3L230.19.00; 2020. 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Reference Source\n\nMeyer AH, Rinke H, Verbeek U, et al.: Neue Novel Food Verordnung 2015/2283, Fälle - Recht - Verfahren. 2. Auflage. München: Eigenverlag – meyer.rechtsanwalts GmbH; 2019. Reference Source\n\nLachenmeier DW, Rajcic de Rezende T, Habel S, et al.: Current case law confirms novel food classification of hemp extracts and cannabidiol (CBD) in foods – narcotic classification of cannabis foods remains unclear. Deut Lebensm Rundsch. 2020; 116(3): 111–19. Publisher Full Text\n\nBVL: Opinion of the BVL on the assessment of hemp extracts is unchanged. Berlin, Deutschland Bundesamt für Verbraucherschutz und Lebensmittelsicherheit; 2020. accessed on: 2020-08-10. Reference Source\n\nEuropean Commission: Rapid Alert System for Food and Feed (RASFF). Brussels, Belgium. European Commission; 2020. 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PubMed Abstract | Publisher Full Text\n\nPavlovic R, Nenna G, Calvi L, et al.: Quality traits of \"cannabidiol oils\": cannabinoids content, terpene fingerprint and oxidation stability of European commercially available preparations. Molecules. 2018; 23(5): 1230. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHazekamp A: The trouble with CBD oil. Med Cannabis Cannabinoids. 2018; 1(1): 65–72. Publisher Full Text\n\nBonn-Miller MO, Loflin MJE, Thomas BF, et al.: Labeling accuracy of cannabidiol extracts sold online. JAMA. 2017; 318(17): 1708–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLachenmeier DW, Bock V, Deych A, et al.: Hemp food products - an update. Deut Lebensm Rundsch. 2019; 115(8): 351–72. Publisher Full Text\n\nEuropean Industrial Hemp Association: European Industrial Hemp Association asked by European Commission to advise on traditional or novel food status of hemp extracts. (Press release 15 January 2019). Brussels, Belgium. European Industrial Hemp Association; 2019. (accessed 2020-08-19). Reference Source\n\nFreedman DH: High on the hype. Newsweek. 2019; 30–41.\n\nPacher P, Kogan NM, Mechoulam R: Beyond THC and endocannabinoids. Annu Rev Pharmacol Toxicol. 2020; 60: 637–59. PubMed Abstract | Publisher Full Text\n\nPacher P, Kunos G: Modulating the endocannabinoid system in human health and disease - successes and failures. FEBS J. 2013; 280(9): 1918–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPacher P, Batkai S, Kunos G: The endocannabinoid system as an emerging target of pharmacotherapy. Pharmacol Rev. 2006; 58(3): 389–462. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajesh M, Mukhopadhyay P, Batkai S, et al.: Cannabidiol attenuates cardiac dysfunction, oxidative stress, fibrosis, and inflammatory and cell death signaling pathways in diabetic cardiomyopathy. J Am Coll Cardiol. 2010; 56(25): 2115–25. 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Cannabis and Cannabinoid Research. 2020; in press. Publisher Full Text\n\nTallon MJ: Cannabis sativa L. and its extracts: Regulation of cannabidiol in the European Union and United Kingdom. J Diet Suppl. 2020; 17(5): 503–16. PubMed Abstract | Publisher Full Text\n\nMarinotti O, Sarill M: Differentiating full-spectrum hemp extracts from CBD isolates: Implications for policy, safety and science. J Diet Suppl. 2020; 17(5): 517–26. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "70375",
"date": "07 Sep 2020",
"name": "Patrick John O'Mahony",
"expertise": [
"Reviewer Expertise I am not a research scientist. I am a scientist (molecular biologist by training) working in the Irish/EU food regulatory arena for 20 years. I have been looking after the novel food area (among others) in Ireland for 20 years and have coordinated the analytical survey of the Irish market for hemp-products as published in February 2020."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSide effects of CBD products - EU food regulators await the final opinion of EFSA on the safety assessment of synthetic CBD. Many claims are made about CBD, some health claims not authorised in the EU, some relating to the mitigating effect of CBD on THC (as yet unproven conclusively). World-wide reports of foods and supplements claiming to contain CBD show that a significant proportion also contain THC, some at unsafe levels and some at levels that could result in the \"high\" associated with recreational cannabis use.\nTHC definition and estimation of daily dose of products - In some EU Member States (MS) there is a threshold for THC contaminants in food, but not in others. EU food law is categorical (Reg 178/2002) food does not include narcotics which means any THC in food is considered a contaminant for which there is as yet no safe limit designated. Some EU MS have developed national limits for THC in food and in the future there could be an EU threshold for THC as a contaminant in hemp seed food products (in development). In some MS police can and do remove food products from sale based on any THC level under national legislation.\nCannabis shot - I agree with the author here. Under food law, a supplement must declare a recommended and/or maximum dosage. A shot is generally considered a small amount of concentrated beverage (usually alcoholic) to be consumed in one go.\nCBD oil - Supplements must declare a dosage by law. If not a supplement with no recommended usage guidance then it is anyone's guess as to appropriate use.\nMitigation of THC effects by interaction with CBD - This is not an argument for food law and has not been discussed by regulators. THC presence in food is not specifically permitted by food law and tolerance thresholds for THC as a contaminant are in effect in some EU MS only, with a possibility of an EU-wide threshold in the future. It is unlikely that any EU food regulatory authority would have such a discussion with the industry.\nIllegality of all hemp products containing isolated CBD or hemp extracts - The novel food catalogue is not a legally binding document as stated. However, it does reflect the agreed outcome of discussions at the novel food working group and therefore is binding in so far as all MS agree to interpret and implement the conclusions accordingly within their jurisdictions. Industry groups have tried unsuccessfully to argue that hemp extracts were on the EU market prior to 1997. Any food or ingredient which is a purified/extracted/concentrated component of an existing (not novel) food is likely to be considered a novel food and this standard has been used for almost two decades with many different examples available. Court rulings in one MS have no bearing on the implementation or interpretation of food law in other MS. At most such national court rulings can result in a case being sent to the European Court of Justice (ECJ), the results of which may then necessitate EU-wide legislation consideration. Novel food status is not based on safety or otherwise as stated by the author, but on a significant history of consumption in the EU before 1997.\nJudgement about food producers of CBD products - The idea that registered CBD producers of hemp extracts would be allowed on the market was dismissed as an irrational proposal of industry regulation by this regulatory body. THC content is not the only regulatory or safety issue with hemp products on the market as pointed out by the author through the many reports cited.\nJudgement of the hemp industry in the food sector - The statement in Newsweek about \"the largest uncontrolled clinical trials in history\" is in my opinion the type of histrionic argument used against GMOs and in other food and non-food areas over the years. The reality is that many foods on the market (particularly supplements) fly under the radar until caught by routine surveillance or by the manifestation of safety issues. Therefore, it could be said that there are many \"large-scale uncontrolled clinical trials\" ongoing around the world in food, cosmetics, etc. This sort of inflammatory statement does not aid a rational discussion. There has been no reliable safety assessment yet of CBD ingestion and until then, safety levels of CBD or the hundred plus other cannabinoids in Cannabis sativa is unclear. A thorough safety assessment as being carried out by EFSA currently will address issues of safe intake levels, interactions of CBD with other cannabinoids or other foods. It will also address stability and breakdown products of cannabinoids like CBD.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "7022",
"date": "16 Aug 2021",
"name": "Dirk W. Lachenmeier",
"role": "Author Response",
"response": "Thank you for your insightful remarks regarding the regulatory status of CBD. As requested, we have removed the histrionic argument from Newsweek in v4 of our article1. References 1 Lachenmeier DW, Habel S, Fischer B et al. Are side effects of cannabidiol (CBD) products caused by tetrahydrocannabinol (THC) contamination? [version 4; peer review: 2 approved, 1 approved with reservations]. F1000Research 2021, 8:1394 (https://doi.org/10.12688/f1000research.19931.4)"
}
]
},
{
"id": "70380",
"date": "07 Oct 2020",
"name": "Katarina Černe",
"expertise": [
"Reviewer Expertise Katarina Černe: experimental and clinical toxicology",
"pharmacology",
"cannabinoids",
"risk assessment. Tomaž Pezdir: analytical chemistry",
"forensic toxicology",
"cannabinoids"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 correspondence article, the authors, Lachenmeier et al., attempt to clarify some points they made in their recent article entitled ''Are side effects of cannabidiol (CBD) products caused by tetrahydrocannabinol (THC) contamination?'' (version 3, 19 Aug 2020). The reason for this response is comments on this article that were made by Kruse and Beitzke (26 Aug 2020) on behalf of the European Industrial Hemp Association (EIHA). The main topic is the safety of cannabidiol (CBD) products as a food or food ingredient for consumers, especially in relation to the tetrahydrocannabinol (THC) content. We believe that this issue is worth clarifying, because consumer exposure to unsafe substances is of particular concern since the exposed population may include people of all ages, both sexes and in all states of health. This area is of additional interest due to the new EU Novel Food Regulation 2015/2283.\nIn order to understand the clarifications of Lachenmeier et al. (2020) in this correspondence, it is necessary first to read the comments of Kruse and Beitzke (2020) and the article of Lachenmeier et al. (2020).\nBelow are the main points of Kruse and Beitzke comments to which Lachenmeier et al. wish to respond:\nRegarding the misunderstanding of the “THC” definition of daily dose of products,\nLachenmeier et al. explain that it should be clear from the method section and their definition of the abbreviation of THC as Δ9-tetrahydrocannabinol that they only include psychotropic Δ9-THC (“pure” Δ9-THC) and not its precursor, non-psychotropic Δ9-tetrahydrocannabinolic acid (THCA), in their risk assessment. From the description of the LC methods, it is obvious that the compounds were separated chromatographically. However, the mass spectrum does not show the difference (the parent masses of both TQS and QTOF are identical and, due to low fragmentation, the daughter ions are mainly the same on both instruments). Only the retention times from the chromatographic system show the difference between the substances. It would therefore be useful to show the chromatograms and note the retention times for each substance. EFSA also gives preference to assessing exposure to “pure” Δ9-THC based on the LC-MS method. When samples are analysed using GC-FID or GC-MS (without a preliminary separation step) Δ9-THC and Δ9-THCA cannot be separated, so results are reported as the sum of Δ9-THC/Δ9-THCA. Additionally, EFSA considered 100 % conversion of THCA to THC. Such a report is thus expected to represent an overestimation of exposure to “pure” Δ9-THC for two reasons: the THCA content in hemp is usually higher than the THC content and it is not known to what extent THCA is converted to THC in food1. Kurse and Beitzke also comment on the very high daily dose of Δ9-THC in some products, e.g. tea products. Since this is an initial exposure assessment, it would be helpful if the authors were to describe major sources of uncertainties and the limitation of the exposure assessment in a separate paragraph.\n\nSide effects of CBD products\nFirst, we would like to say that the term ‘side effect’ is inappropriate. Adverse or toxicological effect is a more appropriate term. However, we will use the term ‘side effect’ to avoid confusion. Since Kurse and Beitzke refuted any side effects of CBD, Lachenmeier et al. provided additional literature to the contrary. They proposed that the causes of the side effects are either a direct toxicological effect of CBD, the degradation of CBD to Δ9-THC due to acidic hydrolysis in the stomach following oral consumption or Δ9-THC directly contained in the products. A side effect such as “feeling high” is likely to be explained by Δ9-THC contamination rather than by CBD. In humans, gastrointestinal effects are the most commonly reported side effect. Non-clinical studies have resulted in concerns about hepatotoxicity, teratogenicity and gut inflammation. They have also emphasized that the absence of acute toxic events does not mean that there are no chronic effects. However, not enough time has elapsed since CBD extracts have been more widely present on the market for chronic effect to show up (e.g., chronic liver injury). In addition, the absence of serious side effects is not enough for current safety criteria. Moreover, there is currently no system of nutri-vigilance implemented, so there is no formal registration of such cases and such events may be unrecognized. There are still many uncertainties and contradictions remaining from the increasing number of published cannabinoid safety studies. This is because these studies vary to the extreme in their methodology and quality, rendering results difficult to compare. Moreover, toxicity is not systematically covered, and there are no chronic toxicity data from well-defined exposure settings. Although Kurse and Beitzke criticize the usage of Epidiolex® as a reliable source of toxicological information on CBD, as a 99 % pure extract from C. sativa, CBD has become the most extensively toxicologically tested cannabinoid. In spite of the fact that Epidiolex® has been approved for treatment-resistant epilepsy, the non-clinical part of testing was independent of this indication2. CBD is extensively metabolised in the liver and gut, mainly by the CYP2C19, CYP3A4, UGT1A7, UGT1A9, and UGT2B7 enzymes. The metabolism of CBD is very complex, especially in hepatocytes. The main human metabolite is 7-carboxy-cannabidiol (7-COOH-CBD; ~90 % of all drug-related substances measured in the plasma)3. Its toxicological profile has not been investigated because experimental animals for toxicological studies (mice, rats, and dogs) do not metabolise CBD to a comparable extent as do humans4. The major concern with 7-COOH-CBD may be its reactive acyl-glucuronide5. CYP-mediated interaction is one of the major concerns in clinical practice. Drug interaction trials to assess the effect of CBD on these enzymes in healthy volunteers will therefore be conducted during the post-marketing period. A full battery of non-clinical oral reproductive and developmental studies has been conducted with purified CBD, showing toxicological effects2. Since the novel food status of CBD extracts was confirmed in January 2019, the Food Standard Agency (FSA) has given CBD companies a deadline of March 31, 2020 to apply for authorisations of their CBD extracts and isolates (for each product). In this regard, toxicity testing should be systematically covered, so the safety of each of CBD product will be clear.\n\nMitigation of THC effects by interaction with CBD\nLachenmeier et al. re-confirmed their risk assessment without considering the interaction with CBD, since the opinion of EFSA is that information on THC/CBD interactions is controversial and not consistently antagonistic. EFSA also re-confirmed their acute reference dose (ARfD) of 1 µg/kg body weight (BW), without considering the interaction with CBD. Additionally, Lachenmeier et al. provided reference to recent research of Solowij et al., in which they found that the effects of Δ9-THC may even be enhanced by low-dose CBD. In spite of its low affinity for CB1 and CB2 receptors, CBD can interfere with some THC adverse effects, particularly in the brain, without interfering with the intended THC effects, such as muscle relaxation6. In terms of the pharmacokinetic CBD/THC interaction, CBD may impair THC hydrolysis by the CYP450 enzyme7. The inhibition of THC metabolism may vary with species, timing of administration (CBD pre-administration vs co-administration), and CYP isoenzymes8. Whether CBD will antagonise or potentiate THC effects also seems to depend on their administration ratio, and this ratio varies with species. Given all these possibilities, prediction of interactions between THC and CBD in food can be quite a challenge, so we do not yet see the possibility of including them in the risk assessment of CBD products. When using ARfD, it is necessary to consider that it represents an estimate of the amount of a substance in food that can be ingested, usually during one meal or one day. This has been established on the base of central nervous system effects and increased heart rate, which were noted at a low Δ9-THC level (2.5 mg/day) in humans and occurred within a short time after dose administration. This dose, corresponding to 0.036 mg/day/kg BW for a person with a body weight of 70 kg, was regarded as the lowest-observed-adverse-effect level (LOAEL) in both single and repeated studies. Using an uncertainty factor (UF) of 3 for extrapolation from the LOAEL to a no-observed-effect-level (NOAEL) and an UF of 10 for interindividual differences, an overall UF of 30 was established (0.036 mg/day/kg: 30 = 0.001 mg/day/kg) (1). When applying the UF, the recommended daily dose for adults is 0.07 mg. At a higher consumption level, there is a risk of influence on the person’s ability to operate machinery and drive vehicles. Interestingly, Lachenmeier et al. used LOAEL in their assessment without applying UF.\n\nIllegality of all hemp products containing isolated CBD or hemp extracts\nAfter the date mentioned above, only products that have a validated novel food application will be allowed to remain on the market. It is therefore our view that regulatory issues are very extensively written and could be less extensive and shorter.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Partly\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": [
{
"c_id": "7023",
"date": "16 Aug 2021",
"name": "Dirk W. Lachenmeier",
"role": "Author Response",
"response": "We thank the reviewers for the assessment of our article. Due to the requests, the following changes were implemented: A representative chromatogram with marked retention times for each substance was included. A short discussion about sources of uncertainties and limitations of exposure assessment was added to the section “THC definition and estimation of daily dose of products”. The term “side effects” was changed to “adverse effects” as requested. Regarding the adverse effects of CBD products, we want to thank the reviewer for the insights and remarks on toxicology and metabolism of the compound. We found that this information was more appropriate for inclusion in our original article and have done so during our recent revision into v4 of the article1. Regarding the application of ARfD and LOAEL for risk assessment, we want to point out that were are using both thresholds and not only the LOAEL. A food containing THC in exceedance of ARfD is considered as being “unfit for human consumption” (Article 14 No. 2 (b) of regulation (EC) No 178/2002), while a food containing THC in exceedance of LOAEL is considered as “injurious to health” (Article 14 No. 2 (a) of regulation (EC) No 178/2002). The distinction is also clearly marked by the colours in Table 2 (last column) of our original article1. Furthermore, this distinction also leads to prioritization of risk management measures, e.g. in terms of urgency, inclusion in rapid alert system RASFF, etc. In conclusion, it must be noted that while having already passed the mentiond FSA deadline of March 31, 2021, no product has been approved so far in the UK, and none in the European Union as well. Therefore, we believe that our regulatory section is still valid, and we have refrained from shortening the section so far. References 1 Lachenmeier DW, Habel S, Fischer B et al. Are side effects of cannabidiol (CBD) products caused by tetrahydrocannabinol (THC) contamination? [version 4; peer review: 2 approved, 1 approved with reservations]. F1000Research 2021, 8:1394 (https://doi.org/10.12688/f1000research.19931.4)"
}
]
}
] | 1
|
https://f1000research.com/articles/9-1051
|
https://f1000research.com/articles/10-813/v1
|
16 Aug 21
|
{
"type": "Research Article",
"title": "Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach",
"authors": [
"Fedik Abdul Rantam",
"Viol Dhea Kharisma",
"Christrijogo Sumartono",
"Jusak Nugraha",
"Andi Yasmin Wijaya",
"Helen Susilowati",
"Suryo Kuncorojakti",
"Alexander Patera Nugraha",
"Viol Dhea Kharisma",
"Christrijogo Sumartono",
"Jusak Nugraha",
"Andi Yasmin Wijaya",
"Helen Susilowati",
"Suryo Kuncorojakti",
"Alexander Patera Nugraha"
],
"abstract": "Background: An immunoinformatic approach may be useful to investigate the conserved region in the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting the conserved regions in the spike glycoprotein to trigger increased multi-variant virus neutralization and memory response for the development of vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia were compared with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates obtained from the NCBI and GISAID databases. The recognition of antigens was carried out directly using B cells through the B cell receptor (BCR). An indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC50 value. In addition, vaccine allergenicity and toxicity were investigated. During the molecular complex examination, the 3D peptide structure was investigated and the lowest amount of energy formed when the vaccine candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved regions which were very similar to reference countries such as China, the United Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was predicted that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidate with antigenic, non-allergen, and non-toxic properties.",
"keywords": [
"COVID-19",
"SARS-CoV-2",
"Infectious Disease",
"Immunoinformatic",
"spike glycoprotein",
"conserved region."
],
"content": "Introduction\n\nCoronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). First identified in December 2019 in Wuhan, China, it then spread around the world and became a global health burden. COVID-19 patients may experience headaches, dizziness, coughing, and a loss of their sense of smell.1 The virus is spread between humans when an infected individual expels droplets and airborne particles which come into contact with a healthy person. SARS-CoV-2 is a virus with RNA as its genetic material, an envelope, and in about 96% of COVID patients it is identified as BatCoV RaTG13.2,3 This virus consists of thousands of variants divided into several clades. The most well-known variants are Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Epsilon (E484K, B.1.429 & B.1.427).4 The emergence of SARS-CoV-2 variants causes an increase in the rates of infection, reinfection, and avoidance of neutralization from the vaccine antibodies.5\n\nThe COVID-19 pandemic has extended to all parts of the world including countries in the Southeast Asia region, especially Indonesia. The number of SARS-CoV-2 cases has increased rapidly in Indonesia, at around 1000 new cases per day since 2020. As of now, the distribution of SARS-CoV-2 vaccination in Indonesia still totally depends on foreign production. Thus, the development of domestic vaccines is necessary.6 In addition, the domestic vaccine development uses various Indonesian SARS-CoV-2 isolates from the NCBI and GISAID databases. Therefore, the vaccines must include multi-variant protection, be immunogenic, and form immune memory.1,7\n\nMoreover, the development of vaccines involves the use of SARS-CoV-2 glycoprotein, which plays an important role in the infection process inside the host.7 Under normal conditions, spike glycoprotein will bind to the angiotensin-converting enzyme 2 (ACE-2) receptor as a viral attachment mechanism. This mechanism has inspired many studies that have developed vaccines focusing on the neutralization of antibodies to viral glycoproteins.8 In addition, SARS-CoV-2 is able to mutate to form a new variant that is capable of changing the residues which can create the spike glycoprotein. This leads to the possibility that the spike glycoprotein could avoid being neutralized by antibodies produced by SARS-CoV-2 vaccine.9 However, a previous study suggested that the development of the SARS-CoV-2 vaccine must target the conserved regions. Conserved regions can be found in every variant of SARS-CoV-2, and are the main target of vaccine design because they are able to trigger an increase in the antibody neutralization’s coverage.10\n\nAdditionally, conserved region-based vaccine development has been carried out on ZIKA, DENV and influenza viruses through an immunoinformatic approach, but is rarely found in SARS-CoV-2 vaccine development.11 This approach was used in this study to determine the conserved region in the spike glycoprotein of Indonesian SARS-CoV-2 isolates, which can be used as vaccine seed candidates. BepiPred methods were employed in determining the B cell epitope to investigate the probability of the antigen region inducing the B cell recognition.12 The candidate peptides that change the epitope of B cells would be expected to have antigenicity, similarity, and toxicity. Then, molecular docking and dynamic simulations would be carried out to determine the stability level of molecular complexes formed by peptides with B cell receptors (BCR).13,14 Furthermore, this study aimed to investigate Indonesian SARS-CoV-2 isolates based on their B cell epitopes by targeting the conserved regions in spike glycoprotein to trigger the increased multi-variant virus neutralization and memory response to develop seed candidates.\n\n\nMethods\n\nThe SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesian isolates and their references were obtained from NCBI and GISAID44 databases with keyword ‘SARS-COV-2 Spike Glycoprotein’ and with filter ‘no partial sequences’.\n\nThen, protein alignment was performed using MEGA X (version 10.2.6, build 10210527, default settings GAP, (Open/Extend: −2,90 & 0.00), Min Dag Length: 24, dan Max literation 16) to identify the position of the conserved region.1,15 The SWISS-MODEL (default settings) was applied in this study for the construction of the 3D spike glycoprotein SARS-CoV-2 structure. It utilized the construction method of homology modelling by considering sequences only where >20% of residues were homologous, and model validation through the Ramachandran plot which only considered sequences considered if >90% of residues were in the favored region.16,17 Additionally, comparisons of the simulation, staining selection, and structure of the SARS-CoV-2 query spike glycoprotein models with the reference sequences were completed using PyMol software version 2.5.0,18 differentiating domain receptor, ligand and secondary protein structures by color.\n\nThe recognition of antigens is performed directly by B cells through the BCR. This consists of immunoglobulin and Cluster of Differentiation (CD) 79, which majorly contribute to signal transduction and activation of B cells in the immune response.19,20 The interaction between the variable region in the antigen-binding fragment (Fab) of the BCR and the epitope allow it to trigger the B cell recognition response, which can be predicted by epitope mapping analysis.21,22 IEDB Server Analysis Tools (default settings) were employed in this study to predict B cell epitopes based on the direct recognition mechanism through the BepiPred version 2.0 method.8,12,23\n\nIndirect B cell activation occurs via the peptide recognition pathway by CD4+ T cells through the major histocompatibility complex (MHC)-II. Investigating binding of a peptide with human leukocyte antigens (HLA) can predict their ability to trigger the formation of memory cells.24,25 MHC-II epitopes were predicted through IEDB’s binding tool (default settings, locus allel MHC type II: Human, HLA-DR, with epitope length 15-mer, sorted peptide by: adjusted rank, output format: XHTML table), by binding with three HLAs (reference set) consisting of HLA-DRB1*01:01, HLA-DRB4*01:01, and HLA-DRB3*02:02.26 Meanwhile, the peptide binding affinity for MHC-II encoded with specific HLA alleles was predicted based on the IC50 value, which was determined through previous research by Zahroh et al. in 201145; high affinity was represented by IC50 <50 nM, medium affinity by IC50 <500 nM, and low affinity by IC50 <5000 nM.11\n\nPeptides with positive predictions (indicated by the IC50 value of the vaccine candidate peptide of <50 nm and the percentage rank value of <0.5) for B and T CD4+ cell epitopes were tested through the VaxiJen v2.0 server (Setting as = “target organism”: virus, threshold: default Output format: sequence Output) for the selection of antigenic properties.27 Then, the level of allergenicity from the vaccine candidate peptides was predicted via the AlerCatPro 1.7 server (default settings).28 The toxicity profile of the vaccine candidate peptides in this study was predicted using the ToxinPred server (threshold SVM: −0,1 with positive prediction (peptide but not toxin) indicated as peptide score below -0,1).29 Lastly, the 3D peptide structure of the vaccine candidate was constructed via the PEP-FOLD 3.5 server (default settings) with de novo modeling methods, and a sample of the protein modeling result was saved in databank format.30\n\nThe Cluspro 2.0 server (default settings) was applied in this study for molecular docking as the analysis aimed to determine the lowest amount of energy formed when the vaccine candidate peptide bound with BCR and MHC-II to create the molecular complex. The docking results were formed through superimposition.13 Furthermore, the CABS-flex 2.0 server (default settings: protein rigidity: 1.0; protein restraints: ss2 3 3.8 8.0; global C-alpha restraints weight: 1.0; global side-chain restraints weight: 1.0; number of cycles: 50; cycles between trajectory: 50; temperature range: 1.40-1.40; RNG seed: 2465) was utilized in this study to validate the docking results through molecular dynamics simulation; when a molecular complex occurs, the dynamic molecular simulation can describe the fluctuations in the interaction of the amino acid residues that make up the peptide with the target protein domain (receptor).14\n\n\nResults\n\nThe SARS-CoV-2 spike glycoprotein sequence of Indonesian isolates that were successfully obtained from the NCBI database had the following IDs: MZ026853.1, MZ026854.1, and MZ026855.1. Additional samples were also generated from the GISAID database, which can be found in the underlying data section.31 These gene samples were then translated via MEGA X (version 10.2.6) software to identify the amino acid residues that formed the SARS-CoV-2 spike glycoprotein. The conserved region was obtained through protein alignment with reference sequences MN908947.3/Wuhan/China, MW980115.1/United Kingdom, MW981442.1/South Africa, MT434757.2/India, MT510724.1/United States, and MT807936.1/Brazil. The total number of spike glycoprotein gene sequences used in this study were 26 samples consisting of 20 queries and six reference sequences.\n\nThe conserved region positions were identified as 18 regions in the SARS-CoV-2 spike glycoprotein consisting of A(1-17), B(23-68), C(81-115), D(117-143), E(145-184), F(186-214), G(216-240), H(244-476), I(485-500), J(502-569), K(571-613), L(615-671), M(683-700), N(702-715), O(717-981), P(988-1117), Q(1119-1139), and R(1141-1273). The 3D structures of spike glycoprotein isolates were obtained from SWISS-MODEL to determine the similarity to the structural templates and quality. The protein modeling results were displayed through the PyMol software with a cartoon display and underwent staining selection. When the results of the modeling of the spike glycoprotein SARS-CoV-2 query were completed, a comparison of the structure with the template was carried out through 3D alignment analysis. The resulting spike glycoprotein SARS-CoV-2 models of Indonesian isolates in this study had similarity values of 90-100% with the references in the database through the 3D alignment process (Figure 1).32\n\nThe structures are displayed in cartoons and colored based on the isolates via PyMol software.\n\nIndonesian isolate MZ026853.1 was chosen for SARS-COV-2 seed vaccine candidate as it is the dominant variant found in Indonesia.33 Prediction of B cell epitope recognition was carried out on the template of Indonesian isolate MZ026853.1 using IEDB Analysis Tools with the BepiPred method. The peptides that showed a positive epitope prediction were selected based on the epitope’s carried conserved region. The epitope/peptide of the B cell-based vaccine candidate refers to a score above the threshold of 0.35 (calculated based on the server’s prediction results, which refers to the Hidden Markov Model and Trend Scale methods) while the T-cell-based vaccine candidate epitope/peptide refers to the IC50 score >50 nM. The results showed that the position of the B cell epitope was identified on the SARS-CoV-2 spike glycoprotein of the Indonesian isolate and had a length of 10 to 11-mer (Figure 2).34 Furthermore, the results also revealed that all identified epitopes had a value above the threshold of 0.35, and based on the identification results, it exhibited all peptides that make up the epitope. In addition, inside the obtained B cells epitope, there were eight peptides with conserved regions from the total of 15 epitopes in this study (Table 1).\n\nRegions with positive predictions are highlighted in yellow and green for negative predictions.\n\nThe prediction of CD4+ T cell epitope introduction was also carried out on the template of Indonesian isolate MZ026853.1 using IEDB Analysis Tools with the default method. In addition, the binding affinity of the vaccine candidate peptide with MHC-II encoded by specific HLA alleles was assessed based on a reference set consisting of HLA-DRB1*01:01, HLA-DRB4*01:01, and HLA-DRB3*02:02. The results showed there were 15 peptides categorized as CD4+ T cell epitopes because they had a high binding affinity for MHC-II encoded by specific HLA alleles. Moreover, there were 11 peptides that produced epitopes identified as having conserved regions and these were utilized for further analysis (Table 2).\n\nThere were 19 peptides which have B and T CD4+ cells with conserved regions. These were then tested for antigenicity considering the threshold value of 0.4 (determined by IEDB’s default settings), which led to 13 peptides categorized as antigens because they had values higher than this. Furthermore, peptides with antigenic properties were tested for allergenicity by taking into account the threshold value of 20% (determined by IEDB’s default settings), which resulted in all 13 obtained peptides being considered non-allergenic. Peptides categorized as non-allergenic then underwent toxicity prediction using the reference sequences with a threshold value of −0.8 (determined by IEDB’s default settings), which incurred 10 non-toxic peptides (Table 3). Thus, based on the analysis of vaccine property prediction, it was concluded that peptides B9, B12, L1, L2, L4, L5, L9, L11, L12, and L13 could act as antigens and were not allergenic, as well as having non-toxic properties. These 10 peptides were then used for further analysis.\n\nThe 3D structures of BCR (ID: 5IFH), HLA-DRB1*01:01 (ID: 1AQD), HLA-DRB3*02:02 (ID: 3C5J), and DRB4*01:01 (ID: 5JLZ) were obtained from RCSB Protein Data Bank. 3D peptide structures of B9, B12, L1, L2, L4, L5, L9, L11, L12, and L13were modelled using the PEP-FOLD 3.5 server. The structures of peptides and proteins were used for docking simulations on Cluspro 2.0 software to determine the lowest energy formed in the molecular complex. The docking models in this study were peptides B9 and B11 which interacted with BCR, peptides L1, L2, L4, L5 with MHC-II coded by HLA-DRB1*01:01, peptides L9 with HLA-DRB3*02:02, and peptides L11, L12, and L13 with HLA-DRB4*01:01. The simulation results showed that the molecular complex BCR_B12 with the lowest energy of -433.0 kcal/mol was more negative than B9 when binding to BCR. Meanwhile, peptide L5 had the lowest energy -905, 6 kcal/mol when interacting with MHC-II encoded by HLA-DRB1*01:01, which was lower than L1, L2, and L4. The most negative values occurred in the interaction between peptide L9 and HLA-DRB3*02:02, which had an energy value of -890.6 kcal/mol, and L13 peptide, which possessed lower energy (-789.3 kcal/mol) compared to L11 and L12 when binding to HLA-DRB4*01:01 (Figure 3).35\n\n(A) Interaction of B12 peptides with variable light (VL) and heavy (VH) chains on the B cell receptor (BCR) through direct B cell activation pathways. (B) Interaction of L5, L9, and L13 peptides bound to region A on MHC-II encoded by HLA-II to trigger activation B cells through an indirect mechanism with the help of CD4+ T cells.\n\nThe molecular complexes of BCR_B12, HLA-DRB1*01:01_L5, HLA-DRB3*02: 02_L9, and HLA-DRB4*01:01_L13 were analyzed for residual fluctuations in their peptide constituent that interacted through root-mean-square fluctuation (RMSF) level and generated the protein region via the CABS-flex 2.0 server. The results of molecular dynamic simulations exhibited that the BCR_B12 molecular complex contained a fluctuating residue with positions A3, A4, A5, A6, A7, A8, A9, and A10 with RMSF values >0.85 Å to <2.22 Å. Concurrently, the molecular complex of HLA-DRB1*01:01_L5 showed fluctuant residue positions of A9, A10, A11, A12, A13, A14, and A15 with RMSF values >0.52 Å to <1.46 Å. Furthermore, the HLA-DRB3*02:02_L9 molecular complex showed fluctuant residue positions of A4, A5, A6, A7, and A8 with RMSF values ranging from >0.95 Å to <1.77 Å. Additionally, the molecular complex of HLA-DRB4* 01: 01_L13 showed fluctuant residues at positions A11, A12, A13, A14, and A15 with RMSF values ranging from >0.46 Å to <1.68 Å (Figure 4).37\n\nThe residues that produce L and H chains are part of the BCR, while chain A is presented in MHC-II, and P is the vaccine candidate peptide. (A) BCR_B12, (B) HLA-DRB1*01:01_L5, (C) HLA-DRB3*02:02_L9, (D) HLA-DRB4*01:01_L13.\n\n\nDiscussion\n\nHomology modeling is a method of determining the 3D structure of a query protein based on the availability of templates in the database. Its accuracy is around 90%, and the model is categorized as similar or homologous to the target protein if it has a modeling similarity value of >20%.16,17 The similarity levels are high if the superimposed query protein on the template is identified during 3D alignment.18,38 In this study, the spike glycoprotein structure of 20 Indonesian isolates of SARS-CoV-2 had high similarities to the isolate references such as those from China/Wuhan, the United Kingdom, South Africa, India, the United States, and Brazil with an average similarity level of 90% to 100% (See Figure 1). In addition, the similarities were also demonstrated between the secondary protein structure of the SARS-CoV-2 spike glycoprotein of the Indonesian isolates and the superimposed reference isolates.\n\nThe structure of the SARS-CoV-2 spike glycoprotein consists of S1 and S2 regions. S1 covers residue positions 13-685 and S2 covers positions 686-1273.39 In the S1 region, there is a N-terminal domain as well as a receptor-binding domain (RBD) covering the sequence positions 319-541, including an integrin-binding motif (403-405), and receptor-binding motif (437-508). S2 consists of fusion peptides 1 and 2 (816-1202).40 The conserved region is specific to the virus, is maintained in each generation of variants and has the potential to be a target for antibodies to neutralize of in vaccine design, since it is predicted to be able to protect against infections with a wide variety of variants.8,13,41 Furthermore, the conserved region obtained from the identification results in this study was detected very high activity in almost all parts of the SARS-CoV-2 spike glycoprotein, especially in S1, RBD, and S2.\n\nThe recognition of B cell epitopes in the conserved region allows activation of B cells through direct and indirect pathways19,20 The epitope position on the SARS-CoV-2 spike glycoprotein recognized by B cells based on the study results can be influenced by the direct activation of conserved regions H, K, O, & R. This allows the production of Immunoglobulin M (IgM)-type immunoglobulins for opsonization response and complement recruitment.42,43 In addition, conserved regions A, J, D, P, O may trigger B cell activation through indirect pathways, through the contribution of CD4+ T cells to produce isotype switching for the production of IgG antibodies and memory cells.44,45 Correspondingly, the peptides with specific regions were B9 (region K), B12 (region O), L1 (region J), L2 (region J), L4 (region J), L5 (region A), L9 (region P), L11 (region O), L12 (region O), and L13 (region O) including antigenic peptides, non-allergens, and non-toxins.\n\nThe direct B cell activation pathway is triggered by peptide binding to the Fab region on the BCR, which allows signal transduction through CD79, and then triggers transcription factors involved in the activation, maturation, and proliferation of plasma cells, resulting in the production of IgM antibodies.19,46 On the other hand, the indirect pathway of activation occurs due to the representation of MHC-II by B cells, and its recognition by TCR on CD4+ T cells.20,47 Peptides with high binding affinity to MHC-II and encoded by specific HLA alleles are predicted to act as T cell epitopes.11 The binding of the vaccine candidate peptide to the B cell receptor is identified by the lowest energy produced by the molecular docking complex. The lowest energy with a more negative value, is estimated to indicate the most stable and active biological response to protein initiation.13 In this study, the activation response of B cells is predicted to be directly initiated by the molecular complex BCR_B12, and indirectly through HLA-DRB1*01:01_L5, HLA-DRB3*02:02_L9, and HLA-DRB4*01:01_L13 because they have the lowest negative energy values.\n\nFinally, the binding stability of molecular complexes can be analyzed by molecular dynamics simulations by examining the level of fluctuation based on the RMSF value of each complex formed.14 RMSF exhibits the movement of interacting atoms on the residues of peptides and proteins with a certain distance, while complex stability is achieved when the resulting distance has a value of ≤4Å.48,49\n\n\nConclusions\n\nThe spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates have a conserved region and are very similar to the reference isolates from China, the United Kingdom, South Africa, India, the United States, and Brazil. It is suggested that the conserved region of Indonesian SARS-CoV-2 isolates can be identified as an epitope of B and T CD4+ cells that produce the vaccine candidate peptides with antigenic, non-allergen, and non-toxic properties. This study recommends that peptides B12, L5, L9, and L13 can be used in the follow-up tests because they may trigger B cell activation responses via direct and indirect pathways. Lastly, the vaccine candidate is predicted to be able to initiate the production of specific antibody isotypes, which play a role in increasing the neutralization of multi-variant viruses and the formation of memory cells to prevent SARS-CoV-2 infection.\n\n\nData availability\n\nThe accession numbers for GISAID and NCBI can be found in the acknowledgments table:\n\nFigshare: GISAID acknowledgment table: https://doi.org/10.6084/m9.figshare.15048513.v1.31\n\nAccess to GISAID data requires registration and agreement to GISAID’s terms.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe gratefully acknowledge the following Authors from the Originating laboratories responsible for obtaining the specimens and the Submitting laboratories where genetic sequence data were generated and shared via the GISAID Initiative, on which this research is based.\n\n\nReferences\n\nTurista DDR, Islamy A, Kharisma VD, et al.: Distribution of COVID-19 and phylogenetic tree construction of SARS-CoV-2 in Indonesia. J. Pure. Appl. Microbiol. 2020; 14(suppl 1): 1035–1042. Publisher Full Text\n\nFahmi M, Kharisma V, Ansori A, et al.: Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. Adv Exp Med Biol. 2021; 1318: 839–857. PubMed Abstract | Publisher Full Text\n\nPei S, Yau SS: Analysis of the Genomic Distance Between Bat Coronavirus RaTG13 and SARS-CoV-2 Reveals Multiple Origins of COVID-19. Acta Math Sci = Shu xue wu li xue bao. 2021; 41(3): 1017–1022. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nTai W, He L, Zhang X, et al.: Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Cell Mol Immunol. 2020; 17(6): 613–620. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVishwakarma P, Yadav N, Rizvi ZA, et al.: Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Based Novel Epitopes Induce Potent Immune Responses in vivo and Inhibit Viral Replication in vitro. Front Immunol. 2021; 12: 613045. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNoviski M, Mueller JL, Satterthwaite A, et al.: IgD B cell receptors differentially respond to endogenous antigens and control B cell fate. eLife. 2018; 7: e35074. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu J, Wang Y, Xiong E, et al.: Role of the IgM Fc Receptor in Immunity and Tolerance. Front Immunol. 2019; 10: 529. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStavnezer J, Schrader CE: IgH chain class switch recombination: mechanism and regulation. J Immunol. 2014; 193(11): 5370–5378. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZabel F, Fettelschoss A, Vogel M, et al.: Distinct T helper cell dependence of memory B-cell proliferation versus plasma cell differentiation. Immunology. 2017; 150(3): 329–342. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRadaev S, Zou Z, Tolar P, et al.: Structural and functional studies of Igalphabeta and its assembly with the B cell antigen receptor. Structure. 2010; 18(8): 934–943. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoche PA, Furuta K: The ins and outs of MHC class II-mediated antigen processing and presentation. Nat Rev Immunol. 2015; 15(4): 203–216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSu Z, Wu Y: Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteins. Phys Chem Chem Phys. 2019; 21(5): 2463–2471. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBepari AK, Reza HM: Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation. PeerJ. 2021; 9: e11261. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElbe S, Buckland-Merrett G: Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017; 1: 33–46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZahroh H, Ma’rup A, Tambunan US, et al.: Immunoinformatics Approach in Designing Epitope-based Vaccine Against Meningitis-inducing Bacteria (Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzaeType b). Drug Target Insights. 2016 Nov 1; 10: 19–29. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "91996",
"date": "09 Sep 2021",
"name": "Mohammad Saifur Rohman",
"expertise": [
"Reviewer Expertise Cardiovascular Medicine",
"Molecular Cardiology",
"Interventional Cardiology",
"Pharmacogenetics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript is promising for initial step of vaccine development. Especially for Indonesian population. Since isolated sequence taken from Indonesian covid-19 patients.\nHowever, as preliminary result the author supposed to propose future direction of the next research for vaccine production.\n\nMolecular docking and dynamic simulation results should be confirm again using in vitro or in vivo models. It could be proven or not according to this result. It is far for realistic the candidate of molecule and the rapid test really occur in vivo.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "98953",
"date": "16 Nov 2021",
"name": "Dur Lashari",
"expertise": [
"Reviewer Expertise immunology and microbiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe current study, “Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach,” which employs an Immunoformatics approach, appears to be a high-quality piece of work with promising results. The use of bioinformatics tools reduces the cost and time required to predict potential epitopes. Furthermore, the current study is appealing as a first step in developing a vaccine because it focuses on the local Indonesian sequences of SARS-CoV-2.\nI recommend this study strongly for indexing due to the following reasons:\nThe current study is well-presented, and the most recent literature is cited.\n\nThe study design was found sound and used immunoinformatic approaches for B-cell, T-cell prediction, 3D structure development, and molecular docking are technically sound approaches.\n\nThe methodology and the discussion section were both clear, explanatory, and technically sound.\n\nThe study's abstract and conclusion were found to be brief and concise.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "98417",
"date": "16 Nov 2021",
"name": "Hesham Mohammed Al-Sharani",
"expertise": [
"Reviewer Expertise Clinical and lab studies in medicine and dentistry. Systematic reviews and meta-analyses as well."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study entitled \"Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach\" was an original article that is well organized and valuable. It checked the possibility of investigating SARS-CoV-2 in Indonesian isolates based on B cell epitopes by marking the conserved regions in the spike glycoprotein to trigger the elevated multi-variant virus neutralization and memory response for the development of vaccine seed candidates.\nMethods included a comparison between SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates collected from the NCBI and GISAID databases. B cell receptor (BCR) was used to recognize antigens on the B cells. Indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC50 value. Vaccine allergenicity and toxicity were also examined.\n\nResults showed similarities between Indonesian conserved regions and the compared mentioned countries, thus the predicted expectations that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidates with antigenic, non-allergen, and non-toxic properties.\nI feel satisfied with the article's frame, methodology and results.\nJust a few English corrections are to be rechecked.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-813
|
https://f1000research.com/articles/10-811/v1
|
16 Aug 21
|
{
"type": "Research Article",
"title": "A pragmatic trial of online interactive webtools for teaching biostatistics to first-year medical students: a constructivism-informed approach",
"authors": [
"Steven Hardy",
"Douglas McHugh",
"Steven Hardy"
],
"abstract": "Background: Statistical reasoning is an important clinical skill that informs evidence-based medicine and is desirable for 21st century practice. Yet many physicians struggle to apply biostatistical techniques correctly, potentially undermining patient care decision-making and adversely affecting outcomes. The overarching concepts of foundational biostatistics and probabilistic reasoning can be challenging to teach and hard for students to internalize given time constraints, lack of intrinsic motivation, and varied pre-existing knowledge or cognitive schema. We investigated how supplemental, interactive online webtools affected first-year medical students’ learning of sensitivity, specificity, negative/positive predictive values, and prevalence. Methods: Online webtool design was informed by constructivism and sought to have learners 1) build conceptual representations by connecting new information to existing knowledge, 2) interact with primary sources of biostatistical data, and 3) begin with whole concepts then explore component parts. A total of 59 students were assigned randomly to two cohorts that had access to the webtools before or after in-class teaching; an additional 35 students had no access and served as the control cohort. Access metrics, summative exam scores, prior knowledge measurements, and qualitative data on learners’ experiences from three focus groups (n = 6/group) were collected. Results: Mean exam scores were 87.5 ± 10.8%, 90.7 ± 11.2%, and 88.9 7 ±12.9% for the before, after, and control cohorts (p = 0.49). Students repeatedly accessed the online webtools: mean access was 4.3 (± 2.6) (before) and 2.6 (± 1.5) (after). Qualitative data showed the webtools facilitated learning in a time-efficient manner. Conclusions: Online interactive webtools facilitated a constructivism-informed learning model and were found by first-year medical student to supplement and enhance their learning experience without detracting from established biostatistical teaching or negatively affecting summative assessment outcomes.",
"keywords": [
"Biostatistics",
"Medical Education",
"Shiny",
"R-software",
"Sensitivity",
"Specificity",
"Positive Predictive Value",
"Negative Predictive Value."
],
"content": "Introduction\n\nThe importance of understanding biostatistics in the context of communicating and health-related probabilities and applying them meaningfully with colleagues and patients has been highlighted as an important 21st century component of medical education.1 Indeed, doctors increasingly strive to practice evidence-based medicine and make clinical decisions that are supported by careful evaluation of peer-reviewed research.2,3 Therefore, an effective physician must be able to interpret biostatistical data competently when necessary. Unfortunately, practicing physicians struggle to parse sound knowledge from statistical data.4,5 To address this, many medical school curricula include dedicated biostatistics teaching grounded in medically relevant data sets. Some challenges that medical students face when pursuing proficiency in biostatistics include limited time, motivation, and prior knowledge or experience with which to scaffold learning.6 These challenges necessitate an engaging and streamlined curriculum so that students can get the most out of the effort they put in. Additionally, medical students tend to have a wide range of scheduling and study habits, so individualized learning is often preferred.7 These factors suggest that online resources are a good option to aide medical students in their pursuit of learning biostatistics due to the flexibility of asynchronous, digital instruction. One category of digital tools being increasingly used in teaching statistics is interactive graphics.8,9 The ability to adjust inputs and see immediate outputs (i.e., receive real-time feedback) enables fast perception of trends. This ability is especially useful in statistics when potential inputs can often range from single digits to numbers in the millions. Unfortunately, interactive graphics for statistical visualization are rarely applied to epidemiology or biostatistics in a medical school context. Instead, materials relying on problem sets and manual calculations predominate. Wider adoption of interactive graphics as a suitable teaching resource may be hastened by the generation of evidence to indicate that they are non-inferior to current educational methods. In this study, we investigated how supplemental, online interactive webtools affected first-year medical student learning of sensitivity, specificity, negative/positive predictive values, and prevalence – all of which are biostatistical concepts that concern the calculation and interpretation of probability information used in medical decision-making. We hypothesized that interactive online biostatistical webtools if offered as supplemental learning resources would be used by first-year medical students. We expected that the inherent properties of asynchronous, online resources (e.g., time-flexibility, fosters independent learning) would make the resources appealing to students. We also expected that a constructivism-based design would facilitate conceptual understanding of biostatistics content. We did not anticipate any decline in test scores of students using the new biostatistics resources.\n\n\nMethods\n\nAll 94 first-year students in the Frank Netter MD School of Medicine (FHNSOM) Class of 2023 were invited to participate in the study via an in-person announcement (given prior to a mandatory lecture), and then again via institutional email. Both the lecture announcement and email gave a brief overview of the study and indicated where students could find consent forms. If a student completed and submitted a consent form, they were considered enrolled in the study. The number of enrolled participants was 59. The Quinnipiac University IRB deemed data collection and analysis of those who did not enroll in this study, and therefore only interacted with the regular educational instructional strategies and practices for teaching and assessing competence with biostatistics at FNHSOM, to meet the exemption criteria for human subjects research (45 CFR 46.104(d)). These 35 students constituted the control cohort who had no access to the online interactive webtools.\n\nEnrolled students were allocated into Before and After subgroups which determined whether they were able to access the online modules two weeks before or immediately after the regular in-person teaching event on ‘biostatistics used in medical decision-making’ in the Year 1 curriculum. Students at FHNSOM learn biostatistics in small groups of 5-6 students; membership of these small groups is determined through the random enroll feature of the Blackboard® learning management system. Random assignment of Before or After status was made at this small group level for participants in order to ensure that they would mainly interact with others in their in-class biostatistics small group who had the same Before or After access status as themselves. For example, if four members of the six-person small group, “Biostatistics Small Group 1” consented to participate in the study, all 4 were assigned status Before; the remaining two students had no access to the interactive online tools. If three members of the six-person small group, “Biostatistics Small Group 2” consented to participate in the study, all 4 were assigned status After; the remaining three students had no access to the interactive online tools. Thus, three cohorts were constructed: the Before group of students had access to the online interactive webtools two weeks before in-person teaching by FNHSOM faculty occurred (n = 28); the After group of students had access to the online interactive tools immediately after in-person teaching by FNHSOM faculty occurred (n = 31); the No Access control group of students who only received in-person teaching by FNHSOM faculty (n = 35).\n\nFocus groups were comprised of three sets of six students (18 total) who were selected randomly from the pool of study participants. Focus groups were 1 hour in duration and scheduled for the week after the FHSOM biostatistics summative exam so that students could reflect and report on the entire learning period of the study. Focus group questions were centered around student motivation, tool usage, and differences in learning (e.g., “Given that using the biostats webtools was completely optional, what was your motivations to use them if you did or didn’t?”). All sessions were audio-recorded with participants using an assigned letter identifier (e.g., “Participant A”, and transcribed in a de-identified manner (by SH)).\n\nThis study lasted for five weeks from August 15, 2019 – September 19, 2019 and was conducted through a mixed methods approach in order to combine “qualitative and quantitative viewpoints, data collection, analysis, and inference techniques for the purposes of breadth and depth of understanding and corroboration”.10 For the qualitative focus groups, we chose an interpretative phenomenological epistemology to explore participants’ experience and interpretation of using or nor using the online interactive tools.11\n\nThe Before cohort were given access to the online interactive webtools two weeks before regular in-person teaching of ‘biostatistics used in medical decision-making’ at FHNSOM and for two weeks afterwards until the summative exam occurred. The After cohort were given access to the online interactive webtools immediately after regular in-person teaching of ‘biostatistics used in medical decision-making’ at FHNSOM and for two weeks afterwards until the summative exam occurred. The No Access cohort had no access to the online interactive tool at all but did participate in the regular in-person teaching of ‘biostatistics used in medical decision-making’ at FHNSOM and the summative exam.\n\nSoftware\n\nR software is a desktop application freely available from the Comprehensive R Archive Project (CRAN) that is well known and widely used in the statistical community.12 R statistical software was chosen as a platform because of SH’s pre-existing familiarity and its diverse statistical capability, online package availability, and open-source nature.13 A recent addition to its functionality has been the development of “Shiny” software that enables R to export a browser compatible HTML file whose functionality may be used to update the R code. By frequently resampling, the R software becomes “reactive” to its own HTML output, enabling an interactive interface. This means that a server with R software on it can be called to produce a webpage to any computer connected to the internet, and the webpage can be used to interact and manipulate with the server-based statistical coding (Figure 1).\n\nR software was used to code the online tools, which were then uploaded to the ShinyApp cloud service. Any student provided the appropriate link to use with a HTML capable web browser (e.g., Chrome, Firefox, or Safari) could access and interact with the online tools hosted on the ShinyApp cloud servers.\n\nSince its development, ShinyApps have been widely used, and have developed their own server hosting service enabling any member of the public to create an account, write code, and make it available for a large audience.14 Links to the ShinyApp webtool pages were displayed to students via the Quinnipiac University Blackboard® ™ page. Blackboard® ™ is a learning management system that allows online availability of electronic curricula as well as a host of analytic tools to enable tracking of web-link access.\n\nWebpage creation\n\nUsing principles of instructional design and constructivism,15 a minimalist design approach was selected to create the interactive tool webtool pages. They had a simple title followed by simple graphics that displayed the biostatistical equations being explored (e.g., sensitivity) as well as a simple two-by-two table indicating relevant inputs. Graphics were screen captures from the regular FNHSOM biostatistics curriculum to signal continuity and cue students to the familiar content.\n\nThe second element of each webtool page was a set of instructions guiding students through the manipulation of input variables. These instructions directed attention to particular relationships. Questions were designed for students to quickly interact with the biostatistical equations in a way that encourages students to create predictions in a rapid estimate-based style and quickly check their results with the interactive tools for immediate feedback (Figure 2). Questions were written as plain text and placed in code that auto-formats based on the width of the users’ web-browser. An example of such a question is as follows\n\nThe third component of the webtool page was the interactive input bar, reactive two-by-two table, and refreshing calculated output values. Slider controls (Figure 3) were chosen for numerical inputs as they may add to the user’s concept of input magnitude. We created an additional feedback mechanism for the user by adding the movement and visualization of sliding numerical input because numerical literacy in the general population is a long-standing challenge and even those with substantial education experience difficulty interacting with, analyzing, and correctly interpreting straightforward numeracy questions.16,17 All slider inputs go directly into equations for the desired statistical parameter (i.e., a/a+b). Slider range was set to start at 1 to avoid confusing divide by zero situations, and preset to begin at the same value so that test values began at a neutral outcome.\n\nNote: sliders are in their default position.\n\nThe interactive two-by-two table (Figure 4) was created to show user inputs and aide understanding. Additionally, a <color_bar> function was added to represent the magnitude of inputs. Output values were simple reactive outputs <renderText> of inputs within the studied equation, rounded to 2 digits to minimize computational overload.\n\nNote: the table is not showing default values to demonstrate the scaling color bars placed behind each input value.\n\nTo promote learner progress from the ‘Understanding’ to ‘Applying’ and ‘Analyzing’ levels of Bloom’s cognitive taxonomy,18 the next portion of the webtool page was designed to allow translation of theoretical concepts to a scenario likely encountered by a first-year medical student (i.e., a peer-reviewed journal article from the PubMed® database, which contains 32 million searchable citations of biomedical literature).19 To do this, PubMed® was searched and article abstracts retrieved that presented relevant biostats concepts complete with reporting sample numbers and calculated results. These abstracts were presented as “Practice in Context” screen captures (Figure 5) within the webpage so as to be as realistic of an encounter as possible. A short set of questions pertaining to the displayed abstract tested the major concepts explored in the previous portion of the webtool page, with a similar style of estimate-based calculation. Some questions encouraged students to use the slider and reactive outputs as a simple calculator to check their work while tying applied scenarios back to basic concepts. Answers with a brief stepwise explanation were provided below for users to check their work and receive immediate feedback (Figure 6).\n\nNote: the complete screen capture of the abstract as displayed in PubMed®. Directly below the abstract image are the section instructions and a single practice question.\n\nNote: the brief notation showing each of the major steps in the cognitive process of coming to an answer denoted by arrows.\n\nThe quantitative data collected consisted of online interactive webtool access metrics (i.e., the number of distinct visits to the relevant webpage by a participant), summative exam scores, and scores for a self-reported prior knowledge survey. An 11-question survey designed to query student prior knowledge of biostatistics used in medical decision-making was collected via Blackboard® before any in-person teaching or access to the online interactive webtools was granted (a copy is provided as Extended data24). Webtool usage data was collected from Blackboard® through individual link clicks. Additional usage trends were observed from charts of server usage provided to the Shiny App administrator account used to host the online webtools. The summative assessment of students’ biostatistical knowledge occurred at the end of the month-long learning period. This exam consisted of 10 single-best answer multiple-choice questions, which were constructed to assess students’ competence of biostatistics used in medical decision-making, including definitions, calculation, and interpretation.\n\nThe quantitative data was imported to s for analysis and descriptive statistics (e.g., mean, standard deviation) calculated. A two-sample independent Student’s t-test was used to compare the access metrics between the Before and After cohorts. One-Way ANOVA with Tukey’s HSD post hoc test was used to make pairwise comparisons of summative exam performance and prior knowledge scores between the three Before, After, and No Access cohorts. Analyses were conducted in SPSS v26 (IBM SPSS Statistics, Armonk, NY, USA) and the alpha level for statistical significance was set at 0.05.\n\nSH facilitated the focus group sessions. De-identified audio recordings were transcribed manually then analyzed using an inductive, constant comparison approach.20 Major concepts were organized iteratively and stated as themes.\n\nThis study was conducted according to the guidelines of the Declaration of Helsinki and approved by the Human Experimentation Committee/Institutional Review Board of Quinnipiac University (#08919; 22 August 2019). Written informed consent to participate was obtained from the participants, including consent to publish audio recordings of the focus groups.\n\n\nResults\n\nPrior knowledge survey\n\nThe mean (± standard deviation) prior knowledge survey scores out of 110 points for the Before, After, and No Access cohorts were 53.8 (± 20.9), 53.6 (± 23.3), and 51.7 (± 22.1) points respectively (Figure 7). These scores were not significantly different from one another (p = 0.91; One-Way ANOVA) indicating that none of the three cohorts were different at the onset of the study. The range of the prior knowledge scores was 1 – 84 points. The median value was 55.5 points.\n\nThese scores were not significantly different from one another (p = 0.91; One-Way ANOVA).\n\nSummative exam scores\n\nThe mean (± standard deviation) summative exam scores as percentages for the Before, After, and No Access cohorts were 87.5% (± 10.8%), 90.7% (± 11.2%), and 88.9% (± 12.9%) respectively (Figure 8). These scores were not significantly different from one another (p = 0.49; One-Way ANOVA) indicating that none of the three cohorts were different at the onset of the study.\n\nThese scores were not significantly different from one another (p = 0.49; One-Way ANOVA).\n\nAccess metrics\n\nThe mean (± standard deviation) number of distinct visits per participant over the 5-week study period for the Before and After cohorts were 4.3 (± 2.6) and 2.6 (± 1.5) visits respectively (Figure 9). These scores were significantly different from one another (p = 0.003; independent t-test) indicating that the Before group chose to engage with the online interactive webtools more often than the After group. The range of the number of distinct visits per participant was 0 – 10 visits for the Before group, and 0 – 6 visits for the After group.\n\nThese scores were significantly different from one another (p = 0.003; independent t-test).\n\nServer usage data available to the Shiny App administrator account showed a bimodal distribution over time, with the majority of student using the apps around the time during which the regular in-person ‘biostatistics used in medical decision-making’ was taught to the Class of 2023 (Figures 10 and 11). There was also a large spike in activity during the few days before the summative exam. These major groups of activity were separated by approximately a week during which there was zero activity.\n\n\nQualitative data\n\nFocus group discussion\n\nComparatively, about 75% of the focus group participants stated that they had opened the links provided to the online interactive webtools. In total, 50% said they used at least some portion of the webtools, while 25% reported engaging with and completing all interactive components of the webtools multiple times. A majority of students reported using the webtools for only one specific component. Some stated that they found the interactive calculators and tutorial most useful, while others found the practice-in-context element most useful. It was not uncommon for students to only use one and not the other.\n\nTwo themes from the focus group discussion emerged: facilitation of learning and time efficiency. Illustrative quotes are identified by the anonymous letter identifies assigned to each participant.\n\nTheme 1 - Facilitation of learning\n\nThere was substantial agreement among the participants that the webtools enabled them to take more control of their learning processes to improve their comprehension and application of the biostatistical content.\n\nA: “Once I hit a spot where I pause and I don’t understand, that’s when I used them [the webtools] for something extra to supplement my studying, something extra to help me understand.”\n\nH: “I used the [webtools] as a way of tuning up for the exam. I wanted to make sure I was a bit more concrete and so it was nice to have something to walk through and play around with and get an actual feel for what that stuff looked like.”\n\nC: “I was looking at the [regular curriculum teaching] slides and felt that they were a lot of definition and not numbers, so I used your [webtools] to play around with numbers and get an understanding of how sensitivity works.”\n\nE: “I kinda struggled to understand some of the concepts or what we wanted to know about each concept from the [regular curriculum teaching] videos, so I used [the webtools] to play around and see how it would change without having to do each individual calculation.”\n\nH: “What I thought was nice about the [webtools] is that you were able to … um … directly change the numbers and see what effect that that had on the calculations without actually having to do all the calculations. So it saved a lot of leg work but you still got the big picture idea. Even though working out methodically can be helpful, it was nice to just see the trends.”\n\nF: “I think I kinda use [the webtools] in conjunction with the [regular curriculum teaching] that we had and there are some examples with real studies and I kinda used that with the [the webtools] like “oh what would happen if I increased the number of people in this.”\n\nTheme 2 - Time efficiency\n\nThere was also substantial consensus that the webtools helped the time investment needed to learn or set an appropriate learning pace.\n\nD: “I like that I could have more control … like for me, the slow parts of traditional lectures are too slow for me, and the fast parts are too fast. [With the webtools] I have the ability to control the pace at which I go … allows me to be more effective and efficient.”\n\nA: “I think that I would have been able to get to apply [my knowledge of the biostatistics] by spending a longer time with the lectures and rereading them, but I think that the [webtools] helped me get there faster than I would have. It was more efficient for me.”\n\nD: “I would agree … that it kind of sped up the getting to applying and being able to broadly conceptualize it.”\n\nD: “I would say that playing with the [webtools] did help me to get to apply faster.”\n\nF: “I definitely would be more confident … just because I didn’t really understand the concepts behind the equations until I use [the webtools] so now I feel like I could explain this to my family if they were gonna get a test done that had those parameters.”\n\n\nDiscussion\n\nThis pragmatic trial study was designed to explore the use of interactive web-based resources to alleviate some of the challenges associated with teaching first-year medical students biostatistics such as a lack of time, motivation, and cognitive scaffolding. To accomplish this goal, constructivism was used as a conceptual framework to design interactive the webtools. Constructivism is a theory of learning that says, “people construct their own understanding and knowledge of the world, through experiencing things and reflecting on those experiences”.15 Put succinctly, it posits that learning is an active process whereby knowledge is constructed through appropriately contextualized experiences rather than mere transmission of information from teachers to learners. The webtools sought to have learners 1) build conceptual representations by connecting new information to existing knowledge, 2) interact with primary sources of biostatistical data, and 3) begin with whole concepts then explore component parts.21,22 The webtools were provided to the students for use alongside the regular biostatistics teaching curriculum at FHNSOM in two temporally spaced groups. Access metrics, summative exam scores, and qualitative focus group data was collected and analyzed. Our findings support our initial hypotheses that medical student users would interact with the webtools and deem them useful, that the constructivism-informed design would facilitate the conceptual understanding of learners, and that there would be no detrimental impact of using the webtools on biostatistical exam scores.\n\nThere was no significant difference in summative exam scores or self-reported prior knowledge between the three study cohorts. These data, along with the interest expressed by the focus group participants and the repeated access metrics, indicate that this new resource could be added alongside existing biostatistics curricula without detrimental effects to learning. Results of access metrics data showed an elevated level of participation from those who chose to access the webtools with an average of 5 clicks per student. This indicated that many students found the webtool content valuable enough to return to after an initial experience. Furthermore, a temporal view of server data showed a significant spike of usage prior to the summative exam date suggesting that students returned to the webtools as a study resource during a high-pressure time period. Additional server data indicated that most webtool interactions were sessions less than 30 minutes in duration, suggesting that students were able to quickly visit the webtools to get what they needed rather than using them for long, unbroken sessions. This may be especially valuable to medical school students who are routinely trying to determine and make choices around what they will focus on learning in a time-scarce environment.\n\nFocus group discussion indicated a positive response to the constructivist design choices with students reporting that they allowed efficient use and increased students ability to experiment. Similarly, students endorsed the webtools’ part in allowing them to explain statistical concepts to others (e.g., friends or family members). Interestingly, one focus group argued against the constructivist design reporting that a more directed process would have been appreciated. This may reflect some learners’ preferences for passive versus active learning.23 The multi-component design and its associated flexibility of the online webtools was prominent in focus group discussion; a large portion of students revealed that they only used select portions of each webtool depending on their perceived personal learning deficits. Students often used the webtools as a way to test the knowledge and comprehension they had built and validate their conceptual understandings; our participants valued a setting where they may quickly experiment with concepts and receive immediate feedback – which is consistent with constructivism.\n\nWhile we cannot claim that students had any increased learning motivation, it should be noted that once the webtools were created and made available to the Before and After cohorts, there was no additional reminder or external pressure to use them. No instructor time was required for their use; therefore, they may be cost effective resources regardless of how many students are motivated to use them. There was consensus in focus groups that given the low resources necessary to keep the webtools running they should be made available to future students to broaden their learning options.\n\nAccess data indicated that students mostly used the webtools during the weeks concurrent with the regular in-class curriculum at FHNSOM. This suggests that students may have desired additional or different types of resources during their active knowledge construction processes. This bore out in focus group discussions when participants mentioned regularly looking for a multitude of resources to be used at their discretion during periods of intensive academic focus.\n\nIn focus groups, some Before cohort students mentioned accessing the webtools to “pre-study” the material. They generally reported finding the webtools alone without introduction or explanation (provided by the regular biostatistics curriculum) confusing and counterproductive. Further, students who found the modules confusing reported abandoning them altogether or stopped using the webtools until a later date.\n\nThe limitations of this study include that it was conducted once with a small sample of learners at a single institution.\n\n\nConclusion\n\nMost curricula for biostatistics follow some variation of the following steps: 1) knowledge acquisition via text or lecture format, 2) knowledge application via problem sets or other use-case based tasks, and 3) testing to assess learner competency. This sequence moves students along Bloom’s cognitive taxonomy from remembering > understanding > application > analysis.18 Due to the constraints of synchronous teaching modalities like timing of lectures or physical presence in student discussion groups, traditional methods offer limited opportunities for the learner to move up and down Bloom’s taxonomy as they might see fit and at their own pace. Through the use of R software and Shiny we created webtools for producing interactive, web-ready data visualizations and practicing learning in context. These resources were valued by learners for facilitating student-paced learning in a time efficient manner and may represent a pragmatic approach to supplementing existing medical school teaching strategies for biostatistics and learners’ abilities to curate their own learning experience.\n\n\nData availability\n\nZenodo: A Pragmatic Trial of Interactive Online Statistical Webtools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach. https://doi.org/10.5281/zenodo.5092290.24\n\nThis project contains the following underlying data:\n\n• Steven Hardy F1000 Data (Quantitative data).xlsx (access metrics, summative exam scores, prior knowledge survey scores).\n\n• Focus Group 1 09-30 Participants A-E.m4a (focus group 1 audio recording).\n\n• Focus Group 2 09-30 Participants F-H.m4a (focus group 2 audio recording).\n\n• Focus Group 3 10-01 Participants I-N.m4a (focus group 3 audio recording).\n\n• Focus Group 4 10-02 Participants O-R.m4a (focus group 4 audio recording).\n\n• Focus Group 1 participants A-E.docx (focus group 1 transcript).\n\n• Focus Group 2 F-H.docx (focus group 2 transcript).\n\n• Focus Group 3 I-N.docx (focus group 3 transcript).\n\n• Focus Group 4 O-R.docx (focus group 4 transcript).\n\nZenodo: A Pragmatic Trial of Interactive Online Statistical Webtools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach. https://doi.org/10.5281/zenodo.5092290.24\n\nThis project contains the following extended data:\n\n• Prior Knowledge of Biostatistics Used in Medical Decision.docx (a blank copy of the self-reported ‘prior knowledge of biostatistics used in medical decision-making’ survey)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nWartman SA: The Empirical Challenge of 21st-Century Medical Education. Acad Med. 2019; 94: 1412–1415. PubMed Abstract | Publisher Full Text\n\nRosenberg W, Donald A: Evidence based medicine: An Approach to clinical problem-solving. BMJ. 1995; 310: 1122. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMasic I, Miokovic M, Muhamedagic B: Evidence Based Medicine - New Approaches and Challenges. Acta Inform Med. 2008; 16: 219. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGigerenzer G, Gray JAM, John AM, et al.: Better Doctors, Better Patients, Better Decisions: Envisioning Health Care. The MIT Press; 2011.\n\nWegwarth O: Statistical illiteracy in residents: what they do not learn today will hurt their patients tomorrow. J Grad Med Educ. 2013; 5: 340–341. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAstin J, Jenkins T, Moore L: Medical students’ perspective on the teaching of medical statistics in the undergraduate medical curriculum. Stat Med. 2002; 21(7): 1003–1006; discussion 1007. PubMed Abstract | Publisher Full Text\n\nFielding S, Poobalan A, Prescott G, et al.: Views of medical students: what, when and how do they want statistics taught? Scott Med J. 2015; 60(4): 164–169. Publisher Full Text\n\nSeeing Theory: a visual introduction to probability and statistics. Accessed March 17, 2019. Reference Source\n\nArtofStat: Web Apps. Accessed July 26, 2021. Reference Source\n\nJohnson BR, Onwuegbuzie AJ, Turner LA: Toward a definition of mixed methods research. J Mixed Methods Res. 2007; 1: 112–133. Publisher Full Text\n\nNeubauer BE, Witkop CT, Varpio L: How phenomenology can help us learn from the experiences of others. Perspect Med Educ. 2019; 8: 90–97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCRAN: The Comprehensive R Archive Network. Accessed July 26, 2021. Reference Source\n\nR: The R Project for Statistical Computing. Accessed July 26, 2021. Reference Source\n\nShinyapps.io. Accessed July 26, 2021. Reference Source\n\nErtmer PA, Newby TJ: Behaviorism, cognitivism, constructivism: Comparing critical features from an instructional design perspective. Performance Improvement Quarterly. 1993; 6: 50–72. Publisher Full Text\n\nPaulos JA: Innumeracy: Mathematical Illiteracy and Its Consequences. New York, NY, USA: HOLT MCDOUGAL; 2001.\n\nLipkus IM, Samsa G, Rimer BK: General performance on a numeracy scale among highly ducated samples. Med Decis Making. 2001; 2: 37–44. PubMed Abstract | Publisher Full Text\n\nAnderson LW, Krathwohl DR, Airasian PW, et al.: A taxonomy for learning, teaching, and assessing: a revision of Bloom's taxonomy of educational objectives. New York, NY, USA: Pearson; 2000.\n\nPubMed®: Accessed July 26, 2021. Reference Source\n\nButler-Kisber L: Constant comparison inquiry. In: Qualitative Inquiry. ; Butler-Kisber L, Ed.; London, UK: SAGE Publications Ltd; 2018; pp. 41–59.\n\nColburn A: Constructivism: Science Education’s “Grand Unifying Theory.”. The Clearing House: A Journal of Educational Strategies, Issues and Ideas. 2000; 74: 9–12. Publisher Full Text\n\nFosnot CT: Constructivism: Theory, Perspectives, and Practice. New York, NY, USA: Teachers College Press; 2013.\n\nEva KW, Regehr G: “I’ll never play professional football” and other fallacies of self-assessment. J Continuing Education Health Professions. 2008; 28: 14–19. Publisher Full Text\n\nHardy S, McHugh D: A Pragmatic Trial of Interactive Online Statistical Webtools for Teaching Biostatistics to First Year Medical Students: A Constructivism-Informed Approach [Data set]. Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "123182",
"date": "22 Feb 2022",
"name": "Craig S Webster",
"expertise": [
"Reviewer Expertise I am a psychologist with 25 years experience in human factors redesign and clinical 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\nThis is a well-written report of a trial of interactive webtools for statistics teaching. The authors report largely nonsignificant findings from their quantitative measures, but demonstrating significant improvements in education research is notoriously difficult, especially in relatively small n studies. Despite this, attempting to make this kind of teaching material accessible and interesting to students is a challenge that many educators face, and so I think this paper will be of interest to many. Specific comments follow.\nPage 2, line 1: “student” should be “students”?\n\nPage 8, line 17: “Major concepts were organized iteratively and stated as themes” – this is an inadequately brief description of your qualitative analysis. Inductive thematic analysis usually starts with the assignment of codes, which are subsequently organised by similarity into themes. A constant comparison approach on the other hand is more often associated with grounded theory rather than thematic analysis, and so this section sounds a little confused – please clarify what you actually did.\n\nPage 11, Qualitative data: Typically, the reporting of qualitative analysis begins with a statement of the median (range) length of the focus groups or interviews in minutes (or an estimate), then the median (range) number of words per transcript. This is the volume of text that undergoes analysis – but you make no mention of this in your paper. Also, why are all your exemplar quotations in red?\n\nPage 13: Are you making the audio recordings of your focus groups available as an additional data resource? This seems inadvisable in terms of the potential ability to identify the participants by recognizing their voices. It also seems unnecessary if you are also making the transcripts available.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "129256",
"date": "29 Apr 2022",
"name": "Tonya Esterhuizen",
"expertise": [
"Reviewer Expertise Biostatistics",
"epidemiology",
"teaching medical statistics at undergraduate and postgraduate level",
"curriculum 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\nThis article addresses an important topic in medical student education, that of enabling the medical student to interpret and critique the literature where biostatistical methods are used. This study uses an innovative intervention of a webtool created in an open-source platform that appears to be user-friendly and interactive. A mixed-methods approach was used to evaluate the effect of this intervention in three cohorts: those who had access to the intervention prior to the lectures and also before the summative exam; those who had access to the intervention immediately post the lectures and also prior to the summative exam; and those who chose not to enroll in the study and used as a control group with no access to the intervention.\n\nIn terms of the study design, it appears to be a quasi-randomized design since the control group was not randomly assigned even though the two intervention groups were. This could have led to a selection bias since those who opted out of the study might have been different in terms of their confidence in the topic and prior knowledge of the subject matter. However, the self-reported prior knowledge test scores were similar between the three groups, indicating that at least by self-report they were equivalent.\n\nThe randomization of the two intervention groups was done at the small group level. This is cluster randomisation and thus the data should have been analysed with this clustering in mind. Additionally, there might have been some \"contamination\" between members of a group who were in the \"no access\" group with members who were in one of the intervention groups. This should be reported as a limitation of this study.\n\nThe summative assessment questions should have also been included in the extended data provided. It appears to have been at a level that was perhaps not challenging enough since most students scored very well in the summative assessment. This might be the reason that no difference was found between the three groups. The authors' indication of the level of the summative assessment in testing the required knowledge would be helpful. There is an error in the results section in the sentence: \"These scores were not significantly different from one another (p = 0.49; One-Way ANOVA) indicating that none of the three cohorts were different at the onset of the study. \" This sentence refers to the summative exam scores, therefore this indicates that the cohorts were not different from each other at the end of the study, not at the onset 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? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-811
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https://f1000research.com/articles/10-809/v1
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16 Aug 21
|
{
"type": "Method Article",
"title": "Pulsed administration for physiological estrogen replacement in mice",
"authors": [
"Carmen Corciulo",
"Julia M. Scheffler",
"Karin L. Gustafsson",
"Christina Drevinge",
"Piotr Humeniuk",
"Alicia M. del Carpio Pons",
"Matti Poutanen",
"Claes Ohlsson",
"Marie K. Lagerquist",
"Ulrika Islander",
"Julia M. Scheffler",
"Karin L. Gustafsson",
"Christina Drevinge",
"Piotr Humeniuk",
"Alicia M. del Carpio Pons",
"Matti Poutanen",
"Claes Ohlsson",
"Marie K. Lagerquist",
"Ulrika Islander"
],
"abstract": "Estrogens are important regulators of body physiology and have major effects on metabolism, bone, the immune- and central nervous systems. The specific mechanisms underlying the effects of estrogens on various cells, tissues and organs are unclear and mouse models constitute a powerful experimental tool to define the physiological and pathological properties of estrogens. Menopause can be mimicked in animal models by surgical removal of the ovaries and replacement therapy with 17β-estradiol in ovariectomized (OVX) mice is a common technique used to determine specific effects of the hormone. However, these studies are complicated by the non-monotonic dose-response of estradiol, when given as therapy. Increased knowledge of how to distribute estradiol in terms of solvent, dose, and administration frequency, is required in order to accurately mimic physiological conditions in studies where estradiol treatment is performed. In this study, mice were OVX and treated with physiological doses of 17β-estradiol-3-benzoate (E2) dissolved in miglyol or PBS. Subcutaneous injections were performed every 4 days to resemble the estrus cycle in mice. Results show that OVX induces an osteoporotic phenotype, fat accumulation and impairment of the locomotor ability, as expected. Pulsed administration of physiological doses of E2 dissolved in miglyol rescues the phenotypes induced by OVX. However, when E2 is dissolved in PBS the effects are less pronounced, possibly due to rapid wash out of the steroid.",
"keywords": [
"Estrogens",
"sex steroids",
"therapy",
"ovariectomy",
"osteoporosis"
],
"content": "Introduction\n\nSteroid hormones control the physiology of the whole body. Alterations of this well-balanced system can lead to organ dysfunction, representing a risk factor for many human diseases1. Women are more subjected to changes in sex-hormone concentrations compared to men due to the menstrual cycle and they also go through menopause, which is defined by lack of the menstrual cycle for more than 12 consecutive months. This phase of women's lives is characterized by reproductive senescence and a decrease of sex-hormone production2. Many medical conditions are associated with menopause, including cardiovascular diseases (affecting 75% of postmenopausal women)3, hot flushes (85%)4, vaginal dryness and genitourinary syndrome (75%)5–8, bone loss and consequent osteoporosis (30%)9,10, emotional symptoms leading to sleep disturbance (50%)11, irritability (42%) and depressive mood (29%)12,13. The association between menopause and these conditions emphasizes the importance of female sex-hormones (estrogens among them) in maintaining women's health. Thus, much research worldwide is focused on determining the effects of estrogens on e.g., bone turnover, behavior and pain sensitivity, cardiac alterations, and influence on the immune system.\n\nEstrogens are expressed in all vertebrate species, as well as in some of the invertebrates. They are produced by the ovaries and are considered the primary female sex hormones14. Natural estrogens comprise a class of compounds including estrone, estradiol (17α-estradiol and 17β-estradiol), and estriol. 17β-estradiol is the most abundant and biologically active form of estrogen produced in non-pregnant premenopausal women15.\n\nAnimal models that mimic human reproductive senescence, including mouse models, are powerful scientific tools to study mechanisms mediated by estrogens-, to discover new and safer hormone-based drugs, and to predict the outcome of therapeutic treatments. Various approaches for estrogen replacement therapy in mice have been described in the literature, all displaying different strengths and weaknesses. In addition, various doses and patterns of administration have been used with distinctive outcomes16–18. The design of an experiment that includes treatment with estrogens is complicated by the difficulty to predict the effect of the hormones at higher doses based on data at lower doses. Indeed, estrogens have different affinity for the estrogen receptors, ERα and ERβ, and the expression and function of the receptors are regulated depending on the dose of the ligand. This mechanism of mutual regulation results, in some tissues, in a non-monotonic dose-response, meaning that increasing doses of hormones generates dissimilar or opposite effects compared with lower doses, giving a U-shaped dose-response curve19.\n\nThe most common methods for estradiol delivery in mice are subcutaneous implants of estradiol pellets or silastic tubes filled with estradiol powder. Neither of these procedures guarantee the release of a controlled amount of estradiol, as a high amount of hormone is delivered during the days directly after the implant, and this peak is subsequently followed by a drastic reduction17,20. Chow supplemented with estrogens has been largely described as a convenient method of administration with low stress for the animals but with uncertainty in the dose delivered18. Implants of an osmotic mini-pump would overcome this problem since the pores in the filters regulate the amount of solution released. Nevertheless, the size of the osmotic pump and consequently the volume of the solution loaded is limited by the small size of the animals. Moreover, the surgical removal of the pump is needed after 4 weeks, making this delivery method un-suitable for longer experiments. Most importantly, for all these techniques, the constant hormone release does not mirror the normal cyclic fluctuations of estradiol in females.\n\nAnother usual method for estradiol delivery to mice is repeated injections. For this technique, the vehicle used to dissolve estradiol needs to be considered. In common practice, estradiol is dissolved in an oil-based vehicle and injected subcutaneously. The oil is slowly absorbed, creating pockets of oil that persist for many days. In this method of administration, it is likely that the injected hormone is not completely absorbed at the time of the next injection, leading to estradiol accumulation and uneven release over time.\n\nThe present study aimed to determine whether pulsed subcutaneous injections with 17β-estradiol-3-benzoate (E2) every 4 days in healthy ovariectomized (OVX) mice can be used to better mimic the physiological dose of endogenously produced E2. Two different preparations of E2 were tested, either suspended in miglyol or in phosphate buffer saline (PBS), in order to determine the optimal solvent for injections of E2. We report the effects of pulsed E2 administration in OVX mice on sex steroid concentration in serum, soft tissues, bone, and motor ability of the mice.\n\n\nMethods\n\nC57BL/6J mice (Taconic, Denmark) were kept in the animal facility at the University of Gothenburg (Sweden) under regular lighting conditions (12 h light/dark cycles), fed with soya-free laboratory chow and tap water ad libitum. Mice were acclimatized for 7 days before initiating the surgical procedures. The experiments were carried out as described in Figure 1. All the experimental procedures were performed in accordance with the ethical permit approved by the Regional Ethical Review Board in Gothenburg, Sweden (Dnr: 2814/2020), which included also the criteria for the earlier termination of the experiment (weight loss and signs of pain and distress), and according to the Institutional Animal Care and Usage Committee (ARRIVE guidelines21). The sample size (n=3group) was decided to minimize the number of animals and allow the statistical analysis. Animals were randomly allocated in the different experimental groups and randomly sacrificed to minimize potential confounders.\n\nThis figure describes the timeline of the experiments and the experimental groups included in the study.\n\nIn this study, 96 female mice, 8 weeks old, were employed and underwent OVX or sham surgery. Mice were anesthetized by a mix of isoflurane and oxygen (1.5-2.5 %). A 10 mm incision was made through the shaved and disinfected skin at the lower back area. Then, a 5 mm incision was done in the peritoneum on one side to carefully pull out the ovarian fat pad and excise the ovary by cauterization. The incision in the peritoneum was closed using absorbable sutures. The procedure was repeated on the other side with the second ovary. The external wound on the skin was closed by surgical clips. In mice undergoing sham surgery, the same procedure was performed, but without excising the ovaries. Meloxicam (5mg/kg) was used as a postoperative analgesic.\n\nThe oil-based stock solution of E2 (17β-estradiol-3-benzoate, SIGMA Aldrich) (1mg/ml) was prepared by mixing E2 with inert miglyol oil (Miglyol812 OmyaPeralta GmbH, Hamburg, Germany). E2 was dissolved by stirring the solution for 3 hours at 150°C and then further diluted with miglyol to 0.5 µg/ml and 1.5 µg/ml concentrations.\n\nFor the PBS-based formulation, a stock solution (1mg/ml) of E2 dissolved in absolute ethanol was prepared and stored at -20°C. At the time of injections, the stock solution was diluted in PBS to 0.5 µg/ml and 1.5 µg/ml final concentrations.\n\nMice were allowed to recover from the OVX procedure for 10 days before the initiation of treatments. Sham and OVX mice were divided into different treatment groups receiving subcutaneous (s.c.) injections (100 µl) every four days of E2 (0.05 μg or 0.15 μg/mouse/injection) dissolved in miglyol or PBS, or vehicle (miglyol or PBS). Mice were sacrificed at 2, 4, 6 or 8 weeks after the start of treatments.\n\nThroughout the experiment, all the efforts were made to minimize the pain and distress of the experimental animals. For this purpose, mice were anesthetized with a mixture of ketamine / dexmedetomidine hydrochloride before the procedure. Their body composition was determined using dual-energy x-ray absorptiometry (DXA) scan (UltraFocusDXA, Faxitron Bioptics, Tuscon, AZ). Anesthetized mice were euthanized by exsanguination followed by cervical dislocation. Blood samples were collected for serum isolation. Uterus, thymus, spleen, and liver were dissected, and weights were noted. Femurs were collected for micro-computed tomography (µCT) analysis.\n\nAfter sacrifice, the left hindleg was excised and the femur dissected. The soft tissue was carefully removed from the bone. Samples were fixed in PFA 4% for 3 days and then stored in 70% ethanol. The area for the trabecular bone evaluation was selected starting at 500 µm from the growth plate and extending a further longitudinal distance of 192 µm in the proximal direction. Cortical measurements were performed in the diaphyseal region of the femur starting at 5195 µm from the growth plate and extending a further longitudinal distance of 192 μm in the proximal direction. The selected area was evaluated in a scanning tube providing a voxel size of 4.49 µm isotropically and scanned at 50 kV, 200 µA (Skyscan 1172 scanner; Bruker MicroCT, Aartselaar, Belgium). Samples were kept in paper soaked in PBS to avoid dehydration. Analysis of the morphology and measurement of bone features by μCT was performed using the software CtAN (1.13.2.1, Bruker microCT, RRID: SCR_021338).\n\nTo assess the effect of E2 replacement on locomotor ability, two motor tests were performed 2 days before termination of the 8 weeks of treatment experiment. Mice were acclimatized in the procedure room for 1 hour before the start of the tests.\n\nSpontaneous locomotor activity was analyzed using the open-field test. Each mouse was placed into the center of a 60 × 60 × 60 cm chamber to allow free exploration. The experiments were performed for 15 min. The motor parameters were measured by computerized analysis at 3 min intervals. Mice behavior was recorded, and videos were analyzed by using Viewer software (RRID:SCR_014337; Biobserve, Germany).\n\nForced locomotor activity was tested by using the rotarod test. Mice were placed on a rotarod apparatus (Panlab, Harvard Apparatus, Spain) and tested for 5 min with constantly increasing acceleration from 4 to 40 r.p.m. The latency to fall was registered for each animal. To exclude differences in learning skills between the groups of mice, each group was assessed over three trials per day for 2 consecutive days. Mice were given a 30 min inter-trial rest interval.\n\nPeripheral blood from all mice was collected at termination in 500 µl tubes containing serum gel with clotting activator (Microvette 500 Z-Gel, Sarstedt). The serum was extracted and stored at -80° C until use. Steroids were extracted from serum (200 µl) and concentrations of estradiol, estrone, progesterone, 17β-hydroxiprogesterone, testosterone, dihydrotestosterone (DHT) and androstenedione were analyzed by Liquid Chromatography-Mass Spectrometry (See underlying data,22).\n\nData on levels of sex steroids in serum are expressed as median (range) with non-detectable values represented as half of the lowest level of quantification (LLOQ). Statistical analysis was not performed on serum steroid levels due to the presence of values under the detection limit for some hormones, in combination with the low number of samples per experimental group. For all other data Gaussian distribution was assumed and results are expressed as mean ± SEMGraphPad Prism software (RRID:SCR_002798; GraphPad, San Diego, CA). No animals were excluded from the data analysis. Among the authors of the manuscript, CC was aware of the group allocation at the different stages of the experiment.\n\n\nResults\n\nMice were subjected to sham or OVX surgery and treated with s.c. injections every 4 days with vehicle (miglyol or PBS) or two different doses of E2 in the corresponding vehicle (Figure 1). The concentrations of estradiol, estrone, progesterone, 17α-hydroxiprogesterone, testosterone, dihydrotestosterone (DHT), and androstenedione were measured in serum from mice terminated at 8 weeks after start of the treatments.\n\nEstradiol and estrone. After 8 weeks of treatment, a reduced concentration of estradiol was shown in the miglyol OVX+veh group compared with miglyol sham+veh mice, and both doses of E2 dissolved in miglyol increased the serum level of estradiol compared to OVX+veh. However, in mice receiving the PBS formulation no differences between OVX+veh and any of the other groups could be detected. A comparison between the miglyol sham+veh and PBS sham+veh groups showed that the PBS treated sham group had a tendency towards lower serum concentration of estradiol (Figure 2A).\n\nThe amount of estradiol (A) and estrone (B) was measured in Sham and OVX mice after 8 weeks of s.c. injections every 4 days with vehicle (miglyol or PBS) or 17 β-estradiol (E2; 0.05 µg/mouse or 0.15 µg/mouse). Data are expressed as median (range); n=3 for each experimental group. (nd = not detectable; LLOQ=lower level of quantification).\n\nThe fluctuations of estrone levels in the miglyol preparation groups, showed a similar pattern to that described for estradiol. Estrone levels were generally low, and under the detection limit in the miglyol OVX+veh group. Treatment with both doses of E2 dissolved in miglyol increased the amount of serum estrone compared to OVX mice. However, animals injected with the PBS preparation of E2 displayed estrone values below the detection limit (Figure 2B).\n\nProgesterone and 17β-hydroxiprogesterone. As expected, OVX induced a reduction in serum progesterone levels. Treatments with E2, dissolved in miglyol or PBS, did not affect the serum concentrations of progesterone (Figure 3A).\n\nThe amount of progesterone (A) and 17α-hydroxyprogesterone (B) was measured in Sham and OVX mice after 8 weeks of s.c. injections every 4 days with vehicle (miglyol or PBS) or 17 β-estradiol (E2; 0.05 µg/mouse or 0.15μg/mouse). Data are expressed as median (range); n=3 for each experimental group. (LLOQ = lower level of quantification).\n\nSerum levels of 17β-hydroxiprogesterone were unaltered between the groups after 8 weeks of treatment (Figure 3B).\n\nTestosterone, dihydrotestosterone (DHT) and androstenedione. The levels of testosterone tended to decrease in OVX+veh groups for both formulations compared to the sham+veh groups in mice terminated after 8 weeks. Testosterone concentrations were not altered by E2 replacement, in neither the miglyol nor the PBS preparation groups (Figure 4A).\n\nThe amount of testosterone (A), dihydrotestosterone (DHT; B) and androstenedione (C) was measured in Sham and OVX mice after 8 weeks of s.c. injections every 4 days with vehicle (miglyol or PBS) or 17 β-estradiol (E2; 0.05 µg/mouse or 0.15 µg/mouse). Data are expressed as median (range); n=3 for each experimental group. (nd = not detectable; LLOQ=lower level of quantification).\n\nSerum levels of DHT were reduced after OVX in both miglyol and PBS preparations. Treatment with E2 dissolved in miglyol resulted in DHT levels under the detection limit after 8 weeks, while E2 dissolved in PBS partially restored the serum levels of DHT (Figure 4B).\n\nThe serum levels of androstenedione in the different groups resembled those for DHT (Figure 4C). Androstenedione was reduced in the OVX groups after 8 weeks of treatment compared to the sham mice, with values under the detection limit in the miglyol OVX+veh and OVX+E2 groups.\n\nThe body weight and the weight of perigonadal fat, uterus, thymus, liver, and spleen were measured at the time of each termination (Figure 5; extended data figure. 121). The miglyol sham+veh mice had constant body weight for the whole duration of the experiment. However, the miglyol OVX+veh group showed a significant increase in body weight compared to the sham+veh group after 8 weeks of treatment, which was efficiently prevented by treatment with both doses of E2 dissolved in miglyol (Figure 5A). On the contrary, the PBS OVX+veh group did not differ in body weight from PBS sham+veh mice at any time-point. Treatment with E2 in PBS resulted in a gradual increase of the body weight compared to body weights of the PBS OVX+E2 groups measured after 2 weeks of treatment and reached a significant increase at 6 and 8 weeks of treatment for the low and high dose of E2, respectively (Figure 5A).\n\nMice were subjected to Sham or OVX surgery and treated with s.c. injections of vehicle (miglyol or PBS) or 17β-estradiol (E2; 0.05µg/mouse or 0.15µg/mouse) every 4 days. Experiments were terminated at 2, 4, 6 and 8 weeks after the start of treatments. Body weight (A), perigonadal fat (B) and uterus (C) weights were determined at sacrifice. Data are expressed as mean±SEM; n=3 for each experimental group. * statistical differences between sham+veh vs OVX+veh; or OVX+veh vs the E2 treatment groups; # statistical difference vs week 2 of the same treatment group. *or #, p<0.05; **or ##, p<0.01; ***or ###, p<0.001; ***** or ####, p<0.0001; Two-way ANOVA followed by Dunnet’s post-hoc test).\n\nConsistent with the results of body weights, the perigonadal fat in the miglyol OVX+veh group increased significantly at 6 and 8 weeks of treatment compared to the miglyol sham+veh group (Figure 5B). Furthermore, miglyol E2 treatment of OVX mice prevented perigonadal fat accumulation. At 6 weeks of treatment, the PBS OVX+veh group had significantly increased perigonadal fat weight compared to the PBS sham+veh group. Consistent with the results of body weights there was a gradual increase in perigonodal fat in mice treated with both doses of PBS E2. After 8 weeks of treatment, the perigonadal fat of the PBS OVX+E2 0.05µg group was also significantly higher compared to the PBS OVX+veh mice (Figure 5B).\n\nAs expected, the uterus weight was substantially lower in the OVX+veh mice compared to sham+veh mice in both miglyol and PBS groups (Figure 5C). An increase of the uterus weight was induced in the miglyol OVX+E2 0.15 µg group, starting at 2 weeks of the treatment. At the termination after 8 weeks of treatment, no differences between the miglyol OVX+E2 groups compared to the OVX+veh group were detected due to the unexpectedly increased uterus weight in miglyol OVX+veh mice (Figure 5C, left). On the contrary, injections of E2 dissolved in PBS did not increase the uterus weight when compared to the PBS OVX+veh mice (Figure 5C, right).\n\nAfter 2 weeks of treatment, the PBS OVX+veh group had increased thymus weight compared to the PBS sham+veh mice, however the differences were equalized during the later time points. No major differences between the groups were detected for liver and spleen weights in either miglyol or PBS preparations (Extended data, figure. 1A–C,21).\n\nBefore each sacrifice, the whole-body bone, fat and lean mass composition were measured using DXA scan (Figure 6A) (Underlying data22). The percentage of fat in miglyol OVX+veh mice increased over time and reached statistically significant differences at weeks 6 and 8 compared to 2 weeks of treatment. After 8 weeks of treatment, both groups of miglyol OVX+E2 displayed decreased levels of body fat compared to the miglyol OVX+veh group (Figure 6B, left). On the contrary, both the low and the high dose of E2 dissolved in PBS induced an increase in whole body fat over time, compared to the same treatment at week 2 (Figure 6B, right). No differences between treatments were detected in lean mass (Extended data, figure. 2A,21).\n\nMice were subjected to Sham or OVX surgery and treated with s.c. injections of vehicle (miglyol or PBS) or 17β-estradiol (E2; 0.05 µg/mouse or 0.15 µg/mouse) every 4 days. The analyses were performed using a dual energy x-ray absorptiometry (DXA) scanner before sacrifice after 2, 4, 6 and 8 weeks of treatment. Representative DXA scan images for the experimental groups after 8 weeks of treatment (A). Percentage of fat (B), bone mineral content (BMC; C) and bone mineral density (BMD; D) were determined for the whole body. Data are expressed as mean±SEM; n=3 for each experimental group. * statistical differences between sham+veh vs OVX+veh; or OVX+veh vs the E2 treatment groups; # statistical difference vs week 2 of the same treatment group. *or #, p<0.05; **or ##, p<0.01; ***or ###, p<0.001; ***** or ####, p7lt;0.0001; Two-way ANOVA followed by Dunnet’s post-hoc test).\n\nIn the miglyol groups, the OVX+veh mice showed an increase of bone mineral content (BMC) and bone area after 8 weeks of treatment compared to week 2 (Figure 6C, left; extended data, figure. 2B, left,21). At week 4, the BMC of PBS OVX+E2 0.15µg mice were higher compared to week 2 of treatment. The other PBS experimental groups also showed an increase of the BMC and bone area at weeks 6 and 8 compared to the same treatment at week 2 (Figure 6C, right, extended data 2B, right,21).\n\nThe bone mineral density (BMD) was significantly lower in miglyol OVX+veh mice compared to the sham+veh group at 8 weeks of treatment. Neither the high nor the low dose of miglyol E2 treatments affected the BMD compared to OVX+veh (Figure 6D, left). Similarly, a decrease in BMD was detected in the PBS OVX+veh group at weeks 6 and 8 compared to the PBS Sham+veh groups (Figure 6D, right).\n\nMicro-computed tomography was performed on dissected femurs of all mice for each time point (Figure 7A) (Underlying data22). After 8 weeks of treatment a decrease in bone volume over total volume (BV/TV) was detected in both miglyol and PBS OVX+veh mice compared to the sham counterparts (Figure 7B). The loss of bone was faster (2 weeks) in OVX mice receiving PBS-vehicle. No significantly protective effects on BV/TV were detected by E2 replacement in the miglyol groups (Figure 7B, left). An early protective effect (2 weeks) was measured in the PBS OVX+E2 mice (Figure 7B, right).\n\nMice were subjected to Sham or OVX surgery and treated with s.c. injections of vehicle (miglyol or PBS) or 17β-estradiol (E2; 0.05µg/mouse or 0.15µg/mouse) every 4 days. Experiments were terminated at 2, 4, 6 and 8 weeks after the start of treatments and femurs were dissected. Trabecular and cortical parameters of the femoral bone were determined by micro-computed tomography (µCT) analysis. Representative µCT scan pictures of the trabecular and cortical femur for the experimental groups after eight weeks of treatment (A). µCT analyses of bone volume/total volume (BV/TV); B), trabecular number (C), trabecular thickness (D), trabecular bone mineral density (BMD; E), and cortical thickness (F) were performed on femur. Data are expressed as mean±SEM; n=3 for each experimental group. * statistical differences between sham+veh vs OVX+veh; or OVX+veh vs the E2 treatment groups; # statistical difference vs week 2 of the same treatment group. *or #, p<0.05; ##, p<0.01; **** or ####, p<0.0001; Two-way ANOVA followed by Dunnet’s post-hoc test).\n\nAfter 8 weeks of treatment with miglyol OVX+veh, mice displayed reduced trabecular number compared to sham+veh. Treatment with both doses miglyol E2 resulted in a trend towards increased trabecular number (Figure 7C, left). In the PBS OVX+veh group, the trabecular number was significantly reduced at all time points compared to PBS sham+veh (Figure 7C, right).\n\nFor trabecular thickness similar patterns were detected between the miglyol and PBS OVX+veh groups at week 8, showing increased trabecular thickness compared to the corresponding OVX+veh groups at week 2 (Figure 7D).\n\nThe trabecular BMD was reduced in the PBS OVX+veh mice compared to the PBS sham+veh group, constantly over time (Figure 7E, right). No significant differences were detected for any of the miglyol experimental groups (Figure 7E, left).\n\nLoss of cortical thickness was detected in the miglyol OVX+veh group after 4 weeks of treatment, and the high dose of E2 (0.15µg) in miglyol protected from the decrease in cortical thickness (Figure 7F, left). In addition, both sham+veh, OVX+veh, and treatment of OVX mice with both doses of miglyol E2, resulted in an increase in cortical thickness over time (Figure 7F, left). For the PBS group the cortical thickness was significantly decreased in OVX+veh compared to sham+veh starting at week 6 and the high dose E2 treatment increased the cortical thickness from 4 weeks of treatment (Figure 7F, right).\n\nThe cortical area increased over time compared to week 2 in all the experimental groups of mice receiving miglyol, as well as in the PBS sham+veh group from 6 weeks of treatment (Extended data, figure. 3A,21).\n\nThe porosity of the bone was decreased in the PBS OVX+veh mice compared to the PBS sham+veh group at 4 weeks after the start of the treatments. Also, an overall reduction over time among the PBS OVX treatment groups were detected starting at week 6 (Extended data, figure. 3B,21).\n\nThe capacity to run on the rotarod (set to a constant acceleration) was reduced in OVX+veh mice compared to the sham+veh in both PBS and miglyol groups (Figure 8A). An improvement in the latency to fall was registered in OVX mice treated with miglyol E2 0.15µg compared to the OVX+veh mice (Figure 8A, left).\n\nMice were subjected to Sham or OVX surgery and treated with s.c. injections of vehicle (miglyol or PBS) or 17β-estradiol (E2; 0.05 µg/mouse or 0.15 µg/mouse) every 4 days. After 8 weeks of treatments, motor behavior was tested using the rotarod test for measurement of latency to fall (A) and the open field test to measure activity (B), track length (C) and average velocity (D). Data are expressed as mean±SEM; n=3 for each experimental group. One-way ANOVA followed by Dunnet’s post-hoc test was used to analyze differences between sham+veh vs OVX+veh; or OVX+veh vs the E2 treatment groups. *, p<0.05; **, p<0.01.\n\nIn the open field test, miglyol OVX+veh mice tended to move less and slower compared to the sham+veh operated mice (Figure 8B–D, left). A similar and more pronounced pattern was registered in the mice from the PBS groups. In this group, E2 replacement with the lower dose was able to restore the activity parameters (Figure 8B–D, right).\n\n\nDiscussion\n\nThere is a clear female bias in the development of certain pathologies and estrogens are associated with differences in disease progression. However, the specific mechanisms underlying the effects of estrogens, are still unclear. Experimental mouse models constitute a powerful tool that can be used to define the effect of estrogen on specific cells, tissues and organs. The goal of this study was to determine a dose and preparation of 17β-estradiol-3-benzoate (E2), which restores ovariectomy (OVX)-induced effects in mice to the physiological levels of sham operated controls. The results from this study are intended to be used as a guide in the planning of experiments that aims to define the specific effects of treatment with a physiological dose of E2 in experimental mouse models.\n\nSurgical removal of the ovaries was performed in order to mimic a postmenopausal state. OVX mice were treated with subcutaneous E2 injections and monitored at 2 weeks intervals for up to 8 weeks of treatment. The doses of E2 used, 0.05µg or 0.15µg per mouse/per injection, were previously reported as concentrations equivalent to estrus and anestrus levels in mice23. E2 was injected every 4 days to resemble the length of the estrus cycle in mice24. Two vehicles for dissolving E2 were tested: miglyol is described as an inert oil used for slow and sustained absorption of the drug from the oily pocket created after the injection in the subcutaneous area; PBS is used for faster absorption25,26.\n\nSex steroid concentrations were analyzed in serum collected at the time of sacrifice. As expected, OVX resulted in reduced levels of estradiol, progesterone, and testosterone, hormones that are primarily produced by the ovaries. The injections of E2 dissolved in oil did not exceed the control (sham) concentrations of serum estradiol after 8 weeks of treatment, indicating that both tested E2 doses were within the physiological range. However, lower levels of estradiol were found in serum when the drug was dissolved in PBS, suggesting a rapid wash out or reduced drug absorption.\n\nLack of estrogen provoked fat accumulation and a consequent increase of body weight, a phenotype that is linked to increased feed efficiency and reduced lipolysis in white adipose tissue27,28. Replacement of E2 starting 10 days after OVX prevented fat accumulation. Interestingly the lower dose of estradiol delivered with PBS had the opposite effect and induced an increase in the body weight as a consequence of perigonadal fat and total body fat accumulation. This difference in response to the same dose injected could be due to a lower absorption of the aqueous formulation or to a rapid washout making the E2 less bioavailable compared to the E2 dissolved in miglyol. The biological effects of E2 and the expression of estrogen receptors are strictly associated with its concentration, a pharmacological mechanism known as a non-monotonic dose-response29.\n\nThe uterus is a fast-responding organ that is sensible to hormone alterations. The uterus size changes during the menstrual cycle, enlarging and shrinking in response to sex hormone availability, in particular estradiol and progesterone. As expected, the lack of ovaries and the consequent reduction of estradiol and progesterone reduced the uterus weight. The uterus was enlarged to the same levels as the sham controls after treatment with E2 dissolved in oil. Unexpectedly, at 8 weeks after the surgery and treatment with oil as vehicle, the uterus of OVX mice had increased and reached similar size as the sham controls. We speculate that this could be related to local production of estrogens in the perigonadal fat30. A slight increase of the uterus weight was detected in mice treated with E2 dissolved in PBS, an indication that the concentration of E2 delivered with PBS as solvent is much lower compared to E2 dissolved in miglyol. A previous study demonstrated that injections of mice with E2 dissolved in peanut oil (2µg/mouse every 4 days) increased the uterus size up to 4 times the size of the control mice31. For studies of pain and mobility in mice, an important characteristic is keeping the uterus at the same size as the control. An oversized uterus and the hypertrophy of the vaginal tract will induce pain, reduced mobility, and will alter the feeding behavior. Furthermore, an increase of urinary infections caused by a large uterus will impair the general health of the animals and alter the final results of the experiment32. Together, this highlights the importance of choosing a physiological dose of E2 for studies where E2 treatment is performed. Bone parameters are also affected by estrogens to a large extent. E2 controls bone formation and bone resorption by effects on osteoclasts and osteoblasts thereby affecting the amount of bone, its microarchitecture, and its quality in terms of strength and physical properties33. For example, estrogen deficiency results in sub-clinical inflammation with increased expression of pro-inflammatory cytokines including Interleukin-1 (IL-1), IL-6 and Tumor Necrosis Factor (TNF), which leads to an increase in osteoclastogenesis34. Development of osteoporosis was visible already at an early point in the OVX mice, with a reduction in the number and thickness of the femoral trabeculae. At 8 weeks, an increase in BMC, bone area and trabecular thickness was detected, most likely representing a compensatory mechanism with the aim to contrast the reduced bone mineral density and trabecular number and maintain bone strength. A similar compensatory effect was previously described in tibia of OVX rats35.\n\nThe fact that some women suffer from depression in the premenstrual, postpartum and perimenopausal periods is well documented36,37. Estradiol affects the central nervous system by promoting spontaneous physical activity, which supports lipolysis in the white adipose tissue and stimulates the reduction of body mass28,38. In this study, OVX mice that were tested for spontaneous locomotor activity, moved less and slower compared to the sham-operated control mice at 8 weeks post-surgery. In the rotarod test, OVX mice showed a pain-associated behavior, which was also described at 8 weeks after OVX in a previous study39,40.\n\n\nConclusion\n\nIn this study we found that subcutaneous injections of OVX mice with low dose E2 (either 0.05 or 0.15µg/mouse dissolved in miglyol) every 4th day, results in serum levels of estradiol comparable to sham operated control mice. Furthermore, both doses of E2 treatment restore body fat composition, rescue the OVX induced decrease in BMD and increase motor ability to the level of sham operated control mice. Thus, pulsed E2 treatment with low dose E2 dissolved in miglyol mimics the endogenous level of estradiol produced by the ovaries in mice. A milder effect was detected when E2 was dissolved in PBS compared to miglyol, indicating a rapid release and wash out of the hormones from the subcutaneous area, and that E2 dissolved in the aqueous vehicle could be more suitable for short term experiments.\n\nThe limitation of this study is the small sample size. Despite this, the study provides a useful tool for the planning of experiments, which aims to investigate the effects of a physiological dose of E2 administered in a pulsed fashion, thereby resembling the cyclic fluctuations of estradiol in normal mice and avoid duplication of effort.\n\n\nData availability\n\nZenodo: Pulsed administration for physiological estrogen replacement in mice.\n\nhttps://doi.org/10.5281/zenodo.503624122\n\nThe project contains the following underlying data:\n\nDXA data: Dual energy x-ray absorptiometry (DXA) measurements for the whole body and lumbar spine of each mouse included in the study.\n\nMotor tests: Video files from the open field test and excel files including raw data from the open field and rotarod test.\n\nSteroid: Excel files including raw data from the steroids measurement.\n\nTissues and body weight: Information about the weight of the body and organs of the animals included in this study. (Description of data).\n\nuCT: Excel files including the raw data obtained from the micro-computed\n\nTomography analysis of the femur collected from each mouse included in this study\n\nZenodo: Pulsed administration for physiological estrogen replacement in mice.\n\nhttps://10.5281/zenodo.514001721.\n\nThe project contains the following extended data:\n\nSupplemental figures: The file includes extra figures and data from the analysis of the organs weight, DXA, and uCT measurement.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: ARRIVE checklist for “Pulsed administration for physiological estrogen replacement in mice”. https://10.5281/zenodo.514001721.\n\nThe file is available under the terms of the Creative Commons Attribution 4.0 International.",
"appendix": "Author contributions\n\n\n\nC.C., J.S., C.D., M.L., U.I., conceived and designed research; C.C., K.G., J.S., C.D., P.H., and A.C. performed experiments; C.C. and U.I. analyzed data; C.C., J.S., C.D., P.H., M.L. and U.I. interpreted results of experiments; M.P. and C.O. provided instrumentations and knowledge for DXA, serum and µCT analyses; C.C. and U.I. prepared figures; C.C. and U.I. drafted the manuscript; all authors revised the draft and approved the final version of the manuscript.\n\n\nAcknowledgements\n\nWe thank Jianyao Wu and Anna-Karin Norlén for excellent technical assistance.\n\n\nReferences\n\nFiacco S, Walther A, Ehlert U: Steroid secretion in healthy aging. Psychoneuroendocrinology. 2019; 105: 64–78. PubMed Abstract | Publisher Full Text\n\nNelson HD: Menopause. Lancet. 2008; 371(9614): 760–70. PubMed Abstract | Publisher Full Text\n\nRocca WA, Grossardt BR, Miller VM, et al.: Premature menopause or early menopause and risk of ischemic stroke. Menopause. 2012; 19(3): 272–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nACOG Practice Bulletin No. 141: management of menopausal symptoms. Obstet Gynecol. 2014; 123(1): 202–16. PubMed Abstract | Publisher Full Text\n\nPortman DJ, Gass ML, Vulvovaginal Atrophy Terminology Consensus Conference Panel: Genitourinary syndrome of menopause: new terminology for vulvovaginal atrophy from the International Society for the Study of Women's Sexual Health and the North American Menopause Society. Menopause. 2014; 21(10): 1063–8. PubMed Abstract | Publisher Full Text\n\nSantoro N, Komi J: Prevalence and impact of vaginal symptoms among postmenopausal women. J Sex Med. 2009; 6(8): 2133–42. PubMed Abstract | Publisher Full Text\n\nPastore LM, Carter RA, Hulka BS, et al.: Self-reported urogenital symptoms in postmenopausal women: Women's Health Initiative. Maturitas. 2004; 49(4): 292–303. PubMed Abstract | Publisher Full Text\n\nGandhi J, Chen A, Dagur G, et al.: Genitourinary syndrome of menopause: an overview of clinical manifestations, pathophysiology, etiology, evaluation, and management. Am J Obstet Gynecol. 2016; 215(6): 704–711. PubMed Abstract | Publisher Full Text\n\nKhosla S: Pathogenesis of age-related bone loss in humans. J Gerontol A Biol Sci Med Sci. 2013; 68(10): 1226–35. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFaienza MF, Ventura A, Marzano F, et al.: Postmenopausal osteoporosis: the role of immune system cells. Clin Dev Immunol. 2013; 2013: 575936. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSherman S, Miller H, Nerurkar L, et al.: Research opportunities for reducing the burden of menopause-related symptoms. Am J Med. 2005; 118 Suppl 12B: 166–71. PubMed Abstract | Publisher Full Text\n\nBromberger JT, Kravitz HM: Mood and menopause: findings from the Study of Women's Health Across the Nation (SWAN) over 10 years. Obstet Gynecol Clin North Am. 2011; 38(3): 609–25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFreeman EW: Depression in the menopause transition: risks in the changing hormone milieu as observed in the general population. Womens Midlife Health. 2015; 1: 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCornil CA, Ball GF, Balthazart J: The dual action of estrogen hypothesis. Trends Neurosci. 2015; 38(7): 408–16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFuentes N, Silveyra P: Estrogen receptor signaling mechanisms. Adv Protein Chem Struct Biol. 2019; 116: 135–170. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStrom JO, Theodorsson E, Holm L, et al.: Different methods for administering 17beta-estradiol to ovariectomized rats result in opposite effects on ischemic brain damage. BMC Neurosci. 2010; 11: 39. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStrom JO, Theodorsson E, Theodorsson A: Order of magnitude differences between methods for maintaining physiological 17beta-oestradiol concentrations in ovariectomized rats. Scand J Clin Lab Invest. 2008; 68(8): 814–22. PubMed Abstract | Publisher Full Text\n\nStrom JO, Theodorsson A, Ingberg E, et al.: Ovariectomy and 17β-estradiol replacement in rats and mice: a visual demonstration. J Vis Exp. 2012; (64): e4013. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVandenberg LN, Wadia PR, Schaeberle CM, et al.: The mammary gland response to estradiol: monotonic at the cellular level, non-monotonic at the tissue-level of organization? J Steroid Biochem Mol Biol. 2006; 101(4–5): 263–74. PubMed Abstract | Publisher Full Text\n\nIngberg E, Theodorsson A, Theodorsson E, et al.: Methods for long-term 17β-estradiol administration to mice. Gen Comp Endocrinol. 2012; 175(1): 188–93. PubMed Abstract | Publisher Full Text\n\nCorciulo C, Scheffler JM, Gustafsson KL, et al.: Extended data and ARRIVE checklist - Pulsed administration for physiological estrogen replacement in mice. 2021.\n\nCorciulo C, Scheffler JM, Gustafsson KL, et al.: Underlying data_Pulsed administration for physiological estrogen replacement in mice.\n\nOffner H, Adlard K, Zamora A, et al.: Estrogen potentiates treatment with T-cell receptor protein of female mice with experimental encephalomyelitis. J Clin Invest. 2000; 105(10): 1465–72. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAjayi AF, Akhigbe RE: Staging of the estrous cycle and induction of estrus in experimental rodents: an update. Fertil Res Pract. 2020; 6: 5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAndersson A, Bernardi AI, Stubelius A, et al.: Selective oestrogen receptor modulators lasofoxifene and bazedoxifene inhibit joint inflammation and osteoporosis in ovariectomised mice with collagen-induced arthritis. Rheumatology (Oxford). 2016; 55(3): 553–63. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOhlsson C, Gustafsson KL, Farman HH, et al.: Phosphorylation site S122 in estrogen receptor α has a tissue-dependent role in female mice. FASEB J. 2020; 34(12): 15991–16002. PubMed Abstract | Publisher Full Text\n\nNishio E, Hayashi T, Nakatani M, et al.: Lack of association of ovariectomy-induced obesity with overeating and the reduction of physical activities. Biochem Biophys Rep. 2019; 20: 100671. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYonezawa R, Wada T, Matsumoto N, et al.: Central versus peripheral impact of estradiol on the impaired glucose metabolism in ovariectomized mice on a high-fat diet. Am J Physiol Endocrinol Metab. 2012; 303(4): E445–56. PubMed Abstract | Publisher Full Text\n\nLagarde F, Beausoleil C, Belcher SM, et al.: Non-monotonic dose-response relationships and endocrine disruptors: a qualitative method of assessment. Environ Health. 2015; 14: 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHetemaki N, Savolainen-Peltonen H, Tikkanen MJ, et al.: Estrogen Metabolism in Abdominal Subcutaneous and Visceral Adipose Tissue in Postmenopausal Women. J Clin Endocrinol Metab. 2017; 102(12): 4588–4595. PubMed Abstract | Publisher Full Text\n\nLitwak SA, Wilson JL, Chen W, et al.: Estradiol prevents fat accumulation and overcomes leptin resistance in female high-fat diet mice. Endocrinology. 2014; 155(11): 4447–60. PubMed Abstract | Publisher Full Text\n\nLevin-Allerhand JA, Sokol K, Smith JD: Safe and effective method for chronic 17beta-estradiol administration to mice. Contemp Top Lab Anim Sci. 2003; 42(6): 33–5. PubMed Abstract\n\nKhalid AB, Krum SA: Estrogen receptors alpha and beta in bone. Bone. 2016; 87: 130–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLei Z, Xiaoying Z, Xingguo L: Ovariectomy-associated changes in bone mineral density and bone marrow haematopoiesis in rats. Int J Exp Pathol. 2009; 90(5): 512–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWaarsing JH, Day JS, van der Linden JC, et al.: Detecting and tracking local changes in the tibiae of individual rats: a novel method to analyse longitudinal in vivo micro-CT data. Bone. 2004; 34(1): 163–9. PubMed Abstract | Publisher Full Text\n\nSoares CN, Almeida OP, Joffe H, et al.: Efficacy of estradiol for the treatment of depressive disorders in perimenopausal women: a double-blind, randomized, placebo-controlled trial. Arch Gen Psychiatry. 2001; 58(6): 529–34. PubMed Abstract | Publisher Full Text\n\nRubinow DR, Johnson SL, Schmidt PJ, et al.: Efficacy of Estradiol in Perimenopausal Depression: So Much Promise and So Few Answers. Depress Anxiety. 2015; 32(8): 539–49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWada T, Sameshima A, Yonezawa R, et al.: Impact of central and peripheral estrogen treatment on anxiety and depression phenotypes in a mouse model of postmenopausal obesity. PLoS One. 2018; 13(12): e0209859. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCrawley JN: Behavioral phenotyping of transgenic and knockout mice: experimental design and evaluation of general health, sensory functions, motor abilities, and specific behavioral tests. Brain Res. 1999; 835(1): 18–26. PubMed Abstract | Publisher Full Text\n\nAbe Y, Iba K, Sasaki K, et al.: Inhibitory effect of bisphosphonate on osteoclast function contributes to improved skeletal pain in ovariectomized mice. J Bone Miner Metab. 2015; 33(2): 125–34. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "92272",
"date": "31 Aug 2021",
"name": "Narendra Verma",
"expertise": [
"Reviewer Expertise Bone disorder",
"Obesity and diabetes"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 nice study, the authors show that distribution of 17β-estradiol-3-benzoate (E2) efficacy depends on the solvent and dose frequency. The authors did compare two solvents miglyol and PBS and showed their profound effects, however, I do have some minor concerns:\nTo add some more literature about the estrogens and their role in bone development.\n\nThere are some typo errors the authors should fix\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": []
},
{
"id": "98755",
"date": "22 Nov 2021",
"name": "Julia O. Fedotova",
"expertise": [
"Reviewer Expertise neuropsychopharmacology",
"psychoneuroendocrinology",
"hormones and behavior",
"affective-related disorders",
"cognitive impairments"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very nice study concerning the effects of pulsed subcutaneous injections with 17β-estradiol-3-benzoate (E2) every 4 days in healthy ovariectomized (OVX) mice. The present work creates a useful tool for the planning of experiments, which aims to investigate the effects of a physiological dose of E2 administered in a pulsed way.\nI recommend to continue this study with OVX animals of different age using a physiological dose of E2 administered in a pulsed regime.\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/10-809
|
https://f1000research.com/articles/10-808/v1
|
16 Aug 21
|
{
"type": "Research Article",
"title": "Early detection of macrovascular complications in type 2 diabetes mellitus in Medan, North Sumatera, Indonesia: A cross-sectional study",
"authors": [
"Rina Amelia",
"Juliandi Harahap",
"Yuki Yunanda",
"Hendri Wijaya",
"Isti Ilmiati Fujiati",
"Zulham Yamamoto",
"Juliandi Harahap",
"Yuki Yunanda",
"Hendri Wijaya",
"Isti Ilmiati Fujiati",
"Zulham Yamamoto"
],
"abstract": "Background: Macrovascular complications occur very frequently in patients with type 2 diabetes mellitus (T2DM) with a high mortality rate, due to the development of cardiovascular disease (CVD), such as stroke, atherosclerosis acceleration, and atrial fibrillation. T2DM is a significant risk factor for CVD and has become the leading cause of death. The purpose of this study was to detect the early risk of macrovascular complications by using the ankle brachial index (ABI) as a marker. Methods: This study was an analytic study with a cross-sectional approach. The study population was patients with T2DM from several primary health care centers in Medan. In total, 89 subjects who met the inclusion and exclusion criteria were recruited with consecutive sampling. ABI was determined as the ratio of systolic blood pressure in the brachial artery to the posterior tibial artery after the subjects had been relaxed and felt comfortable in a supine position. Examination of vitamin D and lipid profile was derived from examination of venous blood. Data were processed using SPSS and analyzed with one-way ANOVA. Results: The study found that there was a relationship between LDL-C, triglyceride, and vitamin D (25OH-D) based on the ABI (p > 0.05). Conclusions: ABI can be used for an early detection of macrovascular complications. Apart from being easy to perform, ABI was non-invasive. Some other risk factors that can also be used to assess complications and have relationships with ABI were LDL-C, triglyceride, and vitamin D (25OH-D). Complications in T2DM patients can be prevented with reasonable blood sugar control and lifestyle changes. Education and motivation need to be given to patients so that they become more independent in controlling their disease and improving their quality of life.",
"keywords": [
"macrovascular complications",
"ankle brachial index",
"hydroxy vitamin D",
"LDL-C",
"triglyceride",
"HDL-C"
],
"content": "Introduction\n\nPatients with type 2 diabetes mellitus (T2DM) are at risks of short- and long-term complications. Long-term complications include macrovascular and microvascular diseases.1 Macrovascular complications occur very frequently in patients with T2DM with a high mortality rate, due to the development of cardiovascular disease (CVD) such as stroke, atherosclerosis acceleration, and atrial fibrillation. T2DM is a significant risk factor for CVD and has become the leading cause of death, whereby almost 50% of the total deaths are due to this disease.1 It is estimated that the mortality rate of CVD increases almost threefold in T2DM.2 Besides CVD complication, peripheral arterial disease (PAD) has also become a serious condition of macrovascular complications. PAD is characterized by narrowing peripheral arteries due to atherosclerosis, and it generally occurs in the leg arteries. Many patients with T2DM are suffering from PAD, and as this disease is non-symptomatic, it is undetected. PAD is one of the T2DM complications associated with CVD.3–6 Atherosclerosis is the most common and important cause of PAD. Dyslipidemia, smoking, hypertension, and T2DM are also known as risk factors for PAD, CVD and coronary artery disease.7 Ankle brachial index (ABI) is a non-invasive tool for detecting vascular status and for measuring lower leg arteries versus upper leg arterial health status.8 ABI is the ratio between the lower limb (ankle) systolic blood pressure and the upper limb (upper arm) systolic blood pressure. ABI reflects vascular resistance, which explains the main factors: the blood vessel diameter, which can be narrowed either from internal factors (plaque and intimal tearing) or from external factors, such as compression by soft tissue.9 ABI examination is a non-invasive gold standard measurement to detect PAD; consequently, the examination is highly recommended for patients with T2DM and others at risk of suffering from PAD. An early detection can reduce the risk of more severe complications, such as neuropathy and CVD disorders.5 The purpose of this study was to detect the early risk of macrovascular complications by using the ABI as a marker.\n\n\nMethods\n\nThis was an analytical study with a cross-sectional approach. The study had the ethical approval from the Research Ethics Commission of Universitas Sumatera Utara (Approval number No:280/KEP/USU/2020).\n\nThe study population consisted of patients with T2DM in Medan. The sample size was determined using one-proportion hypothesis test with an accuracy of 10% and a significance of 95%.10 A total of 89 subjects that met the inclusion and exclusion criteria were recruited with consecutive sampling technique. Patients who participated in this study were recruited from three primary health services in Medan (Medan Tuntungan, Medan Selayang, and Medan Belawan. The research process lasted for six months, starting from determining the patient, taking blood and laboratory examinations to completion.\n\nPatients who regularly visited the primary health service and were willing to participate were included in this study. Patients with a history of vascular disorders before they had diabetes, leg trauma, stroke, and those with clotting blood disorders were excluded from this study. During the recruitment, selected subjects were firstly, explained about this study, the examination procedure, the process of taking blood, and explaining the discomfort experienced by the patient in the process. Next, if they agreed to join the study after they had understood the explanation about the study protocol, they were asked to sign a consent statement.\n\nMost of the data collection was done between 18th Aug 2020 and 10th September 2020. ELISA examination, which had to be carried out in the integrated laboratory of the Faculty of Medicine of Universitas Sumatera Utara, was delayed, and could only be carried out on 10th November 2020 due to the pandemic situation that caused limited active laboratory staff with limited working hours. By early December 2020, all data had been collected and then analyzed. ABI was determined as the ratio of systolic blood pressure in the brachial artery to the posterior tibial artery. Blood pressure was measured after the subject felt relaxed and comfortable for 5 minutes in a supine position. Blood pressure was measured by using a mercury sphygmomanometer (Reister TM). For measuring the blood pressure of the brachial artery, the cuff was placed at the upper arm. The systolic pressure was considered as the first occurrence of rhythmic sounds heard with stethoscope placed on the antecubital fossa. For the posterior tibial blood pressure, the cuff was placed at the ankle, the systolic pressure was considered as the first pulse was palpable on the dorsum pedis during the cuff deflation. ABI lower than 0.90 was considered abnormal, which was then classified into 0.41–0.90 as a mild to moderate decrease in blood flow, while <0.40 as a severe decrease in blood flow.11,12\n\nHydroxyvitamin D (25OH-D) level and lipid profile (total cholesterol, HDL-C, LDL-C, and triglyceride level) were analyzed from the venous blood samples (5 ml) drawn after 10 hours fasting. Hydroxyvitamin D (25OH-D) were measured through enzyme-linked immunosorbent assay (ELISA) with human vitamin D ELISA kit (Cat. No E1543Hu, Brand Bioassay TL). Serum for lipid profile was processed by and Auto Analyzer (Indiko Thermo Scientific™) and the total cholesterol (TC) level was measured using cholesterol oxidase method, HDL-C and LDL-C levels analyzed by enzymatic colorimetric method,13 and triglyceride (TG) level was measured using the GPO–Trinded method.14\n\nDetermination of the patient's nutritional status was done by using the Body Mass Index (BMI), which is defined as body weight in kilograms divided by the square of body height in meters (kg/m2), which is then adjusted to the World Health Organization classification.15\n\nThe data was analyzed with SPSS 22 for Windows and then shown in tables. The data under consideration was complete data; any incomplete data was deleted. We included all participants who satisfied the inclusion criteria until the minimal number of samples was reached.\n\nThe Kolmogorov Smirnov test (p > 0.05) was used to estimate the average of the normal distribution of the sample data. The normality test findings were utilized in the following analysis: parametric analysis was done if the distribution was normal; otherwise, non-parametric analysis was used. To show how ABI influenced average age, diabetes duration, blood pressure, total cholesterol, HDL-C, LDL-C, TG, and vitamin D (25OH-D) (p < 0.05), a one-way ANOVA was used. The method was then followed by least significant difference or Bonferroni testing if a significant result was obtained (p < 0.05).\n\n\nResults\n\nMost patients were female (69 subjects, 77.5%), and from the age group of 46–55 years (37 subjects, 41.6%). Normal nutritional status was noted in 44 subjects (49.4%). Based on the duration of illness, more than half of the subjects (47 subjects, 52.8%) had T2DM for 1–5 years (Table 1).\n\nTable 2 shows that 34 (38.2%) patients were in the borderline PAD category, meaning that the peripheral circulation had begun to be disrupted but not included as having PAD. In contrast, 26 patients (29.2%) had mild PAD.\n\nTable 3 indicated that there were differences in average levels of LDL-C, TG and vitamin D (25OH-D), based on ABI (p < 0.05). However, age, duration of illness, blood pressure, TC, and HDL-C did not show this difference (p > 0.05). It was concluded that there was a relationship between LDL-C, TG, and vitamin D (25OH-D) based on ABI classification.\n\n\nDiscussion\n\nDiabetes with vascular inflammation has become a risk factor for atherothrombotic diseases, such as PAD.16 A low ABI value reflects atherosclerosis in the vessel wall, resulting in a decrease of perfusion and arterial circulation to the distal extremities.17 This reduction in perfusion is usually characterized by loss of peripheral pulses, intermittent claudication, and complicated infection of the legs.18 The pathogenesis of atherosclerosis in PAD is the same as that of the coronary arteries. The lesion in the segment creates stenosis or occlusion that usually takes place in the large or medium-sized vessels. The development of these lesions become atherosclerotic plaques with calcium build-up, thin tunica media, destruction of muscle and elastic fibers, and fragmentation of the elastic internal lamina; and thrombus consisting of platelets and fibrin may happen.19\n\nHypertension and diabetes increase the risk of the development of macrovascular and microvascular complications.7,20 According to a study by Hiramoto (2014), after 30 months of observation, the ABI value decreased in patients with T2DM by 20.7%, with 5% of the patients showing PAD symptoms.19 The factors causing the decrease in ABI were influenced by age, gender, high HbA1c, high serum creatinine, high LDL-C, and retinopathy.21\n\nDyslipidemia is a metabolic disorder associated with diabetes. It is characterized by a spectrum of quantitative and qualitative changes in lipids and lipoproteins, including hypertriglyceridemia, decreased concentrations of high-cholesterol lipoprotein (HDL), and elevated LDL.22 Various studies have proven that the risk factors for cardiovascular disease and death from coronary heart disease are directly related to the concentration of cholesterol in the blood.23 Hypercholesterolemia can directly cause endothelial dysfunction through the production of reactive oxygen species, which converts low-density lipoprotein (LDL) into oxidized low-density lipoprotein (ox-LDL).24 LDL-C and TG are markers that have been used to assess the occurrence of atherosclerosis (atherogenic dyslipidemia).25,26 Atherogenic index of plasma, on the other hand, is an instrument that has been used to assess the occurrence of atherosclerosis by using TG level as a marker.27,28 Ultimately, small dense LDL-C leads to an increased risk for the development of CVD.29–31\n\nThis study indicated that there was no relationship between the length of illness and age with ABI. The results were not in line with other studies that showed that age and length of illness affecting ABI, and that this risk increased in patients aged ≥50 years and a history of diabetes-associated atherosclerosis.7 Complications such as uncontrolled blood sugar levels, i.e., random blood sugar level ≥ 200 mg/dL, and fasting blood sugar level ≥ 126 mg/dL occur in T2DM patients within an average period of 5–10 years.32 The low ABI is influenced by irregular consumption of anti-hyperglycemic drugs, irregular physical activity, irregular foot care, and irregularity in the T2DM diet.33\n\nThis study shows that there was relationship between vitamin D and ABI. Vitamin D is associated with arterial atherosclerosis, which underlies an increased risk of CVD,34–36 and there is a strong association between vitamin D deficiency and the prevalence and severity of PAD,37 however, other studies have demonstrated that serum levels of Vitamin D are not associated with arterial stiffness or PAD.36 Previous studies have reported that vitamin D has a preventive role in patients with CVD.39\n\nThis vitamin inhibits the renin–angiotensin–aldosterone system and modulates macrophage activity and cytokine production.35 T2DM and vascular inflammation have become risk markers and even risk factors for atherothrombotic disease, including PAD. T2DM increases the process of atheroma formation. There is an increase in histamine levels in plasma and cells in patients with T2DM and PAD, which can lead to an increased endothelial permeability.40 The next process is the migration of T-lymphocytes into the intima and the increase in the secretion and the activation of cytokinesis. Monocytes/macrophages ingest oxidized LDL molecules and turn them into foam cells, where the accumulation of these cells will form fatty streaks, which are the precursors of atheroma. Atheroma plaque will become unstable because endothelial cells in patients with T2DM secrete cytokines that inhibit collagen production by smooth muscle cells of the blood vessel. Metalloproteinases are also released by these inflammatory cells, which can destroy the collagen fibrous cap plaque atheroma, increasing the tendency for plaque rupture and thrombus formation.16 Systemic inflammation has also been evident to increase insulin resistance. T2DM is an inflammatory condition, and vitamin D may reduce insulin resistance by reducing the risk of inflammation.\n\nThere is an association between low vitamin D levels and T2DM, and impaired glucose tolerance.41 In populations with vitamin D deficiency and impaired glucose tolerance and T2DM, vitamin D supplementation can improve insulin secretion, glucose tolerance, and decrease HbA1c levels. The provision of vitamin D supplementation in healthy adults with this deficiency has shown to improve insulin sensitivity by 60%, which is better than rosiglitazone and other metformin therapy.42\n\nThe abnormalities in the function of endothelial cells and vascular smooth muscle and the tendency to thrombosis are affected by atherosclerosis and its complications. Endothelial cells can regulate blood vessel function and structure because of the strategic anatomical position between the blood vessel walls and blood flow. Under normal circumstances, many active substances are synthesized and released by endothelial cells to maintain blood vessel homeostasis and to regulate blood flow and nutrients to the tissues while preventing thrombosis and leukocyte diapedesis.43\n\nIndividuals with low serum vitamin D levels have an increased risk of dyslipidemia, insulin resistance, and T2DM. The effect of vitamin D on the improvement of T2DM can be directly obtained through insulin action. Vitamin D enhances insulin response to glucose transport by stimulating insulin receptor expression in peripheral tissues. Moreover, vitamin D improves the level and the integrity of lamellae in the aortic medium tunica and prevents fragmentation of the aortic elastic fibers. Vitamin D supplementation in adult patients with T2DM significantly improves lipid profiles. Therefore, it can be concluded that fat metabolism disorders are caused by vitamin D deficiency.44\n\nThe limitation of this study was that it did not distinguish patients with a history of smoking from non-smoking individuals. The results of other studies also say that a history of or smoking affects blood vessels because it causes atherosclerosis in blood vessels that contributing significantly to the ABI value, and smoking can significantly increase DM patients experiencing diabetic peripheral neuropathy.45\n\n\nConclusions\n\nEarly detection of macrovascular complications is vital to prevent morbidity and mortality in T2DM patients. ABI can be used for the early detection of macrovascular complications. Besides being simple and non-invasive, the ABI is also entirely accurate for detecting macrovascular complications in T2DM patients. The results demonstrated that there was a correlation between the ABI value and the average LDL-C level, triglycerides, and vitamin D.\n\n\nData availability\n\nFigshare: Laboratory Result of type 2 DM Patients, https://doi.org/10.6084/m9.figshare.14915724.v1.46\n\nThis project contains the following underlying data:\n\n• Data file (physical examination results, patient characteristics, and laboratory results of patients (BGL, HbA1c, Total cholesterol, LDL-C, HDL-C, TG, Vitamin D)\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\nSilva EFF, Ferreira CMM, de Pinho L : Risk factors and complications in type 2 diabetes outpatients. Rev. Assoc. Médica Bras. 2017 Jul; 63(7): 621–7. PubMed Abstract | Publisher Full Text\n\nJaiswal M, et al.: Peripheral neuropathy in adolescents and young adults with type 1 and type 2 diabetes from the SEARCH for Diabetes in Youth follow-up cohort: a pilot study. Diabetes Care. 2013 Dec 1; 36(12): 3903–3908. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLin JS, Evans CV, Johnson E, et al.: Nontraditional risk factors in cardiovascular disease risk assessment: updated evidence report and systematic review for the US Preventive Services Task Force. Jama. 2018 Jul 17; 320(3): 281–297. PubMed Abstract | Publisher Full Text\n\nSigvant B, Lundin F, Wahlberg E: The risk of disease progression in peripheral arterial disease is higher than expected: a meta-analysis of mortality and disease progression in peripheral arterial disease. Eur. J. Vasc. Endovasc. Surg. 2016 Mar 1; 51(3): 395–403. PubMed Abstract | Publisher Full Text\n\nLe Bivic L, et al.: The intrinsic prognostic value of the ankle–brachial index is independent from its mode of calculation. Vasc. Med. 2019 Feb; 24(1): 23–31. PubMed Abstract | Publisher Full Text\n\nLi G, et al.: The long-term effect of lifestyle interventions to prevent diabetes in the China Da Qing Diabetes Prevention Study: a 20-year follow-up study. Lancet. 2008 May 24; 371(9626): 1783–1789. PubMed Abstract | Publisher Full Text\n\nPark SY, et al.: Effects of foot complications in patients with Type 2 diabetes mellitus on public healthcare: An analysis based on the Korea National Diabetes Program Cohort. J. Diabetes Complications. 2017 Feb 1; 31(2): 375–380. PubMed Abstract | Publisher Full Text\n\nAlves-Cabratosa L, et al.: Levels of ankle–brachial index and the risk of diabetes mellitus complications. BMJ Open Diabetes Res. Care. 2020 Mar 1; 8(1): e000977. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcClary KN, Index PMAB: Ankle Brachial Index. 2020 May 21. StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan. PubMed Abstract\n\nFosgate GT: Practical sample size calculations for surveillance and diagnostic investigations. J. Vet. Diagn. Investig . 2009 Jan; 21(1): 3–14. PubMed Abstract | Publisher Full Text\n\nAboyans V, Criqui MH, Abraham P, et al.: Measurement and interpretation of the ankle-brachial index: a scientific statement from the. J. Am. Heart Assoc. 2012 Dec 11; 126(24): 2890–2909. PubMed Abstract | Publisher Full Text\n\nAerden D, et al.: The ankle–brachial index and the diabetic foot: a troublesome marriage. Ann. Vasc. Surg. 2011 Aug 1; 25(6): 770–777. PubMed Abstract | Publisher Full Text\n\nRobinet P, Wang Z, Hazen SL, et al.: A simple and sensitive enzymatic method for cholesterol quantification in macrophages and foam cells. J Lipid Res. 2010 Nov 1; 51(11): 3364–3369. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPenumarthy S, Penmetsa GS, Mannem S: Assessment of serum levels of triglycerides, total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol in periodontitis patients. J. Indian Soc. Periodontol. 2013 Jan; 17(1): 30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Body mass index - BMI.Reference Source\n\nMoyer VA: Screening for peripheral artery disease and cardiovascular disease risk assessment with the ankle–brachial index in adults: US Preventive Services Task Force recommendation statement. Ann. Intern. Med. 2013 Sep 3; 159(5): 342–348. PubMed Abstract | Publisher Full Text\n\nReis de Matos M, et al.: Distal Symmetric and Cardiovascular Autonomic Neuropathies in Brazilian Individuals with Type 2 Diabetes Followed in a Primary Health Care Unit: A Cross-Sectional Study. Int. J. Environ. Res. Public. Health. 2020 Jan; 17(9): 3232. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZilliox LA, Ruby SK, Singh S, et al.: Clinical neuropathy scales in neuropathy associated with impaired glucose tolerance. J. Diabetes Complications. 2015 Apr 1; 29(3): 372–377. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHiramoto JS, Katz R, Weisman S, et al.: Gender-specific risk factors for peripheral artery disease in a voluntary screening population. J. Am. Heart Assoc. 2014 Mar 13; 3(2): e000651. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSheng B, Truong K, Spitler H, et al.: The long-term effects of bariatric surgery on type 2 diabetes remission, microvascular and macrovascular complications, and mortality: a systematic review and meta-analysis. Obes. Surg. 2017 Oct; 27(10): 2724–2732. PubMed Abstract | Publisher Full Text\n\nSayin S, Kutlu R, Koçak A: The relationship between atherogenic index of plasma and major risk factors of cardiovascular disease in obese and non-obese individuals. Eur. Res. J. 2019; 5(4): 678–685. Publisher Full Text\n\nWu L, Parhofer KG: Diabetic dyslipidemia. Metabolism. 2014 Dec 1; 63(12): 1469–1479. PubMed Abstract | Publisher Full Text\n\nTucker WD, Arora Y, Mahajan K: Anatomy, Blood Vessels. StatPearls [Internet]. 2020 Jan. Reference Source\n\nHeriansyah T, Wihastuti TA, Sargowo D, et al.: Reduction of histopathological images through a decrease in H2O2 levels in diabetic rats with polysaccharide peptides. Biomarkers Genomic Med. 2015 Mar 1; 7(1): 31–7. Publisher Full Text\n\nArca M, Montali A, Valiante S, et al.: Usefulness of atherogenic dyslipidemia for predicting cardiovascular risk in patients with angiographically defined coronary artery disease. Am J Cardiol. 2007; 100(10): 1511–1516. PubMed Abstract | Publisher Full Text\n\nAmelia R, Sari MD, Virgayanti V, et al.: Effect of duration of illness and lipid profile of type 2 Diabetes Mellitus patients on diabetic retinopathy. IOP Conf. Ser. Earth Environ. Sci. 2021 Mar; 713(1): 012058): 1.\n\nPop-Busui R, et al.: Diabetic neuropathy: a position statement by the American Diabetes Association. Diabetes Care. 2017; 40(1): 136–154. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmelia R, Sahbudin DKN, Yamamoto Z: Stress level and self-concept among type 2 diabetes mellitus patients in Indonesia. Fam. Med. Prim. Care Rev. 2020; 22(2): 111–115. Publisher Full Text\n\nAmelia R, Harahap J, Lelo A, et al.: Risk analysis for cardiovascular complication based on the atherogenic index of plasma of type 2 diabetes mellitus patients in Medan, Indonesia. Fam. Med. Prim. Care Rev. 2020; 22(3): 197–201. Publisher Full Text\n\nWu Y, Ding Y, Tanaka Y, et al.: Risk factors contributing to type 2 diabetes and recent advances in the treatment and prevention. Int. J. Med. Sci. 2014; 11(11): 1185. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmelia R, Harahap J, Wahyuni AS, et al.: Health status of elderly based on daily activities living, cholesterol and uric acid profile in Medan city. IOP Conference Series: Earth and Environmental Science. 2018; 125: 012175. Publisher Full Text\n\nKumar A, Kumar A, Kumar H, et al.: Prevalence of peripheral arterial disease & associated risk factors among type 2 diabetes mellitus patients attending diabetic health camp. Int J Med Res Internet. 2018; 3(2): 90–92. PubMed Abstract\n\nShishehbor MH, et al.: Critical limb ischemia: an expert statement. J. Am. Coll. Cardiol. 2016 Nov 2002; 68(18): 1. PubMed Abstract | Publisher Full Text\n\nMitri J, et al.: Plasma 25-hydroxyvitamin D and risk of metabolic syndrome: an ancillary analysis in the Diabetes Prevention Program. Eur. J. Clin. Nutr. 2014 Mar; 68(3): 376–383. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKang JY, Kim MK, Jung S, et al.: The cross-sectional relationships of dietary and serum vitamin D with cardiometabolic risk factors: Metabolic components, subclinical atherosclerosis, and arterial stiffness. Nutrition. 2016 Oct 1; 32(10): 1048–1056. PubMed Abstract | Publisher Full Text\n\nWang Z, et al.: A systematic review and meta-analysis of tests to predict wound healing in diabetic foot. J. Vasc. Surg. 2016 Feb 1; 63(2): 29S–36S. PubMed Abstract | Publisher Full Text\n\nIbhar AM, Arshed AQ: Vitamin D and Cardiovascular Disease: Controversy Unresolved. J. Am. Coll. Cardiol. 2017 Jul 4; 70(1): 89–100. PubMed Abstract | Publisher Full Text\n\nWang L, et al.: Circulating 25-hydroxy-vitamin D and risk of cardiovascular disease: a meta-analysis of prospective studies. Circ. Cardiovasc. Qual. Outcomes. 2012 Nov; 5(6): 819–829. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNsengiyumva V, et al.: The association of circulating 25-hydroxyvitamin D concentration with peripheral arterial disease: a meta-analysis of observational studies. Atherosclerosis. 2015 Dec 1; 243(2): 645–651. PubMed Abstract | Publisher Full Text\n\nAl Mheid I, Patel RS, Tangpricha V, et al.: Vitamin D and cardiovascular disease: is the evidence solid. Eur. Heart J. 2013 Dec 21; 34(48): 3691–3698. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGregg EW, et al.: Changes in diabetes-related complications in the United States, 1990–2010. N. Engl. J. Med. 2014 Apr 17; 370(16): 1514–1523. PubMed Abstract | Publisher Full Text\n\nPalomer X, González-Clemente JM, Blanco-Vaca F, et al.: Role of vitamin D in the pathogenesis of type 2 diabetes mellitus. Diabetes Metab Syndr Obes. 2008 Mar; 10(3): 185–197. PubMed Abstract | Publisher Full Text\n\nAngellotti E, Pittas AG: The role of vitamin D in the prevention of type 2 diabetes: to D or not to D? Endocrinology. 2017 Jul 1; 158(7): 2013–2021. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDucci K, et al.: Ticagrelor versus clopidogrel in patients undergoing implantation of paclitaxel-eluting stent in the femoropopliteal district: A randomized pilot study using frequency-domain optical coherence tomography. Int. J. Cardiol. 2020 Apr 1; 304: 192–197. PubMed Abstract | Publisher Full Text\n\nClair C, Cohen MJ, Eichler F, et al.: The effect of cigarette smoking on diabetic peripheral neuropathy: a systematic review and meta-analysis. J. Gen. Intern. Med. 2015 Aug; 30(8): 1193–1203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmelia R, Harahap J, Yunanda Y, et al.: F1000-Data_Submit_F1000.xlsx. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "91992",
"date": "31 Aug 2021",
"name": "Mohd Adzim Khalili Rohin",
"expertise": [
"Reviewer Expertise Community Nutrition",
"Functional Foods & Nutraceuticals"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscripts could be improved if the authors include detailed information in methods with sufficient data and supporting evidence in results and discussion sections.\n\nThe introduction needs to be justified, with limited evidence to show the magnitude of the problem.\n\nThe conclusion could be more concise and better worded study implications.\n\nLanguage-wise is good.\n\nLimited references were used in supporting the findings. See Silva et al. (2017[ref 1]), Angellotti et al. (20172) and Palomer et al. (20083).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7113",
"date": "02 Sep 2021",
"name": "Rina Amelia",
"role": "Author Response",
"response": "Dear Prof. Rohin, I really appreciate your willingness to review my manuscript. I will try to add to the information provided and make corrections to improve it. Best regards, Rina Amelia"
}
]
},
{
"id": "91990",
"date": "01 Sep 2021",
"name": "Hari Kusnanto",
"expertise": [
"Reviewer Expertise My areas of research is epidemiology as applied to family medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study is simple yet very powerful in advocating the use of Ankle Brachial Index as a risk measurement for peripheral arterial disease as a manifestation of macrovascular problem. The predictive capability of ABI to measure the risk for peripheral arterial disease is also consistent with the level of LDL-cholesterol and triglycerides known to be risk factors for cardiovascular diseases. Of particular interest, which should be emphasized in the discussion is concerning the positive association between the level of vitamin D and the level of peripheral arterial disease. This is a very important finding now when many people consume high dose of vitamin D to prevent severe COVID-19. Evidence-based explanation of the negative effect of higher level of vitamin D need some more elaboration.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7112",
"date": "02 Sep 2021",
"name": "Rina Amelia",
"role": "Author Response",
"response": "Dear Prof. Kusnanto, I really appreciate your willingness to review my manuscript. I will correct all the input; for Vitamin D, I will try to add it to the discussion about the consumption of Vitamin D and the effect of higher vitamin D levels on health, mainly peripheral arterial disease. Best regards, Rina Amelia"
}
]
}
] | 1
|
https://f1000research.com/articles/10-808
|
https://f1000research.com/articles/10-802/v1
|
13 Aug 21
|
{
"type": "Study Protocol",
"title": "Methods and guidance on conducting, reporting, publishing and appraising living systematic reviews: a scoping review protocol",
"authors": [
"Claire Iannizzi",
"Elie A Akl",
"Lara A Kahale",
"Elena Dorando",
"Abina Mosunmola Aminat",
"James M Barker",
"Joanne E. McKenzie",
"Neal R Haddaway",
"Vanessa Piechotta",
"Nicole Skoetz",
"Elie A Akl",
"Lara A Kahale",
"Elena Dorando",
"Abina Mosunmola Aminat",
"James M Barker",
"Joanne E. McKenzie",
"Neal R Haddaway",
"Vanessa Piechotta",
"Nicole Skoetz"
],
"abstract": "Background: The living systematic review (LSR) approach is based on an ongoing surveillance of the literature and continual updating. A few guidance documents address the conduct, reporting, publishing and appraisal of systematic reviews (SRs), but the methodology described is either not up-to date or not suitable for LSRs and misses additional LSR-specific considerations. The objective of this scoping review is to systematically collate methodological literature and guidance on how to conduct, report, publish and appraise the quality of LSRs. The scoping review will allow the mapping of the existing evidence on the topic to support LSRs authors seeking guidance and identify related gaps. Methods: To achieve our objectives, we will conduct a scoping review to survey and evaluate existing evidence, using the standard scoping review methodology. We will search MEDLINE, EMBASE, and Cochrane using the OVID interface. The search strategy was developed by a researcher experienced in developing literature search strategies with the help of an information specialist. As for searching grey literature, we will seek existing guidelines and handbooks on LSRs from organizations that conduct evidence syntheses using the Lens.org website. Two review authors will extract and catalogue the study data on LSR methodological aspects into a standardized and pilot-tested data extraction form. The main categories will reflect proposed methods for (i) conducting LSRs, (ii) reporting of LSRs, (iii) publishing and (iv) appraising the quality of LSRs. Data synthesis and conclusion: By collecting these data from methodological surveys and papers, as well as existing guidance documents and handbooks on LSRs, we might identify specific issues and components lacking within current LSR methodology. Thus, the systematically obtained findings of the scoping review could be used as basis for the revision of existing methods tools on LSR, for instance a PRISMA statement extension for LSRs.",
"keywords": [
"Living systematic reviews",
"methods and guidance",
"scoping review",
"conducting LSRs",
"reporting",
"appraisal"
],
"content": "Background\n\nSystematic reviews (SRs) are essential to provide evidence-based answers to clinical and public health-related questions. Due to continuous publishing of relevant primary studies in some areas, it is important to keep these SRs up-to-date.1 One could achieve that goal by adopting the living systematic review (LSR) approach, which is based on an ongoing surveillance of the literature and continual updating.2 Regular searches ensure that the SR includes the latest available findings and remains up-to-date.2 Therefore, LSRs are most suitable for high-priority topics with substantial uncertainty and frequent publications.When continually updating a review, it is important but challenging to report changes to the methodology and to the findings in transparent and traceable ways.\n\nFew guidance documents address the conduct, reporting, publishing and appraisal of LSRs. The Living Evidence Network developed the “Guidance for the production and publication of Cochrane living systematic reviews”, but that guidance is now four years old.3 While the recent update of the ‘Preferred Reporting Items for Systematic reviews and Meta-Analyses’ (PRISMA) can be used for reporting living systematic reviews, the statement indicates there may be some additional considerations that need to be addressed.4 On the other hand, the AMSTAR - Assessing the Methodological Quality of Systematic Reviews tool which was developed for the critical appraisal of the quality of SRs, does not consider LSRs.5\n\nTherefore, it is of high interest to summarize the literature evaluating methods of conducting, reporting, publishing and appraising LSRs, as well as any guidance on those methods.\n\n\nObjective\n\nThe objective of this scoping review is to systematically collate methodological literature and guidance on how to conduct, report, publish and appraise the quality of LSRs. The scoping review will allow the mapping of the existing evidence on the topic to support LSRs authors seeking guidance. Also, the scoping review will identify the knowledge gaps in the field and any need to revise existing guidance or develop new ones for conducting, reporting and appraising LSRs.\n\n\nMethods\n\nThis scoping review study will be part of a larger project to develop an extension of the PRISMA 2020 statement for living systematic reviews. To achieve our objectives, we will conduct a scoping review to survey and evaluate existing evidence and literature, especially with regards to the availability of methods papers, evidence gaps and associated primary research gaps.6 A framework is illustrating an overview of the methodological plan for this scoping review from the search to the data synthesis (Figure 1). Scoping reviews are particularly useful in the context of emerging evidence and act as a precursor for other topic-related projects.6 We will use standard scoping review methodology with the following steps:\n\na) identification of the research question;\n\nb) identification of relevant studies;\n\nc) study selection;\n\nd) charting the data; and\n\ne) collating, summarizing and reporting of the results.7\n\nWe will include articles that devoted at least two paragraphs to discuss methods or conceptual approaches for how to conduct, report, publish or appraise LSRs. Such articles should ideally include methodological or concept papers describing methods for LSRs, guidance (e.g. handbooks) for undertaking LSRs, issued by organizations that conduct evidence syntheses, and commentaries or editorials that discuss methods for LSR.\n\nWe will exclude from our search, LSRs themselves, as well as LSR protocols.\n\nWe will search in MEDLINE, EMBASE, and Cochrane from 2013 using the OVID interface. The search strategy was developed by a researcher experienced in developing literature search strategies with the help of an information specialist (LH) as part of a larger project to develop an extension of the PRISMA 2020 statement for LSRs.8,9 The strategy was peer-reviewed by an information specialist (IM) who will also run the search planned for July or August 2021. Please see Box 1 for the complete search strategy.\n\nMedline\n\n1. exp Meta-Analysis as topic/\n\n2. Systematic Reviews as Topic/\n\n3. (meta-analysis or review or systematic review).pt. or search*.tw.\n\n4. 1 or 2 or 3\n\n5. ((continuous* or continual* or continue or periodic*) adj3 (updat* or search*)).mp.\n\n6. 4 and 5\n\n7. ((living adj3 (review* or metaanaly* or (meta adj analy*))) or lsr).mp.\n\n8. 6 or 7\n\n9. limit 8 to yr=\"2013 -Current\"\n\nEmbase\n\n1. 'meta analysis'/exp OR 'meta analysis (topic)'/de\n\n2. 'systematic review'/de OR 'systematic review(topic)'/de\n\n3. 'meta analys$s':ti OR review*:ti OR metanalys$s:ti OR search:ti,ab\n\n4. #1 OR #2 OR #3\n\n5. ((continuous* OR continual* OR continue OR periodic*) NEAR/3 (updat* OR search*)):ti,ab,kw\n\n6. #4 AND #5\n\n7. ((living NEAR/3 (review* OR metaanaly* OR 'meta analy*' OR metanaly*)):ti,ab,kw) OR lsr:ti,ab,kw\n\n8. #6 OR #7\n\n9. #8 AND (2013:py OR 2014:py OR 2015:py OR 2016:py OR 2017:py OR 2018:py OR 2019:py OR 2020:py OR 2021:py)\n\nCochrane:\n\n1. MeSH descriptor: [Meta-Analysis] this term only\n\n2. MeSH descriptor: [Meta-Analysis as Topic] explode all trees\n\n3. MeSH descriptor: [Systematic Review] this term only\n\n4. MeSH descriptor: [Systematic Reviews as Topic] this term only\n\n5. ((((meta-analys?s or review* or metanalys?s or metaanalys?s)))):pt\n\n6. (((search*))):ti OR (((search*))):ab\n\n7. #1 OR #2 OR #3 OR #4 OR #5 OR #6\n\n8. ((((continuous* OR continual* OR continue OR periodic*) NEAR/2 (updat* or search*)))):ti,ab,kw\n\n9. #7 AND #8\n\n10. (((living NEAR/2 (evidence OR metaanaly* OR meta-analy* OR metanaly*))) OR LSR):ti,ab,kw\n\n#9 OR #10 with Cochrane Library publication date Between Jan 2013 and April 2021\n\nAs for searching the “grey literature”, we will seek existing guidelines and handbooks on LSRs from organizations that conduct evidence syntheses (e.g. Cochrane handbook, Living Evidence network, JBI) using the Lens.org website. Additionally, we will conduct a step-backwards citation approach to identify relevant LSRs handbooks and guidance documents from the reference list of published LSRs. We will also use forward searching, using certain seminal documents (e.g. papers defining LSRs and Cochrane guidance) and track their citations via google scholar.\n\nTwo authors (CI, AM) will independently and in duplicate screen titles and abstracts. We will use a web-based systematic review software Rayyan (RRID:SCR_017584) for the screening process. To ensure a consistent screening procedure and optimize agreement, we will develop and use a detailed written instruction form. We will then screen for full text assessing eligibility, based on our predefined eligibility criteria. Disagreements and conflicts will be solved by a third author.\n\nTwo review authors will extract and catalogue the study data on LSR methodological aspects into a standardized and pilot tested data extraction form in Microsoft Excel (RRID:SCR_016137); an open-access alternative is Google Sheets (RRID:SCR_017679). All reviewers will participate in calibration exercises before data abstraction to improve reliability, and the senior investigator will serve as a third independent reviewer for resolving disagreements. The predefined categories of data extraction will be piloted, and we will chart data regarding proposed methods for (i) conducting LSRs, (ii) reporting of LSRs, (iii) publishing and (iv) appraising the quality of LSRs. Even though we extract and classify the data according to these categories, we consider that elements from one category (e.g. conducting LSR) can have an impact on elements from another category (e.g. publishing LSR) and might even overlap. We will specifically extract data on the following items:\n\n(i) Regarding the conduct of LSRs\n\n• Inclusion criteria (change, re-evaluation)\n\n• Search (frequency, when, database)\n\n• Data extraction (who, frequency, tool)\n\n• Quality and bias assessment of identified studies (who, frequency, tool)\n\n• Data synthesis with meta-analysis if applicable (who, frequency, tool)\n\n• Certainty of the evidence (who, frequency, tool)\n\n(ii) Regarding the reporting of LSRs:\n\n• Title (identified as LSR)\n\n• Methods\n\n• Results\n\n• Discussion\n\n• Registration and protocol (New protocol for each version with or without changes)\n\n• Support\n\n• Funding and competing interests\n\n• Availability of data\n\n(iii) Regarding the publication of LSRs:\n\n• Publication types of new findings (full revised manuscript or letter)\n\n• Communicating review status\n\n• New citation (visibility)\n\n• Publication of an update/decision on update (frequency, when, trigger)\n\n• Between updates\n\n• Transition out of living mode (when, trigger)\n\n• Peer review\n\n(iv) Regarding the appraisal of LSRs:\n\n• PICO structure applied\n\n• Methods established prior to the conduct and justification of protocol deviations\n\n⁰ Difference between protocol and review assessed\n\n⁰ Difference between review versions assessed\n\n• Study selection explained\n\n• Use of comprehensive search strategy\n\n• Study registry search\n\n• Ongoing studies search\n\n• Study selection and data extraction performed in duplicate\n\n• List of excluded studies with justification\n\n• Description of included studies\n\n• Adequate tool for risk of bias assessment\n\n• Appropriate methods for meta-analysis\n\n• Usage/handling of preprints\n\n• Funding sources, COI\n\nWe will collect, summarize and report the extracted study data according to the predefined categories. Therefore, we will first be presenting a table with the extracted methods unique to LSRs classified into the pre-defined categories, along with the contributing sources. Second, we will develop a visual evidence map framework of these methods and map our findings against the existing standard tools (e.g. Cochrane guidance for conducting LSR, PRISMA 2020, AMSTAR 2) to determine differences and suggestions for adaptations. The evidence map and the summary table will be double-checked by a second review author. These systematically obtained findings of the scoping review could be used as basis for the revision of existing guidance and method tools for LSR, such as the PRISMA statement for instance.\n\nWe plan to disseminate the findings by submitting the resulting scoping review for publication to F1000Research.\n\nWe are currently developing and piloting the data extraction form and the next step will be to run the search and start screening.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nLayal Hneiny, medical librarian at AUB\n\nIna Monsef, information specialist from the university hospital of Cologne\n\nScreeners of related previous LSR project: Ibrahim El Mikati, Rayane El Khoury; Hector Pardo; Assem Khamis\n\nContributors of this scoping review protocol: Gladis Honein; Matthew Page\n\n\nReferences\n\nElliott JH, Turner T, Clavisi O, et al.: Living Systematic Reviews: An Emerging Opportunity to Narrow the Evidence-Practice Gap. PLoS Med. 2014; 11(2): e1001603. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElliott J, Synnot A, Turner T, et al.: Living systematic review 1: Introduction - the Why, What, When and How. J Clin Epidemiol. 2017; 91. PubMed Abstract | Publisher Full Text\n\nCochrane: Guidance for the production and publication of Cochrane living systematic reviews: Cochrane Reviews in living mode.2019.\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ (Clinical research ed). 2021; n71:372. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShea BJ, Reeves BC, Wells G, et al.: AMSTAR 2: a critical appraisal tool for systematic reviews that include randomised or non-randomised studies of healthcare interventions, or both.2017; 358: j4008. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeters M, Godfrey C, McInerney P, et al.: Chapter 11: Scoping Reviews (2020 version) JBI Manual for Evidence Synthesis. JBI. 2020. Reference Source\n\nArksey H, O'Malley L: Scoping studies: towards a methodological framework. Int J Soc Res Methodol. 2005; 8(1):19–32. Publisher Full Text\n\nKhamis A, Kahale L, Pardo-Hernandez H, et al.: Methods of conduct and reporting of living systematic reviews: a protocol for a living methodological survey [version 2; peer review: 2 approved].2019; 8(221). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKahale L, Elkhoury R, El Mikati I, et al.: Tailored PRISMA 2020 flow diagrams for living systematic reviews: a methodological survey and a proposal [version 2; peer review: awaiting peer review].2021; 10(192). Publisher Full Text"
}
|
[
{
"id": "96319",
"date": "19 Oct 2021",
"name": "Zachary Munn",
"expertise": [
"Reviewer Expertise Systematic reviews",
"guidelines",
"evidence synthesis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 to the editors for providing the opportunity to peer review this scoping review protocol investigating methods and guidance on conducting, reporting, publishing and appraising living systematic reviews. The choice of a scoping review approach is methodologically sound and it is encouraging to see the authors have planned their scoping review a priori with this protocol. This is important and interesting work and I commend the authors for taking on this project. I have relatively few minor comments below, which are all at the author’s discretion and none are essential as the article is methodologically sound in its current form.\n\nMinor comments:\nIt may be worth mentioning the final scoping review will be reported in line with PRISMA ScR.\n\nFor your eligibility criteria, it would be useful to know if you are including all living review guidance, regardless of discipline/field.\n\nJustify the 2013 search date (i.e. living reviews are a recent innovation…)\n\nHow will the visual evidence map be created? If using software, it would be good to mention this.\n\nWhat contribution will this study provide in addition to the protocol/planned study by Khamis et al.? It might be worth mentioning this in the background.\n\nTypos/copyediting\n\n\"A framework is illustrating an overview of the methodological plan for this scoping review from the search to the data synthesis.\" – consider rephrasing.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "7576",
"date": "15 Dec 2021",
"name": "Claire Iannizzi",
"role": "Author Response",
"response": "Dear Reviewer, Thank you very much for your review and comments on our protocol. We will incorporate your suggested edits for our final scoping review. We will mention the reporting of the final scoping review in line with PRISMA ScR, the eligibility criteria will be slightly specified, we will elaborate more on the evidence map and the background."
}
]
},
{
"id": "98640",
"date": "07 Feb 2022",
"name": "Lyndsay A. Alexander",
"expertise": [
"Reviewer Expertise Member of JBI Scoping review methodology group."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the invitation to review this scoping review protocol. This is an interesting and well presented protocol on a timely topic.\nI do not have many comments on this manuscript:\nI would be interested in why the authors cite Arksey & O'Malley as the scoping review methodology when there is more up to date and expanded scoping review methodology available (e.g. JBI Scoping review methodology- Peters et al. 2020).\n\nWhy was 2013 chosen as the starting search date?\n\nFor the grey literature search - what are the amended search terms that will be used? From the manuscript, I would not be able to replicate this aspect of the search as currently presented.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-802
|
https://f1000research.com/articles/10-285/v1
|
12 Apr 21
|
{
"type": "Research Article",
"title": "Transition in successors’ behavior and mindset while managing long-lived small and medium-sized manufacturing enterprises: a qualitative study",
"authors": [
"Hiroo Suzuki",
"Yasunobu Kino",
"Yasunobu Kino"
],
"abstract": "Background: There have been many studies conducted on succession, which can be considered as the most important issue in family businesses. However, most of these previous studies have focused only on the early stage of succession, uncovering the role of the predecessor and the successor. Only a few studies have made efforts to examine the total lifecycle of succession. The purpose of this study is to explore the process of the transition in successors' behavior and mindset while managing long-lived small and medium-sized manufacturing enterprises throughout the lifecycle of succession. Methods: Semi-structured interviews were conducted with six successors of small and medium-sized manufacturing companies who are more than half a century old. Their answers were analyzed using the Modified-GTA method to construct a hypothetical model. Results: In total, 46 concepts, four categories, 17 subcategories, and one core category were generated. An analysis result diagram using all concepts and categories was formed. From the observation of this diagram, the successors gained confidence in management through the dilemma between autonomy and constraint in the early stage of succession, which was found in previous research. Following the initial stage, the successors responded to the crisis caused by market constraints and created autonomous strategies in their businesses. Conclusions: By experiencing repetitive crises, the successors tend to acquire new perspectives toward the naturally occurring crises. This change of premise by the successors is considered as the process of double-loop learning. Relationships inside and outside the company influence the generation of this viewpoint. From a long-term perspective, a sense of unity with employees, stable employment, and the pursuit of enjoyment constitute the successors' own values in this model.",
"keywords": [
"Succession",
"successor",
"family business",
"long-lived SMEs",
"qualitative study",
"grounded theory approach",
"M-GTA"
],
"content": "Introduction\n\nJapan has more old companies than any other developed nation in the world. The number of centuries-old companies in Japan is 3,937, which is almost double than that of Germany, which has the second largest number of centuries-old companies with 1,850 (The Nikkei, 2012). According to the database of a research company, there were around 33,000 centenarian companies in 2018 (Teikoku Databank, 2019). Almost all of these companies are family owned, with 80.5% of them having net worth values that are below one billion yen. This means that the old companies in Japan comprise small or medium-sized family businesses.\n\nGoto (2014) is known to have collected century-old company data on a worldwide basis. As per his findings, around 40% of century-old companies in Italy experienced ownership transfer to unrelated families. With respect to Switzerland, Goto (2014) found 56% of family-owned households to have experienced ownership transfers to another family. However, the transfer of ownership is extremely rare in century-old Japanese companies. This action is taken as the last resort to survive. By drawing from a comparison of countries via the worldwide survey, the traits of Japanese long-lived businesses have been family-owned.\n\nRecently, small and medium-sized enterprises (SMEs) have become a serious issue with their succession of management. This tendency can be found from the symptoms of increasing aged-management and declining retiring ratio. While the average ratio of retiring CEOs was around 5% in the 1970s, it was 2.46% in 2011 (The Small and Medium Enterprise Agency, 2016). The average age of the CEOs of companies is steadily increasing, and has currently reached 59.9 years old in 2019, the oldest ever recorded (Teikoku Databank, 2020).\n\nWith the difficulty of succession in SMEs, the number of suspension firms is increasing (The Small and Medium Enterprise Agency, 2019). The Japanese government is concerned that this may lead to the loss of employment and GDP in Japan in the future. Another survey (The Small and Medium Enterprise Agency, 2016) shows that around half of the CEOs over 60 years are planning to abandon their businesses. Further, 44.9% consider their businesses to have at least 10 years of future possibility. As a result, the reason for the suspension is not the business itself, but the issue of the successor. From this viewpoint, one of the issues concerning the basic longevity of Japanese SMEs is the difficulty in tackling the succession problem.\n\nThe study of family businesses does not have a long history. In the mid-90s, the researchers of Harvard Business School focused on the uniqueness of family business and started studies in both U.S. and European business schools. At the same time, while Japan has a stronghold as the “family business nation,” the study of family business in Japan has a relatively short history (Okumura, 2015). One of the reasons might be the overlapping of “ownership” and “management,” which is recognized as an obsolete style. The closed nature of family business might also be a reason for the lack of public information. This study attempts to explore the process of successors’ progress in long-lived SMEs to help the current CEOs and potential successors handle succession smoothly, which is the most important issue for SMEs.\n\nThree-circle model\n\nThe modern form of the company is based on the separation of “ownership” and “management,” which has been advocated by Berle and Means (1932). Many business theories are based on this idea, such as agency theory, which illustrates that the adjustment of conflict between a company’s owner and manager is the main issue of company governance.\n\nWith respect to the case of family business, Tagiuri and Davis (1982) presented the “Three-circle model”, which explains the crossover of “Ownership,” “Family” and “Business” as an essential aspect of family business, and claims family business decision making to be determined by balancing the interests of three stakeholders.\n\nThe 4Cs model\n\nMiller and Le Breton-Miller (2005) researched the factors for successful family-controlled businesses by comparing 46 successful and 24 struggling family-controlled businesses. Successful factors founded from their qualitative study are concluded as “the 4Cs”: continuity, community, connections, and command. A brief explanation of these factors is provided in Table 1. Okumura (2015) is of the opinion that the balancing of these factors is important for family business operations.\n\nEmpirical studies on family business\n\nAsaba (2015) also summarized previous studies on family businesses. In the early stage, the researcher conducted a direct comparison of the performance of family-owned and non-family firms. However, the superiority or inferiority of family businesses pertaining to performance is unclear from the standpoint of Japanese cases (Saito, 2008; Mehrotra et al., 2013) as well as worldwide cases (Anderson & Reeb, 2003). Thus, the interest of studies has shifted from benefit to behavioral characteristics such as investment or market strategies.\n\nHaving examined the research on investment in family and non-family businesses, Asaba (2013) concluded that family businesses continued their investment under volatile and stagnant economic conditions, which is difficult for non-family businesses. From the R&D investment viewpoint, family businesses are “avoiding radical innovations and pursuing incremental innovations” (Asaba & Wada, 2019, p.277). These studies imply that family businesses have long time horizons and consider continuity, which is one of the traits of their strategy.\n\nSuccession of family businesses\n\nChrisman et al. (2003) examined papers on family business management from 1996 to 2003. They found 29 of the 190 strategy-related papers, 22.1% of the total, that were related to the succession of companies (Category 1). The other categories include economic performance (15.3%) and corporate governance (9.5%). This research study brings to light the fact that succession constitutes a major interest among researchers. Having reviewed worldwide studies related to family business succession, Iguchi (2019) found that there are three major research questions: 1) which factors affect the choice of the successor of a family business; 2) which factors affect the success or failure of a family; and 3) how much does succession impact the performance of the family business. These questions were derived from the top 50 cited papers on economics and management. Iguchi (2019) concluded that the impact on performance, including financial analysis should be studied as empirical studies (research question 3). However, previous studies have only covered the factors responsible for the selection of successors (research question 1), and the factors responsible for the success or failure of succession (research question 2), which were were mainly derived from case studies. The many parameters of the family business, such as family connections or emotional factors make empirical studies on these fields difficult, the exception being performance analysis. Thus, the accumulation of case studies is important for the maturation of this field of study. Iguchi (2020) extended his study to find the correlation between the preparation of the successor and the intention for long-term investment by the current CEO. This is fruitful research, as it should that the CEO’s current decision-making affects the expectations of his/her successors.\n\nKamiya (2018) defined these five factors as the unique issue of SME management and innovation, and created an analytical framework by combining these five items with the timeframe, starting from “Unfreeze,” to “Change,” and then to “Freeze,” introduced previously by Lewin (1947). By interviewing the management of a certain food company, Kamiya (2019) presented the matrix of the five factors of SMEs and Lewin’s three-step transition (unfreeze, change, freeze) as the process illustration of SME transformation.\n\nModeling of the succession process\n\nLe Breton-Miller et al. (2004) created a diagram of an “integrative model of the succession process” by combining empirical research, theoretical research, and anecdotal evidence. In particular, they demonstrated the industrial context and social context, which was previously neglected in the inner-process of the family business. Moreover, a broader viewpoint is required to model the succession process of family businesses. In this study, in order for the transition in family business to be complete and smooth, not just the factors within the family or company, but also industry and social factors should be considered.\n\nOchiai (2016b) presented the idea of the successor’s dilemma between autonomy and constraints, which is drawn from the expansion of the observation of many case studies carried out by Gersick et al. (1997).\n\nPrevious studies have recognized that the successors from owners’ families are more likely to introduce discontinuous change than the internally promoted managers, for the successors from the owners’ families do not have to consider the predecessors and current employees (Kagono, 2008). From this explanation, the successors seem to conduct autonomous activities. Ochiai stated that the successors from the owners’ families are ascribed status of being the future management and are treated as special person in the family-owned company. Ochiai further stated that they negotiate equally with the current president and have little concern about the employees. However, the successors are under constraints such as limited choice of occupation, restriction from the current management team, or psychological distance from the employees. The intention of reducing this dilemma is to establish the successors’ achieved status and gain acquired legitimacy as future CEOs with their innate legitimacy from the family.\n\nOchiai (2016a) also found a systematic approach to reduce this dilemma in well-established family-owned companies by conducting interviews with both the current CEOs and the successors from several well-established Japanese companies. This resulted in the formulation of the diagram “autonomy under guardianship”. This diagram presents the current CEO’s role as that of a guardian who gives proper assignments to the successor in order for him/her to adjust to their autonomous behavior and acquire legitimacy. Such modeling of the successor’s behavior is a unique study to understand the wisdom of a well-established family business.\n\nThe duration of CEOs in a family-owned company is generally 20 years long, for it has been proven that the family-owned businesses’ peak profits and growth usually come at the end of their long tenure (Yamaguchi, 2014; Miller & Le Breton-Miller, 2005). However, many previous studies operated within the framework of business succession, and the research that ended during the period of succession had been completed for several years. Only a few studies have brought out the complete lifecycles of successors, right until the end of their tenure as top management. Ochiai (2017) also stated that current studies focused only on the transition process itself, such as the analysis of the early stage of succession or the transition process of president influence, not covering the entrepreneurship of the successors during the middle of their managerial experience.\n\nThe purpose of this study is to try and find the process of succession in long-established family-owned SMEs and understand how successors established their mindsets as the owners of companies and top management post the early stage of succession. The modeling of these processes might be of help to potential successors during their preparation for a smooth succession.\n\n\nMethods\n\nFrom April to August 2020, semi-structured interviews were conducted with the management of six companies. The interviewees were selected by purposive sampling to meet the following criteria: pre-, current, and former CEOs of family-owned manufacturing SMEs that are more than 50 years old and have been managed by three generations. Methods of approach for participants were face to face, email, telephone, or online. The list of interviewees with their attributes and the contact measures for participation is shown in Table 2.\n\nIn accordance with the ethical guidelines of University of Tsukuba, Faculty of Business Science, concerning human beings or specimens, no ethical approval was sought for this study. This is due to the study not involving any physical or mental intervention on the participants. Written informed consent to participate was obtained from each participant prior to the interview.\n\nThe interview time ranged from a minimum of 50 minutes to a maximum of 100 minutes (average time was 78 minutes). All interviews were conducted at their workplace face-to-face or online without the presence of any other participants (Table 2).\n\nPrior to the interviews, the participants agreed on the purpose of the interview and the expected questions, and they granted permission to audio recording for research purposes.\n\nThe verbatim transcriptions were made from the entire recorded data so that the field notes were not created through the interviewing process. Transcripts were not returned to the participants.\n\nThe interview items are as follows: 1) self-introduction, 2) the business domain and the transition of the main business, 3) how to tackle the past market change, 4) how to access the new market, 5) the creed related to the organization, human resources, and management philosophy, 6) future perspectives on business, and 7) anything else.\n\nThe data were analyzed using the modified grounded theory approach (M-GTA) (Glaser & Strauss, 1967). The GTA is a qualitative study method to generate “grounded theory” based on actual data by creating “concepts” from the original data and finding the relationship between these concepts. One of the features of the original GTA is the process of fragmentation of sentences to create the concept by removing the researcher’s bias (Saiki-Craighill, 2014). M-GTA is a modified version of the original grounded theory approach, which holds the intention of being rigorous and scientific with the symbolic methodology of fine fragmentation of sentences constituting as raw data for research. Kinoshita (2003), who developed the M-GTA method, noticed that the original GTA method lost the context, including the cultural aspect, and hindered the formulation of richer concepts from the data (Kambaru, 2018). One of the key features of M-GTA is its avoidance of the fragmentation process by keeping the rigorousness of the original GTA method intact and introducing the procedure of creating the “concept,” which refers to the analytical theme and analytical person, by using an “analytical worksheet” to balance the deep interpretation of data and the rigorous procedure.\n\nM-GTA is a tested method for finding the process in social human interaction and solving the actual problem via a generated theory (Kinoshita, 2007); therefore, this method is judged to be appropriate for this study. The analytical theme of this study is finding the process of succession and developing the management principle in long-lived small and medium-sized manufacturing enterprises. The analytically focused persons are successors in long-lived family-owned manufacturing SMEs, up to some hundred employees with a history of more than a half-century.\n\nThe analytical procedure consists of the following steps based on Kinoshita (2003).\n\n1) Select the most detailed and richest transcription and select relevant parts of the statement from the selected transcription based on the analytical theme.\n\n2) Determine the “concept name,” “definition” from “examples,” and the statement with “theoretical note” as the process of forming Analysis Worksheets, which is prepared for each concept.\n\n3) During the process of determining the “definition” and “concept,” similar sentences from another transcription are selected and collected in the field of “examples” to prove the variety of sentences. Questions or ideas brought out from examining the sentences, but are not adopted in the definition, should be written in a theoretical note, and be confirmed and resolved during the progression of the analysis.\n\n4) An important process while generating worksheets is to try and find not only “similar examples,” but also “polar examples” in the total data via concept generation to reduce the possibility of arbitrary interpretation. An example of an analytical worksheet in this study is presented in Table 3.\n\n5) The generation of concepts is finished when no new concepts are distilled, which is considered to reach the “theoretical saturation.” In this study, the new concept was not generated during the analysis of the sixth interviewee so that the data saturation was considered to be achieved in this stage.\n\n6) Examine the relationship of each concept, and create a “category,” which is the integrated idea of several concepts. The “analytical result diagram” showing the relationship between “categories” is formed as the result of the analysis. Figure 1 presents the overall analysis procedure for the M-GTA method.\n\n\nResults\n\nAs a result of the analysis, 46 concepts, 17 subcategories, four categories, and one core category were generated and reached theoretical saturation. These categories and concepts are listed in Table 4. The analysis result diagram integrated with these elements is shown in Figure 2.\n\nThe results are presented using the storyline or detailed explanations of the analytical result diagram shown in Figure 2 via the use of core category, category, sub-category, and concept, with examples of the statement using quotes selected from the interview data.\n\nThe successors of long-lived manufacturing SMEs join the company sometimes by having the feeling of conflict with regard to succession. They experience a dilemma between constraints under the predecessor and autonomous action by accumulating their business experiences. This model is not directly the same as the “Autonomy Under Guardianship Model” (Ochiai, 2016a), however, it can be regarded as a similar transitional process of succession with there being a conflict between constraint and autonomy (Ochiai, 2016b).\n\nDuring the first stage of joining the company, the successor starts performing tasks using the successor’s expertise and improves his/her business performance by carrying out tasks related to his/her educational background or experience before joining the company, such as expanding domestic/overseas sales channels and launching the R&D/production facility.\n\nWhile gaining work experience by following the instructions of the founder, the successor inherits the basic philosophy and management spirit. Besides, he/she acquires the awe toward previous management by knowing the predecessors’ excellent decision making during the past business development and their deep relationship of trust with customers. This way, the inheritance of the basic values from the predecessors is observed by following the examples of the following statement:\n\n“Well, the most important creed for me is developing people. I told my employees the other day if there were people A, B, and C who made products using the same milling machine program, the appearance of products will be different, depending on each person. This idea was taught to me by my father, and it is the reality.” (Interviewee D).\n\nAnother example is the idea of frugality taught by the predecessor. When sales were increasing due to the bubble economy, the (predecessor) often said: “suppress the spending.” Another thing that often remarked was “when you make a profit, you should store it, you shouldn’t use it just because you made a profit.” (Interviewee A).\n\nAt the same time, the successor’s unique movement against company constraints were also observed at the same time. Since the successor is a special person in the company, he/she makes efforts to foster informal interaction with employees to have a close relationship, such as having a meal with them or holding sports events after business hours. Also, the successor starts forming their own management team to gradually build people of the same generation who meet his/her values as a management team for creating their own organizational system.\n\nWhile accumulating management experiences, the successor often encounters friction with the previous CEO or conflict with previous executives, which is the opportunity to clarify his/her ideas. And his/her proactive effort to establish one’s own creed by joining a gathering of employers’ groups or summarizing one’s thoughts in the notebooks can be found at the same time as the process of the establishment of individuality.\n\nThe typical conflict between the previous CEO and previous executives is a different perspective toward business expansion. An example of a conflict with the pre-CEO case is as follows:\n\n“When changing the company name (from Family-name to the new brand name), I felt the process to be quite difficult because of my predecessor. He told me, ‘I have been this name since I was born … On the contrary, I am not that name when I was born (for the successor is the son-in-law). The impact of changing the company’s name to a general brand had a great impact on the market. Even when opposed, I have challenged various things.” (Interviewee A).\n\nAnother case is that of a conflict with the executive who supported the previous CEO:\n\n“There was a person who was the executive supporting my father. He worked with me for two or three years after previous CEO passing away, However, we had to part ways, as there was a difference in opinion. I wanted to expand the business proactively, but he stated that our business should move steadily and gain money from customers as a result. Aggressive business style made eventual deficit. I was worried about such a different perspective for business.” (Interviewee D).\n\nFrom the examples of conflict mentioned above, it is clear that the successors tended to acquire business expansion in the first stage. At the same time, they deepened the confidence of management via the accumulated business experience and having the confidence to manage their companies. Successors sometimes successfully overcome the hardship or limitations confronted by the predecessors, and these experiences help the successors build their confidence. The preparation for debt guarantee is also seen as the determination of being prepared for succession.\n\nFor the successors who gained certain confidence by overcoming the difficulty of the company, which was difficult for the predecessor, it will be inevitable for them to face new crises that are represented by external factors such as economic recession or internal factors such as strategic failure, one of the turning points for the successors.\n\nThe typical occurrence of crisis for successors is the demise of the previous CEO, and the successors recognize that they possess a weak social status and a heavy responsibility. There are external crises (stalemate in new market) caused by market changes, economic fluctuations, and technological shortages in the new markets. Or, the successors may face unjustified treatment from customers, such as unreasonable price reduction requests from customers, which can be seen as bullying. The successors can be overwhelmed by the harsh reality.\n\n“My predecessor suddenly disappeared in 1991 when he was 67 years old. I was 45 years old at that time. Overall, this period was severe. The previous president suddenly disappeared, and the bubble economy had burst and sales fell steadily, resulting in about half of the sales.” (Interviewee A).\n\nWhen they entered the new market, the effort to improve the quality of products is a countermeasure to tackle the crisis in the market. This is because the requirement from the customer is unexpectedly higher than the conventional customers. However, these experiences lead to an improvement in the company’s technological strength. However, in some cases, withdrawal from market is unavoidable because of the sudden decline in the market. In addition to such a market struggle, they also face difficulty in securing funds. Their assets should be collateral, or they face the challenge of the funding support being denied by their relatives. Another case of trouble is the difficulty in building good relationships with employees, such as letting go a trusted employee when the company is going through a difficult phase. These are the processes of response to crisis and accepting its effect.\n\nAfter overcoming the crisis this way, they have an opportunity to reconsider customers and markets as a reviewing corporate strategy, such as reviewing the position in the market or focusing on profitability than sales. In addition, they use the experience of the crisis as an opportunity to learn about the reconfirmation of strengths of the company:\n\n“Do not produce products and services that are totally different from the conventional one. After all, our greatest strength is in (a certain domain). Even if we already have cutting-edge IT, even if we can use AI, I allow them to give the green light when this technology is related to our domain business.” (Interviewee C).\n\nIn the above example, the successor coined original phrases to redefine their business domain again after the succession. Thus, having a crisis experience confirms their original or strongest business domain.\n\nAfter reviewing the strategy through the experience of the crises, the successors try to scaffold the existing resources to make future preparations for handling a crisis during a normal or peaceful occasion. They conduct institutional approaches such as establishing HR development policy or preparing long-term working environment, as well as share common values with employees about business ethics. The following example is the sharing of important values with employees as a company policy:\n\n“In fact, there are some occasions when the customers ask us to do a strange or unreasonable business activity, but every employee is expected to say we can not do that activity in order to set ethical boundaries. If we do something wrong, the company will collapse in the future.” (Interviewee C).\n\nThe successors expand new resources through the business network and enhance conventional in-house resources. Typical examples are acquiring new resources by merger and acquisition (M&A), utilization of external brains pertaining to financial support or improvement of the productivity in daily routine, and application of digital technology and internet, such as in-house digitization and utilization of e-commerce. Additionally, there are cases where collaborative market development with another group is undertaken with public institutions such as universities or large branded companies. While some are successful, the others are only a trial. However, these activities are derived from the successors’ interests and uniqueness toward the process of acquiring new resources.\n\nAfter preparing the resource-based matters, the successors challenge to enter the new market by investing in the new market or going to the market as top management. Further, they emphasize direct communication with customers to increase the opportunities to hear the customers’ voices directly, even if they had utilized the internet and e-commerce channels. One example is that of the successor often making unannounced visits to the potential customers:\n\n“The employees hesitate to do sales activity for a new customer without an appointment because it’s usual to be refused. However, in my case, there is a possibility of not being refused by the potential customer because I am the president. Even if I am refused, I think it is a poor story for this customer to lose a good opportunity and I do not have so much pride. Direct visits are also a good opportunity for finding the reality of the customer who has a good reputation, but I can sometimes notice that doing business with this customer is risky.” (Interviewee C).\n\nHowever, the challenges posed by the new markets do not always go well, the sales do not grow as expected, and there are ups and downs because of the business cycle. The term of the presidency is around four or six years in general; however, the management of family-owned businesses continues their role a rather long time, around a couple of decades. This is because they seem to have an acceptance of repetitive crisis, such as economic or natural disaster, and even have strategic failures as the preconditions of business cycles.\n\n“My father, my grandfather, as well as me, made many mistakes. And I have prepared myself assuming that these kinds of incidents would happen repeatedly, and manage to continue the business today.” (Interviewee C).\n\nAfter accepting the possibility of making failures or facing the market difficulties repeatedly, the successors not only respond to the crisis but also try utilizing the crisis so that their response aligns with the employees in the crisis to facilitate new market entry or improvement in the execution of daily activities.\n\nFor example, the successor experienced employees’ alignment for a new strategy after experiencing a couple of repetitive economic crises.\n\n“The bubble-economy burst and sales had fallen considerably. Then, when sales recovered slightly, another depression, the “Lehman shock” occurred. Therefore, I wanted to recover from this sales decline by entering a new field. When I decided to enter it, the employees did not show much resistance; on the contrary, everyone aligned with my idea.” (Interviewee A).\n\nAnother successor appreciated the crisis time because a period of crisis can clarify the weakness of a company:\n\n“I am very grateful for this kind of crisis because I can see that our weaknesses were exposed and clarified, the weakness, which had been recognized as a strength.” (Interviewee C).\n\nThrough the experience of the crisis, the successor will redefine the domain of the business and provide clarification on the company’s uniqueness to focus on the points of differentiation with the competitors. Besides, as a small and medium-sized enterprise with limited resources, the focus will be on a specific field, such as reviewing the variety of product and service lineups and limiting the sales’ geographical region. These are a part of the clarification of corporate characteristics, which is carried out during the last stage of tackling the crises.\n\nAs shown in Figure 2, the process of experience and acceptance of crises consists of two branches, which explains the reason why the recognition of crisis changed from the first stage to the experienced stage. Based on the scenarios of facing and recovering from the crisis, they acquired the viewpoint that the occurrence of the crisis is regarded as a “precondition” of management. It is a change of perspective from a passive to proactive handling of the crisis. This is the most unique point of successors who are aware of their predecessors’ past hardships and their own difficult experiences. Therefore, this process was determined as the core category in this research.\n\nIn Figure 2, the large loop between experience and acceptance of crisis and building uniqueness is shown. Between these processes, the successors experience human interactions inside or outside the company. This human interaction affects the mindset of the successors.\n\nWhile overcoming such a crisis, they experienced conflicts with employees. However, at the same time, the remaining employees and long-term customers supported the critical situation. As a result, support from employee and customers lead to the supported experience in crises, or they may experience an unexpected approval from customers amidst a deadlock in the new market. Such an unexpected emotional experience might have a considerable influence on the feelings of the successors. One interviewee recalled the appreciation of the customers and employees who supported the company during the crisis:\n\n“Two factors made us survive. One is help from the customers. Perhaps there was a rumor among the customers that we would collapse. However, customers continued to trade, support, and purchase from our company. The other factor is employees. Of course, some employees quit when we were in a difficult situation. Still, we had 20 employees who had stayed back and done their best.” (Interviewee C).\n\nThe successor may also be affected by the encounter with the master or influence from another businessperson in management. For example, the successor reflects on the employees’ perspectives by meeting an honorable business person who cares about their employees. Another successor who inherited the family business was also inspired by the encountered businessperson who started the business in his favorite field and applied a unique perspective in developing a new business. It is often found that such social interactions with people inside and outside the company lead to the experience of being enlightened by human interaction. In one case, the successor was inspired by a certain founder of the business based on his interest or hobby, which is opposite to doing the business seriously:\n\n“The businessperson who influenced me was Mr. A, who forced me to buy a motorcycle. When he participated in motorcycle racing, he asked me to come to an event in the U.S. At the same time, Mr. B joined an exhibition in the U.S. The teacher of the Toyota style may get angry, but that is not the world I am used to living in. Japanese tend to be serious, but that is a different world; it is a kind of an extension of their hobbies.” (Interviewee E).\n\nIn the early stages of succession, the successors’ values were created in relationship with the preceding CEO. However, due to the experience of the crisis and the interaction with employees and customers via the business network, the successors’ new perspective on creations has come to be observed. As a typical example, the successors turned out to have long-term perspectives, have the intention to protect employees with the willingness to maintain employment, and uphold the element of pursuit of fun in business in the succeeded work or new business development to motivate themselves and employees. A successor did try to include enjoyment at the workplace even under the current crisis:\n\n“I’ve been saying lately that we’ve been in the job for at least eight hours, and I don’t even see my partner’s face for eight hours. Working hours is the longest time in daily life and we cannot stay for eight hours in the workplace. If we feel sad at the workplace, then why do we all not create it that makes us happy and excited? I have been saying this since the pandemic started.” (Interviewee D).\n\nOther successors emphasized that the important factors for family business are unity and a long-term viewpoint:\n\n“For a major company, the term of the presidency is generally four or five years. However, since I have been the president for 20 years, I can look after the business for a long time, and I do not have to worry about the stock price.” (Interviewee E).\n\nAs a long-existing company, preparing for the next generation is also an important theme. To stabilize the management as an owner company, training provided to the CEO’s successor or consolidation of shares in the owner-family are important preparations to have sustainable management. One interviewee shared with their successor the grave reality to help him/her understand the company’s total financial responsibility:\n\n“It is not special that the company may collapse and our own house may disappear. I realized that it is also natural that everything will disappear and I always keep such possibilities in mind, and I am telling the same thing to my son (who is the next successor). I also said to my son that there is no meaning in possessing the house, for such an asset will be taken away when the company will bankrupt.” (Interviewee C).\n\nOn the other hand, the successors have been considering future markets by being sensitive to social change. Furthermore, they prepare business succession to the next generation by having a perspective based on corporate social responsibility such as local contribution and social action. Finally, they reconsider the inheritance of basic values from the predecessor again, and such basic values are passed on to the next generation.\n\n\nDiscussion\n\nIn the early stages of the succession process, the dilemma of the successors, which is described by Ochiai (2016b), is observed by the concepts ‘following the instruction of the founder/predecessor’ and ‘conflicting with the previous CEO’. However, strict frameworks such as the “Autonomy Under Guardianship” model (Ochiai, 2016a), which is defined as “autonomy with intergenerational conflict, restraint, and discipline acting as constraints and guardianship from the preceding CEO” have not been clearly observed in this study. One reason might be that the research subject of Ochiai’s study was large companies, in contrast to the companies in this research, which assign several divisions to the successors periodically. Some successors in this study joined the company to help the predecessors overcome hardship when the market was shrinking or the economy was declining; thus, there was little room to prepare for a gradual succession process. The early stage of the succession process is not simple in order to bring out the successors’ proactive behavior. However, the dilemma might be the inevitable process for overcoming the conflict and creating their axis and confidence as businesspersons, as well as accumulating legitimacy as successors.\n\nIn traditional crisis management theory, the next crisis is averted by elemental preparations through a single feedback loop (Pearson & Mitroff, 1993). However, on real occasions, such preparations do not work well because the crisis has a dynamic framework that ensures that the static and elemental reduction analysis of crisis does not clarify the mechanism of the occasion and address the crisis; thus, the approach of double-loop learning is required (Maenaka et al., 2006).\n\nIn the initial stage of formulating the analysis result diagram in this study, the crises were modeled as repeating cycles. However, as the analysis progressed, the successors seemed to change their premise of crisis, that is, the occurrence of crises and failures is a common issue for experienced successors. This can be interpreted as higher-order learning represented by double-loop learning (Argyris & Schon, 1974). Namely, the single loop learning in this study is the preparation of countermeasures for the crisis. However, the successors change their assumption from preparing the crisis to accepting and utilizing the crisis. This can be interpreted as double-loop learning.\n\nThis means that preparing the countermeasures learned from the crisis is a part of the preparation. For a potential crisis, however, building a firm relationship that is supported by both the customers and employees might be supplemental, but an essential preparation to make a sustainable organization.\n\nThe part of the crisis that is caused by the limitation of the resources of the company such as technology or organization capability, which is functioning as the “constraint in the market,” and the process of building uniqueness is recognized as “business autonomy.” From this interpretation, the dilemma between “constraint” and “autonomy” does not conclude in the early stage of the succession process but continues throughout the entire business practice. It might be said that the dilemma of family business successors with regard to their predecessors is the preparation for the dilemma in their entire business lifecycle. These arguments are presented in Figure 3.\n\nAs mentioned in the section Theory and literature, the 4Cs theory is a collection of four priorities in strategies, organizational, and leadership priorities in family-owned companies derived from qualitative research on successful family businesses carried out by Miller and Le Breton-Miller (2005). The corresponding concepts in this study for these 4Cs elements are the following: continuity is a long-term perspective; community is the fostering of informal interaction with employees, sharing common values with employees, or having a sense of unity with employees; connection is corporative market development with another organization or local contribution and social action; and command is investing in a new market or going to the market as top management. The relationship between the 4Cs in the family business and the experience of crises have not been clearly described in previous research. However, the results of this study suggest that the repetitive crisis experience might affect the creation of such unique initiatives in family business.\n\nOur model is created based on the interviews with six persons, which is the methodological limitation of M-GTA. As a result, one should be cautious of making generalizations. Another limitation is the lack of comparison with other categories such as the manager of startups and the successor in service sectors, or another country case to clarify the uniqueness of the long-lived small and medium-sized manufacturing family businesses. This is also a limitation of M-GTA, which is focused on a specific group as an analytically focused person.\n\n\nConclusions\n\nThe dilemma of the successors can be observed in long-existing family-owned companies, as previously described in the literature. However, this dilemma is considered to decrease as soon as successors have acquired legitimacy. In this study, the successors continue to experience dilemmas, even after taking over the presidency from the predecessors, by facing market constraints such as crises, and having autonomy in business creation. During business practice, the process of building perspective, right from tackling crises to accepting crises, is one development process of successors. Through these experiences, they formulate the principle of management, such as a long-term perspective or a sense of unity with employees. These perspective changes are also affected by the double-loop learning during crises and human interaction both inside and outside the company.\n\n\nData availability\n\nThe interviews were conducted under the agreement of keeping the participants anonymous and their interviews private. Therefore, the raw transcript data are not openly available. Quotes in the manuscript provide intermediate data. Transcripts will be reserved for at least five years; any interested readers can contact the corresponding author (suzuki.hiroo.s5@nifty.com) to facilitate data access. Data will be shared under the following conditions: bona fide researchers with a proposal for how they wish to use the data.",
"appendix": "References\n\nAnderson RC, Reeb DM: Founding-family ownership and firm performance: Evidence from the S&P 500. J Finance. 2003; 58(3): 1301–1328. Publisher Full Text\n\nArgyris C, Schone DA: Theory in practice: Increasing professional effectiveness. 1974; San Francisco, CA:Jossey-Bass.\n\nAsaba S: Patient investment of family firms in the Japanese electric machinery industry. Asia Pacific J Management. 2013; 30(3): 697–715. Publisher Full Text\n\nAsaba S: Family business research in Japan. Hitotsubashi business review. 2015; 63(2): 20–30 (in Japanese).Reference Source\n\nAsaba S, Wada T: Contact hitters or power hitters? R&D behavior of family firms in the Japanese pharmaceutical industry. Family Business Review. 2019; 32(3): 277–295. Publisher Full Text\n\nBerle AA, Means GC: The modern corporation and private property. 1932; New York:Commerce Clearing House.\n\nChrisman JJ, Chua JH, Sharma P: Current trend and future directions in family business management studies: Toward a theory of the family firm. Coleman White Paper Series. 2003: 1–62.\n\nGersick KE, Davis JA, Hampton MM, et al.: Generation to generation: Life cycles of the family business. 1997; Boston:Harvard Business School Press.\n\nGomez-Mejia LR, Cruz C, Berrone P, et al.: The bind that ties: Socioemotional wealth preservation in family firms. Academy of Management Annals. 2011; 5(1): 653–707. Publisher Full Text\n\nGoto T: Family business and its longevity. Kindai Management Review. 2014; 2: 78–96.\n\nGlaser BG, Strauss AL: The discovery of grounded theory: Strategies for qualitative research. 1967; New York, NY:Aldine Publishing Company. Publisher Full Text\n\nIguchi T: Succession in family business: A review of the research. The Waseda Commercial Review. 2019; 454: 29–66 (in Japanese).Reference Source\n\nIguchi T: Uncertainty of business succession and long-term investment behavior in family-owned companies. Org. Sci. 2020; 53(3): 4–17 (in Japanese).\n\nIriyama A, Yamanoi J: The research trend of family business. Org. Sci. 2014; 48(1): 25–37 (in Japanese).Reference Source\n\nKagono T: Business administration and family business studies. Trends Science. 2008; 13(1): 68–70 (in Japanese).\n\nKambaru A: Qualitative research and a modified grounded theory approach. The Tsuru University Review. 2018; 88: 47–58.\n\nKamiya N: Theoretical study in successions and innovations by successors of SMEs. Oikonomika. 2018; 55(1): 15–37 (in Japanese).\n\nKamiya N: Theoretical analysis of management innovation triggered by business succession: From the perspective of issues unique to SMEs and organizational change processes. The doctoral dissertation. 2019;Nagoya City University. (in Japanese).\n\nKinoshita Y: Practice of grounded theory approach, invitation to qualitative research.2003; Koubundou Publishers Inc. (in Japanese).\n\nKinoshita Y: Live lecture M-GTA Practical qualitative research method.2007;Koubundou Publishers Inc. (in Japanese).\n\nLe Breton-Miller IL, Miller D, Steier LP: Toward an integrative model of effective FOB succession. Entrepreneurship Theory and Practice. 2004; 28(4): 305–328. Publisher Full Text\n\nLewin K: Frontiers in group dynamics. Human Relations. 1947; 17(4): 502–513. Publisher Full Text\n\nMaenaka M, Terakawa M, Kobayashi T: A study of crisis management: From the viewpoint of response to the crisis and organizational learning. The Economic Society of Osaka University. 2006; 56(2): 70–80 (in Japanese with English abstract).\n\nMehrotra V, Morck R, Shim J, et al.: Adoptive expectations: Rising sons in Japanese family firms. J Financial Economics. 2013; 108(3): 840–854. Publisher Full Text\n\nMiller D, Le Breton-Miller IL: Management insights from great and struggling family businesses. Long Range Planning. 2005; 38(6): 517–530. Publisher Full Text\n\nMiller D, Le Breton-Miller I: Managing for the long run, Erasmus center for family business academic symposium.2012. Reference Source\n\nOchiai Y: Business Succession and Successor Legitimacy in well-established family company in Japan. Int J Business Information. 2016a; 11(3): 316–340.\n\nOchiai Y: Successor’s dilemma – How do successors manage dilemma between constraints and autonomy under predecessor’s generations? Hakuto-Shobo. 2016b. (in Japanese).\n\nOchiai Y: Entrepreneurial behavior process in family businesses. The Economic Review of Japan University of Economics. 2017; 47(2): 13–22 (in Japanese with English abstract).\n\nOkumura A: On theories of family business. Hitotsubashi Business Review. 2015; 63(2): 6–19 (in Japanese).\n\nPearson CM, Mitroff II: From crisis-prone to crisis prepared: A framework for crisis management. Academy of Management Perspectives. 1993; 7(1): 48–59. Publisher Full Text\n\nSaiki-Craighill S: Overview of grounded theory approach. Keio SFC Journal. 2014; 14(1): 30–43 (in Japanese).\n\nSaito T: Family firms and firm performance: Evidence from Japan. J. Jap. Int. Economies. 2008; 22(4): 620–646. Publisher Full Text\n\nTagiuri R, Davis J: Bivalent attributes of family firms. Family Business Review. 1982; 9(2): 199–208. Publisher Full Text\n\nTeikoku databank: A survey of well-established companies.2019. (in Japanese). Reference Source\n\nTeikoku databank: Analysis of the age of CEO in Japan.2020. (in Japanese). Reference Source\n\nThe Nikkei: Why are so many companies celebrating their 100th anniversary this year? The Nikkei plus-one 9th June. 2012. (in Japanese).\n\nThe Small and Medium Enterprise Agency: The guideline of succession.2016. (in Japanese). Reference Source\n\nThe Small and Medium Enterprise Agency: The white paper of small enterprises in Japan.2019. Reference Source\n\nTokyo Chamber of Commerce and Industry: Teaching from Well-Established Company. 2015. (in Japanese). Reference Source\n\nYamaguchi K: Developing Effective Successor in Family Firm: Research Questions, Propositions, and Future Study. The bulletin of the Graduate School of Commerce, 78. Waseda University. 2014; 39–65. (in Japanese)."
}
|
[
{
"id": "83249",
"date": "27 Apr 2021",
"name": "Yi Zhu",
"expertise": [
"Reviewer Expertise Organizational management"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper uses modified GTA to explore the transition of successors at SMEs in Japan. It gives insights into the behavioral and mindset changes of the successor from a relatively long time span.\nMy comments for each section as below:\nAbstract:\nYou may want to state the reason why the behavior and mindset of successors matter (the value of your research).\n\nConsider revising the title as it could be slightly long.\n\nTo avoid misunderstanding, GTA may need a full name.\n\nClarify what is the uniqueness of your research (some of the descriptions could be moved to the Conclusions).\n\nNeed to explain further what type of crisis you refer to.\n\nIntroduction:\nSecond paragraph: Isn't a Japanese company well known for having a successor from outside the family (i.e. 'mukoyoushi')?\n\nThird paragraph: you may want to specify which country/region you are referring to.\n\nNeed discussion on the importance of SMEs in Japan (e.g. size of the economic loss).\n\nUnclear how the successor is an issue for the failing SMEs.\n\n5th paragraph: the flow was unclear (how is short research life relates to the overlapping of ownership and management, could explore more on the latter topic).\n\nTheory and literature:\nIt seems too sudden to start this section: need introduction to the section.\n\nNeed to clarify the relationship among these theories (e.g. how could 4Cs model relevant to the research by Asba?).\n\nSuccession of family businesses: Which five factors that Kamiya is talking about?\n\nStudy purpose: Could emphasize more on the uniqueness of this study which is to bring out the discussion on complete lifecycles of successors in Introduction and Abstract.\n\nFigure 2 is difficult to comprehend: could have two types of figures, one with a simpler contents; need clarification on the changes of the successors' behaviors and mindsets.\n\nClarify how your research is different from Ochiai 2016a.\n\nSome codes are difficult to understand (e.g. what do you mean by 'Acquiring a higher perspective'?).\n\nMore clarity on the transformation of the management viewpoint: discuss in early-stage in this section what kind of transformation you are referring to.\n\nDiscussion:\nSome early studies were only mentioned in this section, not in the literature review section, which may confuse the reader (e.g. single/double loop learning; crisis management).\n\nConclusions:\nAdd the implications of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "6978",
"date": "13 Aug 2021",
"name": "Hiroo Suzuki",
"role": "Author Response",
"response": "We appreciate the fruitful comment by Dr.Zoe, and the following are the responses to each comment. You may want to state the reason why the behavior and mindset of successors matter (the value of your research). →Definition of \"mindset and behavior\" is vague so that changed the title to \"growth process\". Consider revising the title as it could be slightly long. →Changed the title to the shorter one. To avoid misunderstanding, GTA may need a full name. →Used full name instead of the abbreviation. Clarify what is the uniqueness of your research (some of the descriptions could be moved to the Conclusions). →Described the difference and uniqueness of this study in literature review and conclusions. Need to explain further what type of crisis you refer to. →market and customers issues have been described. Introduction: Second paragraph: Isn't a Japanese company well known for having a successor from outside the family (i.e. 'mukoyoushi')? →Described \"mukoyoshi\" or succession by sons-in-law, which is considered as the expansion of continuation of family-ownership in Japan. Third paragraph: you may want to specify which country/region you are referring to. →Stated this is a Japanese case. Need discussion on the importance of SMEs in Japan (e.g. size of the economic loss). →Stated the economic impact of the SMEs succession issue Unclear how the successor is an issue for the failing SMEs. →Stated the economic impact of the SMEs succession issue 5th paragraph: the flow was unclear (how is short research life relates to the overlapping of ownership and management, could explore more on the latter topic). →The paragraph has replaced the explanation of the current government approach to tackle the succession issues as the background requires information and standardization of the succession process. Theory and literature: It seems too sudden to start this section: need introduction to the section. →The introduction part has been added. Need to clarify the relationship among these theories (e.g. how could 4Cs model relevant to the research by Asba?) →Divided case studies part and other studies including Asaba's study. Succession of family businesses: Which five factors that Kamiya is talking about? →Elaborated Kamiya's studies with five factors Study purpose: Could emphasize more on the uniqueness of this study which is to bring out the discussion on complete lifecycles of successors in Introduction and Abstract. →Changed the study object to the “exploring the growth process of successors” and stated study purpose related to the object. Figure 2 is difficult to comprehend: could have two types of figures, one with a simpler contents; need clarification on the changes of the successors' behaviors and mindsets. →Figure 3 was modified as the simpler version of Figure 2. Clarify how your research is different from Ochiai 2016a. →Described the difference with Ochai2016a from the timeframe of the study. Some codes are difficult to understand (e.g. what do you mean by 'Acquiring a higher perspective'?). →\"Acquiring higher perspective\" has changed to \"Changing Perspective on crisis\" \"Transformation of management viewpoint\" has changed to \"Establishing management principles\". More clarity on the transformation of the management viewpoint: discuss in early-stage in this section what kind of transformation you are referring to. →The concept name has changed and recognized as the process of \"establishing management principles\". Discussion: Some early studies were only mentioned in this section, not in the literature review section, which may confuse the reader (e.g. single/double loop learning; crisis management). →Double-loop learning and Crisis management have been explained in the literature section with previous studies. Conclusions: Add the implications of the study. →Academic and practical implications were added."
}
]
},
{
"id": "83250",
"date": "04 May 2021",
"name": "Chika Yoshida",
"expertise": [
"Reviewer Expertise Software Engineering",
"Requirement Engineering",
"Project Management"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments for each section:\nAbstract:\nThe purpose of this study is \"to explore the process of the transition in successors' behavior and mindset,\" but it would be better to describe what you studied them for.\n\nAs for the Conclusion, it is difficult to see not only what the common trends from the survey are, but also what they mean and how the results can be used.\n\nIntroduction:\nThe data source in the third paragraph is a survey conducted in Japan, and it should be clearly stated as such.\n\nThe second paragraph included examples from overseas, but the data source in the third paragraph is a survey conducted in Japan, and it should be clearly stated as such.\n\nThe fifth paragraph describes the succession problem of family businesses. It would be better to indicate the direction of the study, such as whether this study can be used for that problem, or whether the data can be used to determine mergers and acquisitions like those of large companies, or succession outside the family.\n\nTheory and Literature:\nIn \"Theory and literature,\" it is unclear whether the sections in that section are divided by model or category.\" For \"Three-circle model\" and \"The 4Cs model,\" it would be better to title the section with what the research model is, so that it is consistent with other sections (such as \"Empirical studies on family business\").\n\nIt is not clear the difference between this research and Ochiai (2016a).\n\nIn the Discussion section, it is written that Ochiai (2016a) focuses on large corporations. That should be clarified in this chapter too.\n\nStudy Purpose:\nIn the Abstract, you mentioned “The purpose of this study is to explore the process of the transition in successors' behavior and mindset while managing long-lived small and medium-sized manufacturing enterprises throughout the lifecycle of succession.” In the Introduction, you describe that “This study attempts to explore the process of successors’ progress in long-lived SMEs to help the current CEOs and potential successors handle succession smoothly, which is the most important issue for SMEs.”\nAs with my comment for the Introduction, It would be better to indicate the direction of the study, such as whether this study can be used for that problem.\n\nDiscussion:\nThere are some continuous descriptions for the previous studies, so it would be better to shift part of the discussion to the previous studies and summarize the discussion here.\n\nConclusion:\nThere is a tendency to state all the issues of the study as limitations of the M-GTA method here. It is better to state how the issues of the M-GTA method will be resolved and studied in the future.\n\nGeneral comments:\nI have confirmed that this paper is of an acceptable scientific standard, but I would like the authors to revise the above comments and present the fundamental purpose of this research paper, how it can contribute to academia and what suggestions it can provide in practice.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6979",
"date": "13 Aug 2021",
"name": "Hiroo Suzuki",
"role": "Author Response",
"response": "We appreciate the comment by Prof.Yoshida and the following are the responses to each comment, which will be modified in Version 3. Abstract: The purpose of this study is \"to explore the process of the transition in successors' behavior and mindset,\" but it would be better to describe what you studied them for. →Owing to the ambiguity of \"behaviors and mindset\", the research object described in the title and research purpose was changed to \"exploring the growth process of successors. As for the Conclusion, it is difficult to see not only what the common trends from the survey are, but also what they mean and how the results can be used. →In the discussion section, the academic and practical implication has been added. Introduction: The data source in the third paragraph is a survey conducted in Japan, and it should be clearly stated as such. →Stated. The second paragraph included examples from overseas, but the data source in the third paragraph is a survey conducted in Japan, and it should be clearly stated as such. →Stated as the Japanese case in the third. The fifth paragraph describes the succession problem of family businesses. It would be better to indicate the direction of the study, such as whether this study can be used for that problem, or whether the data can be used to determine mergers and acquisitions like those of large companies, or succession outside the family. →The purpose and benefits of the study were described from the perspectives of both the successors and the professionals who support them, along with the background of the problem of the business succession of SMEs in Japan and the government's measures to deal with it. Theory and Literature: In \"Theory and literature,\" it is unclear whether the sections in that section are divided by model or category.\" For \"Three-circle model\" and \"The 4Cs model,\" it would be better to title the section with what the research model is, so that it is consistent with other sections (such as \"Empirical studies on family business\"). → The 4Cs model is categorized as \"case studies\" with another Japanese one. It is not clear the difference between this research and Ochiai (2016a). →Ochai(2016a) is covering the period when the predecessors are in the top management, This study is following after the successors become the top. and different types of the dilemma is observed in early-stage and top management period, which are stated in the literature section and discussion. In the Discussion section, it is written that Ochiai (2016a) focuses on large corporations. That should be clarified in this chapter too. →Reconsidering Ochiai(2016a), the main finding was the successors' transfer between several departments as the preparation of succession and does not clearly state the large company cases. And the uniqueness of Ochiai's study was interviewing both predecessors and successors in the same company so that the explanation of the context of his study has been amended. Study Purpose: In the Abstract, you mentioned “The purpose of this study is to explore the process of the transition in successors' behavior and mindset while managing long-lived small and medium-sized manufacturing enterprises throughout the lifecycle of succession.” In the Introduction, you describe that “This study attempts to explore the process of successors’ progress in long-lived SMEs to help the current CEOs and potential successors handle succession smoothly, which is the most important issue for SMEs.” →The study purpose is unified as exploring the growth process of successors in long-lived small and medium-sized manufacturing companies both As with my comment for the Introduction, It would be better to indicate the direction of the study, such as whether this study can be used for that problem. →Adding the benefit of the study in the study purpose section. Discussion: There are some continuous descriptions for the previous studies, so it would be better to shift part of the discussion to the previous studies and summarize the discussion here. →Description of previous studies such as single and double-loop learning and crisis-management has shifted in the theory and literature part. Conclusion: There is a tendency to state all the issues of the study as limitations of the M-GTA method here. It is better to state how the issues of the M-GTA method will be resolved and studied in the future. →The necessity of further study based on a quantitative study in the part of the limitation of the study has been stated. General comments: I have confirmed that this paper is of an acceptable scientific standard, but I would like the authors to revise the above comments and present the fundamental purpose of this research paper, how it can contribute to academia and what suggestions it can provide in practice. →Study purpose with practical benefit has stated in the study purpose and implications."
}
]
}
] | 1
|
https://f1000research.com/articles/10-285
|
https://f1000research.com/articles/10-801/v1
|
13 Aug 21
|
{
"type": "Method Article",
"title": "An in vitro model for the cultivation of polymicrobial biofilms under continuous-flow conditions",
"authors": [
"Thomas James O'Brien",
"Marwa Mohsen Hassan",
"Freya Harrison",
"Martin Welch",
"Thomas James O'Brien",
"Marwa Mohsen Hassan",
"Freya Harrison"
],
"abstract": "The airways of people with cystic fibrosis (CF) are often chronically colonised with a diverse array of bacterial and fungal species. However, little is known about the relative partitioning of species between the planktonic and biofilm modes of growth in the airways. Existing in vivo and in vitro models of CF airway infection are ill-suited for the long-term recapitulation of mixed microbial communities. Here we describe a simple, in vitro continuous-flow model for the cultivation of polymicrobial biofilms and planktonic cultures on different substrata. Our data provide evidence for inter-species antagonism and synergism in biofilm ecology. We further show that the type of substratum on which the biofilms grow has a profound influence on their species composition. This happens without any major alteration in the composition of the surrounding steady-state planktonic community. Our experimentally-tractable model enables the systematic study of planktonic and biofilm communities under conditions that are nutritionally reminiscent of the CF airway microenvironment, something not possible using any existing in vivo models of CF airway infection.",
"keywords": [
"Cystic fibrosis (CF)",
"polymicrobial",
"biofilms",
"in vitro models",
"3Rs"
],
"content": "\n\nAllows for direct comparison of biofilm and planktonic microbial lifestyles.\n\nAllows for longitudinal and real-time analysis of interspecies interactions among polymicrobial biofilms.\n\nReduces the need for vertebrate infection models when studying microbe-microbe interactions in the context of cystic fibrosis.\n\nInexpensive and simple to operate.\n\nChemically defined culture conditions, allows for the reproducible study of subtle interspecies interactions.\n\nExperimentally tuneable, allows for different species combinations or disease states to be studied.\n\nStudying changes in ecology of polymicrobial biofilm formation during co-culture on different solid substrata.\n\nStudying changes in gene expression and behaviour of polymicrobial biofilms comprising of different species combinations.\n\nStudying response of polymicrobial biofilms and planktonic communities against treatment with antimicrobials for the development and validation of polymicrobial biofilm dispersal/treatment regimens.\n\n\nIntroduction\n\nCystic fibrosis (CF) is a life-limiting genetic disorder estimated to affect 70,000 people worldwide (Cystic Fibrosis Foundation). Although a systemic multi-organ disease, the most striking manifestation of CF is chronic obstruction of the airways via an overproduction of viscous, nutrient-rich airway secretions. These secretions block the airways and predispose people with CF to life-long microbial infection. These infections are frequently polymicrobial and comprise both bacterial and fungal species (Ahmed et al., 2019; Boutin et al., 2015; Carmody et al., 2015; Hogan et al., 2016; Jorth et al., 2019; Mahboubi et al., 2016; Rogers et al., 2010; Sibley and Surette, 2011; Zhao et al., 2012). CF airway infections contribute towards a decline in pulmonary function and it is estimated that ~90% of persons with CF succumb to respiratory failure as a direct result of microbial infection (Chmiel and Davis, 2003; Elborn, 2016; Lubamba et al., 2012; Lyczak et al., 2002; Rajan and Saiman, 2002; Sibley et al., 2006).\n\nRecent years have seen increasing recognition that inter-species interactions between the airway microbiota may play a role in modulating the behaviour, virulence, and even the response to therapeutic intervention (Antonic et al., 2013; Armbruster et al., 2016; Baldan et al., 2014; Barnabie and Whiteley, 2015; Beaume et al., 2015; Briaud et al., 2019; Dalton et al., 2011; Diggle et al., 2007; Elias and Banin, 2012; Hotterbeekx et al., 2017; Hibbing et al., 2010; Korgaonkar et al., 2013; Mastropaolo et al., 2005; O'Brien and Fothergill, 2017; Peters et al., 2012; Weimer et al., 2010). Moreover, co-culturing bacterial species in vitro and in vivo has been shown to lead to significant alterations in the expression of core essential genes (Ibberson et al., 2017; Ibberson and Whiteley, 2020). One particularly important unaddressed question relates to the impact of co-habiting species on the biology of Pseudomonas aeruginosa (PA). PA is a common inhabitant of the CF airways, and a model organism for the study of biofilms. However, the paucity of experimentally tractable in vivo or in vitro models of CF infection has severely hampered the in-depth and longitudinal study of such polymicrobial communities (O'Brien and Welch, 2019b).\n\nIt has been estimated that at least 60% of bacterial infections in the western world involve the formation of biofilms (Fux et al., 2005) and CF is no exception. One crucial feature of microbial biofilms is their increased ability to bypass effective immune clearance and resist antimicrobial action. Indeed, some bacterial biofilms are up to 1000 × more resistant to antimicrobial intervention compared with their planktonic cell counterparts (Parsek, 2003). The formation of biofilm-like aggregates in the CF airways is often cited as a reason why therapeutic strategies aimed at eradicating keystone CF pathogens such as PA fail (Bjarnsholt et al., 2009; Döring et al., 2011; Elias and Banin, 2012; Folkesson et al., 2012; Leekha et al., 2011; Lopes et al., 2012; Lopes et al., 2014; Mowat et al., 2011). However, our understanding of how inter-species interactions alter biofilm physiology remains limited. This is important because agonistic and antagonistic interactions between species almost certainly confer a significant selection pressure, thereby driving adaptive divergence in members of the polymicrobial community (Markussen et al., 2014; Schick and Kassen, 2018; Winstanley et al., 2016).\n\nThere are three key vertebrate models of CF available to researchers: the CF mouse, the CF ferret and the CF pig (reviewed recently by O'Brien and Welch, 2019b). Although the porcine airways share a remarkable degree of genetic and structural homology with human airways (Judge et al., 2014; Rogers et al., 2008), the cost and technical/ethical complexity of using porcine models ensures they are rarely used in research. CF ferrets are also rarely used, since they develop severe airway infections soon after birth and subsequently succumb to respiratory failure (Hoffman and Hajjar, 2018; Sun et al., 2010), although this situation may change as in utero administration of cystic fibrosis transmembrane conductance regulator (CFTR) modulators can rescue this severe phenotype (Sun et al., 2019). By contrast, the CF mouse is widely used, with >14 different distinct models available (Guilbault et al., 2007). However, and despite the widespread availability of these murine CF models, their usefulness for studying chronic airway infection is limited. CF mice do not develop spontaneous airway infections (Bayes et al., 2016; Cash et al., 1979; van Heeckeren et al., 2006), and artificially-induced infections of the airways are rapidly cleared if the inoculated microbial species are not immobilised using agar/agarose/alginate beads (Chattoraj et al., 2010; Hoffmann et al., 2005; Moser et al., 2009; Munder et al., 2011). As with CF ferrets, this prevents the long-term study of polymicrobial communities and interspecies interactions.\n\nDue to inherent limitations in the way in which the data is reported, the exact number of animals used for research into CF airway infections is difficult to ascertain. Yet a systematic review of the literature up to 2015 has found 12,304 publications discussing the use of CF animal models. Of those that are primary research articles (799 publications), 636 report the use of CF mice, rats, pigs, ferrets or zebrafish (with the remaining publications not reporting the use of any genetic CF models) (Leenaars et al., 2020). Given that this literature review only accounts for publications up to 2015, and given the recent surge of interest into understanding the polymicrobial communities associated with CF airway infections, the number of CF animals used in research will have certainly increased over the last six years. Despite the importance of biofilms in CF pathology, and their well-known link with increased patient mortality rates, there is currently no suitable in vivo model for the study of polymicrobial biofilm communities in the context of CF. Furthermore, none of the aforementioned 636 studies report the use of CF models to study polymicrobial biofilm communities. Practical limitations when sampling the airway microbiota in infected animal models mean that the animals must be sacrificed and their lungs excised before histopathological examination. Not only are there significant ethical implications associated with these approaches, but the longitudinal/long-term study of microbial populations becomes impractical. More recently, ex vivo models of CF have redressed some of these issues, enabling the study of microbial biofilm lifestyles reminiscent of those observed in situ (Harrington et al., 2020; Sweeney et al., 2021). However, owing to the intense competition observed among microbial species, existing ex vivo models do not yet permit the study of more than one microbial species at a time. This is a significant experimental limitation when studying long-term polymicrobial infection scenarios such as CF. Hence, the in vitro model we describe here provides a novel tool for the study of mixed-species biofilms that is not currently possible using existing in vivo CF models.\n\nThe primary limitations of in vitro infection models, compared with in vivo models, is a lack of host cells and a functional immune system (which may contribute towards clearing microbial infections in situ). However, it should be noted that impaired immune clearance of microbes in an inherent feature of CF, which somewhat mitigates the lack of a functional immune system in in vitro models (Cohen and Prince, 2012; Bonfield and Chmiel, 2017). Although in vitro models do not capture all aspects of human disease pathophysiology, they do provide an ideal tool for studying interspecies interactions between microbes (O'Brien and Welch, 2019b). Emerging evidence suggests that chemical, not spatiotemporal, factors have the greatest impact on driving changes in microbial lifestyles (Lopes et al., 2017; Quinn et al., 2015). Hence, the defined and experimentally-perturbable nature of in vitro models are an attractive option for studying microbial behaviour in a reductive manner. Furthermore, the development of artificial sputum medium (ASM), closely mimicking the nutritional composition of CF airway secretions, provides an unparalleled opportunity for the study of polymicrobial populations under conditions that chemically recapitulate the CF microenvironment (Haley et al., 2012; Sousa et al., 2018; Sriramulu et al., 2005; Turner et al., 2015; Frapwell et al., 2018). However, simply mixing CF airway-associated species together in ASM and hoping for the best is not a recipe for success. This is because the co-cultures display compositional instability, and the initially diverse community rapidly become dominated by just one or a few species. To remedy this, we developed an in vitro model of CF (O'Brien and Welch, 2019a). Importantly, our model permits planktonic microbial communities of three distinctly different species associated with CF airway infections (PA, Staphylococcus aureus (SA) and Candida albicans (CA)) to be maintained, indefinitely, as a stable steady-state community. In this report we build upon our existing model and describe a simple, yet versatile, method of culturing polymicrobial biofilms on different solid substrata.\n\nThe model described in this work permits the simultaneous cultivation of steady-state planktonic and biofilm communities, allowing for direct comparisons to be made between these two modes of microbial growth. In principle, any combination of microbial species associated with CF airway infections could be cultured using the setup. As such, not only does our system reduce the need for in vivo CF infection models for studying microbe-microbe interactions; it enables the real-time, longitudinal study of polymicrobial communities in an experimentally reproducible, controlled setup. It has not escaped our notice that this model system is also well-suited for the road-testing of interventions aimed at preventing the formation of biofilms in chronic CF airway infections.\n\n\nMethods\n\nMicrobial strains\n\nAll microbial strains used in this work are shown in Table 1. Strains were routinely cultured in lysogeny broth (LB) (Formedium) on a 40 cm diameter rotating drum with mild aeration (0.5 rotations per second) at 37°C overnight.\n\nContinuous-flow culture vessel and biofilm container\n\nArtificial sputum medium (ASM) was used as the main growth medium for all experiments and was prepared as previously described (O'Brien and Welch, 2019a). The continuous-flow culture system has also been previously described (O'Brien and Welch, 2019a). Both are described in more detail in the protocol below. Briefly, the culture vessel consists of a 100 mL Duran flask, fitted with an assembled 4-port HPLC GL80 screw cap (Duran). A 24-channel IPC ISM934C standard-speed digital peristaltic pump (Ismatec) was used to deliver sterile ASM from a media reservoir at a defined flowrate (Q) through 1.5 mm bore sterilin silicon tubing (Fisher Scientific) to the culture vessel. A different channel of the same pump was used to remove waste culture into a discard jar at the same flowrate (Figure 1). Biofilms were allowed to develop in the continuous-flow culture vessel on two types of solid substratum; agar chunks and ex vivo porcine lung tissue (EVPL) sections, which have been previously reported to closely mimic the airway surface environment (Harrison et al., 2014; Harrison and Diggle, 2016; Sweeney et al., 2021; Harrington et al., 2020). These substrata were suspended in bespoke cylindrical biofilm containers (25 mm diameter × 35 mm length) constructed from stainless steel wire gauze (Fisher Scientific) (Figure 2A,B). Containers were then suspended in the culture vessel hanging from a piece of silicon tubing threaded through two of the unused HPLC ports (Figure 2C). The entire culture system was maintained at 37°C and the liquid contents of the vessel were kept homogenous by stirring (100 rpm) using a round magnetic stir bar (length 20 mm, diameter 8 mm).\n\nThe main culture vessel (centre) is a 100 mL Duran bottle fitted with a 4-port HPLC GL80 screwcap lid, containing four sealable inlet/outlet ports from which the biofilm container is suspended. A multichannel peristaltic pump delivers fresh media (ASM) into the culture vessel from a reservoir (left), and also removes waste culture into a discard jar (right) at the same rate of flow (Q). Arrows show the direction of media flow. The culture vessel and media reservoirs are incubated at 37°C and the contents are kept homogenous through gentle stirring (100 rpm). The value of Q depends on the microbial species being cultured within the vessel.\n\nThe biofilm container constructed from stainless steel gauze for this study. Biofilm containers consisted of a cylinder, 35 mm in length and 25 mm in diameter (Ø), connected to two stainless steel arms (45 mm in length), which suspend the container from the HPLC screw-port lid. (A) Side view of the container with dimensions. (B) Bottom view of the container. Single strands of stainless-steel wire were threaded across the bottom of the container to form a mesh and prevent the biofilm substratum from falling through. A small gap (~3 mm Ø) was also included for the outlet tube to be threaded through to allow the removal of culture media during incubation. (C) View of the 4-port HPLC screw cap lid. The left port is the media inlet, the right port is the media outlet and the two remaining ports are threaded with a single piece of rubber tubing (1.5 mm bore) to hold the arms of the mesh container. (D) The biofilm container in situ in the assembled setup. Note that the container is completely submerged in the growth medium but is separated from the magnetic stir bar to prevent interference with the continual stirring of the culture vessel.\n\nPreparation of biofilm substratum\n\nAgar plates (2.5% w/v agar in milliQ water) were poured to a depth of 5 mm. Using a sterile number 21 scalpel and a set of sterile 12.7 cm curved forceps, cubes of approximately 5 mm x 5 mm were cut from the plate and transferred into the sterile biofilm container. Biofilm work using EVPL sections was performed in collaboration with Dr Freya Harrison at the University of Warwick, using previously described methods (Harrison and Diggle, 2016). Briefly, fresh pig lungs were collected from the butcher (John Taylor, Earlsdon, UK) and processed within the hour. To remove surface contaminants, a 25 cm palette knife was heated until red-hot using a Bunsen burner and briefly tapped (< 1 s) on the area to be dissected. Working with aseptic technique, a sterile razor blade was used to excise the bronchiole and remove all alveolar tissue; a cleaned bronchiole can be seen in Figure 3. Bronchioles were washed in Dulbecco's Modified Eagle Medium (DMEM)/Roswell Park Memorial Institute 1640 Medium (RPMI) solution (50:50 ratio, 40 mL) and cut into 5 mm wide strips with sterile dissection scissors. The strips were washed in DMEM/RPMI and cut into 5 mm × 5 mm squares. EVPL sections were washed again in DMEM/RPMI, then transferred to a petri dish containing 40 mL ASM and irradiated in UV lightbox for 5 min before being aseptically transferred to the biofilm container [Full dissection methods for the production of EVPL tissue sections are also demonstrated in an open access video protocol (Harrington et al., 2021)].\n\nA single bronchiole excised from porcine lung tissue after cleaning and a single wash in DMEM/RPMI solution. All alveolar and vascular tissue was removed using a razor blade and dissection scissors. After cleaning, bronchiole tissue was cut into 5 mm × 5 mm squares for use as solid substratum to promote biofilm growth.\n\nCulture vessel inoculation and incubation\n\nOvernight cultures of the microbial strains (grown in LB as described above) were washed three times in phosphate-buffered saline (PBS) prior to inoculating the culture vessel. Pre-warmed ASM (37°C, 100 mL) was added to the culture vessel and inoculated with the required combination of microbial species. The optical density (at 600 nm; OD600 nm) of the washed microbial cultures was then measured using a spectrophotometer (Eppendorf BioSpectrometer kinetic) and each species was introduced into the culture vessel to achieve a starting OD600 nm of 0.05. The culture vessel was then incubated for three hours with stirring prior to starting the flow of medium (Q = 145 μL min−1).\n\nSample collection\n\nFor characterisation of biofilm populations, pieces of substratum were aseptically removed at the indicated times and transferred to 500 μL PBS in 24-well microtiter plates. Loosely attached planktonic cells were removed from the substratum by briefly swirling the plates. The substratum was then transferred to a second well in the same plate and washed once more. Finally, after a third wash, the samples were transferred into 2 mL bead beating tubes containing 1 mL PBS and eighteen metal beads (2.38 mm diameter, Qiagen). The tubes were them agitated in a FastPrep-24 5G benchtop homogeniser (MP Biomedicals) for 40 s at 4 m s−1 to liberate the cells. CFU mL−1 counts were performed as described below. Three separate substratum pieces were sampled at each time point (yielding three biological replicates per timepoint, per independent biological experiment). Samples of the planktonic culture (1 mL) were removed directly from the culture vessel using a sterile serological pipette. Independent biological experiments were then performed over separate independent weeks using fresh microbial cultures and pieces of biofilm substratum without any deviation from the methods detailed in this article.\n\nCFU mL−1 enumeration\n\nColony forming units (CFU) were determined using the single plate-serial dilution spotting method, as described previously (Thomas et al., 2015). Briefly, 10-fold serial dilutions of the microbial cultures were made in sterile PBS and 20 μL of each dilution was spotted (approximately 2 μL per drop) onto the appropriate selective agar. Three types of selective agar were used to enumerate microbial cell counts of the different species present in a single sample: PA was isolated using Pseudomonas isolation agar (PIA, Oxoid), SA was isolated using mannitol salt agar (MSA, Oxoid) and CA was isolated onto BiGGY agar (Oxoid). When enumerating cell counts from the polymicrobial cultures, the agar plates used to isolate PA and SA were further supplemented with 5 μg mL−1 itraconazole to inhibit the growth of CA. The different selective media only permit the growth of a single microbial species of interest and inhibit the growth of the other species present. This enables CFU mL−1 counts for each species in the polymicrobial culture to be determined with confidence [note that when studying other co-cultures containing other combinations of microbial species, different types of selective media may be required for the selective enumeration of other species]. All plates were incubated at 37°C. PIA and MSA plates were incubated overnight (16 h) and BiGGY agar plates were incubated for 24 h. Three independent samples of biofilm substratum from the same culture vessel were removed per timepoint (corresponding to three biological replicates). For each biological replicate, three independent serial dilutions were made and plated out for CFU enumeration (constituting three technical replicates per each piece of substratum sampled), non-blinded CFU mL−1 counts were then recorded as the average of the technical replicates. Two independent samples of culture supernatant were removed from each culture vessel per timepoint (corresponding to two technical replicates) to enumerate planktonic CFU mL−1 counts of each species.\n\nWe tested whether there was any significant difference in cell counts determined on non-selective vs selective agar, and there was not (Figure 4 and underlying data (O'Brien et al., 2021)). To test this, we performed serial dilutions of overnight microbial cultures (routinely grown in LB as described above) and plated the same dilution series onto LB-agar (non-selective) and the appropriate selective agar for the cultured species [see notes above]. Plates were then incubated in the same static incubator at 37°C. Plates containing PA or SA incubated for 16 h and plates containing CA incubated for 24 h (as described above). Two independent serial dilutions of the same overnight culture were prepared and plated in parallel from the same overnight culture (constituting two technical replicates) and three independent biological replicates for each microbial species were performed across separate days using fresh microbial cultures and freshly prepared agar plates.\n\nThe figure shows the viable cell counts (expressed as CFU mL−1) of overnight single-species cultures of P. aeruginosa PAO1 (PA), S. aureus 25923 (SA) and C. albicans SC5314 (CA) plated on non-selective agar media (black bars) and selective agar media (grey bars). Data represent the mean ± standard deviation from two technical replicates collected from three independent biological experiments. P > 0.05 is considered as not significantly different (ns).\n\nStatistical analysis\n\nAll biofilm data are represented as the mean ± standard deviation (SD) of three separate biological replicates (collected simultaneously from the same culture vessel at each point of sampling) per timepoint across three independent biological experiments (conducted across different weeks) that were performed using fresh: ASM, microbial cultures and pieces of biofilm substrata [note that experiments using agar chunks or EVPL sections were performed independently of one another]. All planktonic data are represented as the mean ± standard deviation (SD) of two technical replicates (collected simultaneously from the same culture vessel) per timepoint across three independent biological experiments. Planktonic and biofilm CFU mL−1 counts were performed in parallel from the same culture vessel. All statistical analysis was performed using GraphPad Prism version 8.2.0, with P < 0.05 being considered statistically significant [statistical analysis can also be performed using R/Python packages stats/SciPy, respectively]. Paired group two-tailed t-tests were used to analyse: changes in CFU mL−1 counts of the different species present in single- or mixed-species biofilm samples collected at T = 24 h or 96 h; differences in CFU mL−1 counts of the microbial species present on either agar chunks or EVPL sections; and for comparisons of cell viability on selective and non-selective media. Changes in planktonic CFU mL−1 counts across the timepoints for each experiment were analysed using one-way repeated measures ANOVA. Differences in planktonic CFU mL−1 counts in cultures containing the different biofilm substrata across the timepoints for each experiment were analysed using two-way repeated measures ANOVA.\n\nHere we describe step-by-step the procedure used to prepare ASM and to set up/inoculate the continuous-flow culture vessel for the study of polymicrobial biofilm and planktonic communities. Reagents and equipment used in this study are listed in Table 2 and Table 3, respectively.\n\n1. Step 1 Assembly of the biofilm containers. This can be done any time prior to making ASM. A wire “bucket” was crafted by hand from stainless steel wire gauze (Fischer Scientific). Figure 2 shows an image of a completed container and dimensions. Wire cutters are used to trim a mesh of stainless-steel gauze to a rectangle approximately 150 mm x 40 mm. The gauze was then carefully rolled into a cylinder with an approximate diameter of 25 mm. The protruding cut ends of the wire mesh on the side of the cylinder were threaded through the adjacent mesh to secure the side of the cylinder in place. The height of the bucket was then adjusted to 35 mm via trimming with the wire cutters. Spare lengths of wire thread were then woven across the base of the container to generate a bucket-like structure (Figure 2B). Note that we ensured that there was a hole in the bottom of the bucket large enough to fit the out-flow tubing (~ 3mm diameter) (Step 6). To keep the stainless-steel container from interfering with the magnetic stirrer, and to allow easy removal of substratum material during cultivation, we suspended the bucket via two wire “arms” from a loop of silicone tubing threaded through two unused ports of the HPLC screw cap lid (Figure 2C). The wire arms were made by entwining three strands of stainless-steel wire and threading these through the mesh at the top of the bucket. The protruding portion of the arms were bent to allow the bucket assembly to be draped over the silicone tubing support loop and trimmed in length to 45 mm. The correct length of these container arms is important to ensure that the bucket is completely submerged in the culture medium throughout incubation (Figure 2D).\n\n2. Step 2 Preparation of ASM (day 1). Add 5 g of Type II mucin from porcine stomach to 250 mL phosphate buffered saline (pH 7.4) and leave to dissolve overnight with stirring (~400 rpm) at 4°C. On the same day, add 4 g of deoxyribonucleic acid from salmon sperm to 250 mL autoclaved milliQ water and leave to dissolve overnight in a shaking water bath (200 rpm, 30°C). While the mucin/DNA is dissolving, prepare the amino acid and salt/buffer stock solutions (50 mL of each) according to Table 4. Most amino acid stock solutions can be kept for one month in the dark at 4°C. However, stock solutions of tyrosine, threonine, cysteine, phenylalanine and histidine must be made freshly for each batch of ASM.\n\n3. Step 3 Preparation of ASM (day 2). Add ammonium chloride (0.124 g), potassium chloride (1.116 g), sodium chloride (3.032 g) and 3-(N-morpholino) propanesulfonic acid (MOPS, 2.092 g) to a 1 L beaker and dissolve in 250 mL milliQ water with gentle stirring (50 rpm). Then add the remaining salts and amino acids from the pre-made stock solutions as shown in Table 4. Next, combine the dissolved DNA and mucin solutions and add to the beaker with gentle mixing (50 rpm) for 5 min, or until the solution is homogenous. Adjust to pH 6.8 with 0.1 M acetic acid or 0.1 M potassium hydroxide. Following this, prepare the remaining media solutions and add them to the beaker according to Table 5 alongside 5 mL egg yolk emulsion. Once fully homogenous, adjust the total volume to 1 L with milliQ water. The ASM is then filter sterilised using a 1 L disposable Stericup filter unit (0.22 μM pore size) attached to a large diaphragm vacuum pump. Note that the filtering process is slow and may take 2–3 days to complete. Half-way through filtering we recommend carefully decanting (into a clean beaker) the unfiltered ASM from the Stericup unit and rinsing the top of the filter membrane with several mL of sterile PBS (that is then discarded) and then continuing with the filtration to speed up this process.\n\n4. Step 4 Assembly of continuous-flow culture vessel (day 3). While the ASM is being filter-sterilised, assemble the continuous-flow culture vessel as outlined below with inclusion of the biofilm bucket constructed in Step 1. The continuous-flow culture vessel consists of a 100 mL Duran flask fitted with an assembled GL-80 4-port HPLC screw cap (Duran). Two lengths of 1.5 mm bore sterlin silicone tubing (Fisher Scientific) were fed into two of the HPLC ports to act as an inlet/outlet (respectively) for the medium. To prevent contamination of the media reservoir with motile bacteria, ensure that only the outlet tube is in contact with the culture medium when the vessel is filled with ASM. A short piece of silicone tubing was threaded through the two-remaining unused HPLC ports (diagonal from one another) and secured tightly before sealing any gaps around the HPLC ports with parafilm. The biofilm bucket (assembled in Step 1) was hooked onto the suspended tubing and, using forceps, the outlet tube was gently pulled through the meshed hole in the base of the bucket (see step 1). A clean magnetic stir bar was placed in the culture vessel and the fully-assembled lid was fitted. Finally, the inlet tubing was wrapped in aluminium foil and the entire assembly was autoclaved. The setup was allowed to completely dry overnight (in a drying cabinet) before use.\n\n5. Step 5 Preparation of biofilm substratum (day 3). (i) Using agar chunks as a solid substratum for biofilm formation, prepare the substratum by suspending 2.5 g of agar in 100 mL milliQ water. Autoclave. Once cooled, but still warm (~65°C), pour the agar to a depth of 5 mm in a sterile 90 mm petri dish. Once set, the agar plates can be wrapped in parafilm and kept at 4°C until the day of use. (ii) Ex vivo porcine lung (EVPL) tissue sections can also be used as an alternative substratum for biofilm formation. Please refer to Step 7 (day 4) for the protocol detailing the inclusion of EVPL tissue sections in the model.\n\n6. Step 6 Preparation of overnight microbial cultures (day 3). Place a nichrome 5 μL microbial inoculation loop into the blue flame of a Bunsen burner for 5 s. Allow the loop to cool then pick a single microbial colony from an agar plate and use to inoculate 10 mL of LB in a sterile 30 mL universal tube. Repeat for all microbial strains to be inoculated into the culture vessel, then place the tubes on a rotating drum (200 rpm) and incubate at 37°C overnight.\n\n7. Step 7 Preparation of EVPL biofilm substratum (day 4). This work was conducted in collaboration with Dr Freya Harrison at the University of Warwick following their previously published protocol for the preparation of EVPL sections (Harrison et al., 2014) Prior to culture vessel assembly and inoculation (see steps 8-9 below), fresh pig lungs were collected from the butchers and processed within the hour. To remove surface contaminants, a 25 cm palette knife was heated using a Bunsen burner and briefly tapped (< 1 s) on the area to be dissected. A sterile razor blade was used to excise the bronchiole and remove all alveolar tissue. Bronchioles were then washed in DMEM/RPMI solution (40 mL, 50:50 ratio) and cut into 5 mm wide strips with sterile dissection scissors. The strips were washed in DMEM/RPMI and cut into 5 mm × 5 mm squares. EVPL sections were washed again in DMEM/RPMI, then transferred to a petri dish containing 40 mL ASM and irradiated in UV lightbox for 5 min before being aseptically transferred to the biofilm container (as in Step 8).\n\n8. Step 8 Assembly of the culture vessel (day 4). Working in a microbiological safety cabinet, cut the agar into 5 mm × 5 mm cubes using sterile (autoclaved) scalpel/forceps and aseptically transfer these into the wire mesh container so that they sit loose (not stacked) at the bottom of the bucket. The number of substratum pieces used for an experiment may differ, depending on the type of experiment, length of incubation and number of time points to be sampled. In the current work, we simply report the microbial composition of polymicrobial biofilms at two time points (T = 24 h and 96 h). Hence, only six pieces of substratum were incubated in the culture vessel (three for each time point). However, we note that each biofilm container can easily hold 30+ pieces of substratum. Next, aseptically transfer 100 mL of fresh ASM to the culture vessel and secure the lid, ensuring that the biofilm container does not interfere with the magnetic stir bar and is fully submerged in the ASM. The inlet tubing was carefully unwrapped from the foil and placed into the remaining ASM (forming the media reservoir) with the top sealed well with sterile parafilm to prevent contamination. Finally, place the end of the outlet tubing into a discard jar and connect the inlet/outlet tubing to a peristaltic pump. Figure 1 shows a schematic diagram of the assembled continuous-flow culture vessel. The entire system can then be primed with media. The setup was pre-warmed at 37°C prior to microbial inoculation.\n\n9. Step 9 Culture vessel inoculation and incubation (day 4). In this report we describe the formation of polymicrobial biofilms of Pseudomonas aeruginosa (PA), Staphylococcus aureus (SA) and Candida albicans (CA), although in principle, any combination of microbial species could be used for co-culture. Overnight cultures (prepared on day 3) of each species were washed three times in sterile PBS prior to inoculation. Once washed, the optical density (OD600) of the cultures was measured and each species was introduced into the culture vessel to achieve a starting OD600 of 0.05. The culture vessel was incubated at 37°C, with 100 rpm stirring using a round PTFE magnetic stir bar (8 mm diameter × 20 mm length), for three hours prior to starting the flow of medium. For the current study, a continuous flow rate of 145 μL min−1 was applied for the remaining period of incubation (96 h). From our previous study (O'Brien and Welch, 2019a), we note that the flow rate may need to be experimentally optimised if the goal is to maintain steady-state cultures of other species or strains.\n\n10. Step 10 Sample removal and viable cell counts (Day 4–9). At the desired time point(s) (in this study, T = 24 h and 96 h for the biofilms and T = 24, 48, 72 and 96 h for the planktonic samples) remove 1 mL aliquots of the liquid culture using a sterile serological pipette, or pieces of the biofilm substratum from the biofilm bucket, as necessary. For enumeration of colony forming units (CFU mL−1) from the biofilm samples, remove pieces of solid substratum using sterile forceps, taking care to flame and cool the forceps between the collection of individual samples. Pieces of the substratum were aseptically transferred to 500 μL sterile PBS in a 24-well plate. To remove any loosely attached planktonic cells, gently swirl the plates for approximately 5 s then transfer the substratum to another 500 μL of fresh PBS. Repeat the process two more times. A washed piece of substratum was then transferred to a 2 mL bead beating tube containing 1 mL PBS and eighteen 2.38 mm diameter metal beads (Qiagen). The sample was homogenised in a Fast-Prep 5G benchtop homogeniser (MP biomedicals) for 40 s at 4 m s−1. Using a pipette, and taking care to avoid any solid pieces of biofilm substratum, the cell supernatant was removed and CFU mL−1 counts were determined as described in the Methods section above.\n\n\nResults\n\n(i) Agar as a solid substratum\n\nWe first sought to discern changes in the microbial composition of single-species and polymicrobial biofilms grown on agar chunks as a substratum (Figure 5 and underlying data (O'Brien et al., 2021)). Viable cell counts were determined on selective agar plates after rinsing each 5 mm agar chunk (with attached biofilm) and resuspending the attached cells in 1 mL PBS. When examining the single-species biofilm populations, titres of attached SA and CA were similar (ca. 106–107 CFU mL−1) after 24 h incubation, whereas titres of attached PA were >10-fold greater (at just under 108 CFU mL−1). However, over the next 72 h, PA titres increased only slightly (albeit significantly) to >108 CFU mL−1, and SA titres rose to around the same level (i.e. to a titre 2 logs greater than the titre at the 24 h time point). By contrast, CA titres remained essentially unchanged at the 96 h time point compared with the 24 h time point. These data suggest CA biofilms establish rapidly with little overall change in cell titres over time. By contrast, PA and SA biofilms also establish quickly, but continue to grow significantly between sampling points.\n\nP. aeruginosa PAO1 (PA), S. aureus 25923 (SA) and C. albicans SC5314 (CA) cell counts (expressed as CFU mL-1) adhered to 2.5% (w/v) agar chunks after incubation for 24 h (black bars) or 96 h (white bars) in the continuous-flow culture model. Asterisks indicate significant (**P < 0.01, ***P < 0.001) differences in CFU mL-1 counts between the 24 h and 96 h time points. Data represent the mean ± standard deviation of three independent biological experiments in which three pieces of biofilm substratum were sampled per culture vessel per timepoint.\n\nThe situation was different in the polymicrobial cultures. Here, the titres of PA, SA, and CA present on the biofilm substrata removed sequentially from the same culture vessel remained essentially unchanged at the 24 h and 96 h sampling points (at around 107 CFU mL−1 for PA and SA, and around 105 CFU mL−1 for CA). These data suggest that growth in a polymicrobial culture constrains the population size of individual species in a biofilm.\n\n(ii) EVPL tissue sections as a solid substratum\n\nWe next examined biofilm formation on a different biofilm substratum, EVPL tissue (in place of agar chunks) (Figure 6 and underlying data (O'Brien et al., 2021)). No PA, SA or CA cells could be isolated from uninfected EVPL sections after any period of incubation. In the single-species biofilm populations, there was no appreciable difference in PA or SA titres adhered to the substratum at the initial point of sampling (107–108 CFU mL−1 at 24 h). Adhered CA titres were consistently 10-fold lower (ca. 106 CFU mL−1) at the same sampling point. After a further 72 h growth, PA and SA titres increased to >108 CFU mL−1, whereas CA titres remained essentially unchanged compared with the titres measured at 24 h. These data indicate that the dynamics of SA biofilm formation varies on different substrata; SA clearly shows more robust initial colonisation of EVPL substrata compared with agar chunks.\n\nP. aeruginosa PAO1 (PA), S. aureus 25923 (SA) and C. albicans SC5314 (CA) cell counts (expressed as CFU mL−1) adhered to sections of ex vivo porcine lung tissue after incubation for 24 h (black bars) or 96 h (white bars) in the continuous-flow culture model. Asterisks indicate significant (***P < 0.001, ****P < 0.0001) differences in CFU mL−1 counts between the 24 h and 96 h time points. Data represent the mean ± standard deviation of three independent biological experiments in which three pieces of biofilm substratum were sampled per culture vessel per timepoint.\n\nIn the triple-species polymicrobial culture, there was no statistically significant difference in adhered PA or SA titres at the 24 h sampling point (both species achieving 106–107 CFU mL−1 at 24 h). We note that this is 10-fold lower than the PA and SA titres at the same time point in the corresponding biofilms from axenic cultures. Similarly, CA titres in the polymicrobial biofilms were also 10-fold lower than the CA titres in axenically-cultured biofilms. However, and whereas adhered CA titres in the polymicrobial biofilms remained unchanged over the following 72 h, PA titres displayed a marked increase (attaining ca. 108 CFU mL−1 by the 96 h time point) and SA titres displayed a marked decrease (falling to ca. 105 CFU mL−1) in adhered cell counts. We conclude that the population dynamics of each species can vary by orders of magnitude, depending on the nature of the biofilm substrata.\n\nIn parallel with the analysis of species titres in adhered biofilms, we also examined the corresponding titres of each species in the planktonic (i.e. non-attached) fraction (Figure 7 and underlying data (O'Brien et al., 2021)). Consistent with our previous findings (O'Brien and Welch, 2019a), steady-state microbial communities were established by 24 h incubation. There was no appreciable change in CFU mL−1 counts of any species cultured as part of an axenic or polymicrobial population across any point of sampling. Furthermore, there was no discernible difference in CFU mL−1 counts of the planktonic communities grown in the culture vessel flasks containing agar chunks (Figure 7A) or EVPL tissue sections (Figure 7B). These data indicate that the population dynamics of the biofilms is distinct from the population dynamics of the surrounding planktonic culture.\n\nP. aeruginosa PAO1 (PA), S. aureus 25923 (SA) and C. albicans SC5314 (CA) cell counts (expressed as CFU mL−1) in the planktonic fraction of single-species and polymicrobial cultures incubated in ASM in the continuous-flow model containing (A) agar chunks or (B) ex vivo porcine lung tissue sections as the solid substrata. Data represent the mean ± standard deviation of two technical replicates collected per timepoint from three independent biological experiments. P > 0.05 is considered as not significantly different (ns).\n\n\nDiscussion\n\nHere we report a simple method for the robust and reproducible growth of single- and multi-species biofilms on different substrata. Our model system has been designed to mimic the nutritional environment associated with CF airways. We previously showed (O'Brien and Welch, 2019a) that the model can maintain very stable steady-state polymicrobial populations of planktonic cells, even among species that would ordinarily outcompete one another during ex situ co-cultivation. In the current work, we extend these findings to show that polymicrobial biofilms can be similarly maintained. Remarkably, we also show that the biofilm composition is far more dynamic than that of the surrounding planktonic culture, and can vary substantially, even when the planktonic species profile is stable.\n\nA major benefit of our model over existing in vivo approaches is that is inexpensive to set up and requires no specialist equipment or training to operate. Indeed, the only perceived barrier preventing wider uptake of the model is in preparation of the ASM culture medium. Mitigating, this generally requires only a few minutes of effort each day (once the stock solutions have been made up). The primary benefit of the model is that very stable polymicrobial communities can be rapidly established and maintained for extended periods of time, and that the planktonic and biofilm modes of growth can be studied concurrently in a single experiment. This enables the facile longitudinal study of polymicrobial communities in vitro, enabling experimental analyses that were previously not possible due to population instability. As such, the model allows researchers to explore previously inaccessible problems pertaining to microbial ecology, gene expression and metabolism in polymicrobial communities. For example, we are currently exploiting the system to examine how mixed-species biofilms such as those found in the CF airways form over time. We are also using the model to examine how the inclusion of different species or treatment with antimicrobial compounds affect the stability and dynamics of polymicrobial biofilms longitudinally.\n\nAlongside the ethical benefits and accessibility of an in vitro model for microbial culture, the experimentally tuneable nature of our model system provides several inherent benefits over existing in vivo CF models (O'Brien and Welch, 2019b). ASM is a chemically-defined synthetic growth medium that has been formulated to closely mimic the nutritional composition of CF airway secretions (Kirchner et al., 2012; Palmer et al., 2005; Palmer et al., 2007; Turner et al., 2015; Cornforth et al., 2018). This allows subtle interspecies interactions to be quantified, in real-time, with great reproducibility. By contrast, the existing animal models display much greater variability, even within a single host species. Furthermore, culture conditions can be readily modified to enable the detailed study of how a particular variable (such as iron, for example) impinges upon the formation of polymicrobial biofilms (Mashburn et al., 2005; Palmer et al., 2005). This level of environmental control is near impossible to achieve with in vivo infection models. We also note that the experimentally facile nature of our system should permit the study of biofilm formation in other clinically-relevant polymicrobial infection scenarios such as non-CF bronchiectasis, asthma, or chronic obstructive pulmonary disorders (COPDs). This can be accomplished through the simple expedient of appropriately modifying the nutritional composition of the culture medium.\n\nThe key finding in this report is that mixed-species biofilms comprised of three very different CF-associated pathogens (a Gram-positive species (SA), a Gram-negative species (PA), and a fungal species (CA)) display distinctly different compositional dynamics compared with their planktonic counterparts. In particular, we note that the species profiles in polymicrobial biofilms are consistent with both antagonistic and synergistic interactions. For example, irrespective of the substrate, adhered CA titres were lower in the polymicrobial biofilms compared with CA titres in biofilms from axenic CA cultures.\n\nThe primary limitation of in vitro models of infection is a lack of spatial organisation and exclusion of host cells present when utilising in vivo infection models. We therefore attempted to redress this issue through the introduction of EVPL tissue sections as biofilm substrata. Porcine airways share a remarkable degree of structural homology with human airways (Judge et al., 2014; Rogers et al., 2008), and pig lungs are readily available from most butchers as a by-product of the food industry. Hence, the inclusion of ex vivo bronchiole tissue sections provide an ethically sustainable approach to introduce an element of host-microbe interaction and spatial organisation to the model (Harrington et al., 2020; Sweeney et al., 2021). Indeed, we note that growth on different solid substrata had a profound effect on the compositional dynamics of polymicrobial biofilms, especially with regards to S. aureus. SA is an effective early coloniser of the CF airways (Bogaert et al., 2004). When grown on EVPL sections, SA rapidly established a mono-species biofilm with significantly higher titres compared with the biofilm formed on agar chunks. This increased microbial attachment is consistent with the notion that SA adheres tightly to epithelial cells in the CF microenvironment (Josse et al., 2017), but is less effective at adhering to abiotic surfaces (agar chunks). However, and whereas SA titres on the agar chunk substrata were stable between the 24 h and 96 h sampling points, the SA titres on EVPL sections displayed a substantial decline over this period. By contrast, PA titres in the same biofilms increased, suggesting that the PA progressively displaces SA on the tissue surface. This reciprocal response (in terms of cell titres) by PA and SA was not observed when agar chunks were used as a substratum, suggesting that recognition of both airway epithelial cells and SA are required to drive the increased competitiveness by PA.\n\nDespite the introduction of some level of spatial organisation (in the form of EVPL tissue), the major physiological limitation of our model compared with in vivo systems is a lack of live host cells and the absence of any accompanying host-microbe interactions that may modulate microbial behaviour. Nevertheless, and through our comparison of EVPL tissue and agar chunks as biofilm substrata, we note two things. First, the diminution in SA titres in polymicrobial biofilms after 96 h growth on EVPL tissue – a diminution not seen on agar chunk substrata – suggests that microbial interaction with the host tissue may up-regulate the localised production of virulence factors and enhance interspecies competition (Döring et al., 2011; Malhotra et al., 2019). The implication of this is that the growth of EVPL-associated biofilms in our continuous-flow model may enable the capture specific temporally-sensitive interactions between the host tissue and infecting microbes. Second, agar is a more suitable substratum for examining the long-term, steady-state growth of polymicrobial biofilms.\n\nThe ability to maintain very stable (in terms of composition) long-term polymicrobial biofilms in our setup using agar chunks as a solid substratum can be exploited for several other applications. First and most obviously, the setup can be used to investigate the species specificity (for example) of novel antimicrobial or anti-biofilm agents. Using our system, it is possible to test both a sustained treatment regimen (achieved by adding the test compound(s) at the desired concentration to the media reservoir) or a short-term treatment regimen, via adding a compound directly to the culture vessel through the injection ports. The latter may loosely mimic the metabolism and excretion of antimicrobials in situ. This degree of temporal control is not possible using existing in vivo or in vitro models. Second, new species or strain variants can be introduced to pre-established polymicrobial biofilms (e.g. addition of PA to a PA-negative community), allowing facile examination of the impact made by new species or variants. This is directly analogous to the situation seen in CF, where the acquisition of new microbial species or variants can lead to major prognostic changes in the patient. It is important to note that whenever a new species is introduced, the medium flowrate (Q) may need to be re-optimized. If Q is too high, slower-growing organisms may be “washed out” and lost from the culture vessel. Conversely, if Q is too low, species will grow faster than the rate of media displacement, causing elements of the population to exhaust key nutrients and enter the stationary phase of growth.\n\n\nConclusions\n\nIn summary, we present here a simple system for the study of CF-associated polymicrobial biofilms. Importantly, we have shown that polymicrobial biofilms display distinctly different population dynamics compared with the surrounding planktonic cells. Moreover, the compositional dynamics of the biofilms depends very much on the substratum employed. To further extend the utility of our model, we are currently adapting it for use with a wider range of CF-associated pathogens and testing the possibility of inoculating the system directly with CF patient-derived sputum.\n\n\nData availability\n\nFigshare: Underlying data for ‘An in vitro model for the cultivation of polymicrobial biofilms under continuous-flow conditions’. https://doi.org/10.6084/m9.figshare.14974479.v1 (O'Brien et al., 2021).\n\nThis project contains the following underlying data:\n\n• EVPL Biofilms CFUs\n\n• EVPL Supernatant CFUs\n\n• Agar chunks Biofilm CFUs\n\n• Agar chunks Supernatant CFUs\n\n• Selective vs non-selective agar\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbberson CB, Stacy A, Fleming D, et al.: Co-infecting microorganisms dramatically alter pathogen gene essentiality during polymicrobial infection. Nat Microbiol. 2017; 2: 17079. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbberson CB, Whiteley M: The social life of microbes in chronic infection. Curr Opin Microbiol. 2020; 53: 44–50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJorth P, Ehsan Z, Rezayat A, et al.: Direct Lung Sampling Indicates That Established Pathogens Dominate Early Infections in Children with Cystic Fibrosis. Cell Rep. 2019; 27: 1190–1204.e3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJosse J, Laurent F, Diot A: Staphylococcal Adhesion and Host Cell Invasion: Fibronectin-Binding and Other Mechanisms. Front Microbiol. 2017; 8: 2433. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJudge EP, Hughes JM, Egan JJ, et al.: Anatomy and bronchoscopy of the porcine lung. A model for translational respiratory medicine. Am J Respir Cell Mol Biol. 2014; 51: 334–343. PubMed Abstract | Publisher Full Text\n\nKirchner S, Fothergill JL, Wright EA, et al.: Use of artificial sputum medium to test antibiotic efficacy against Pseudomonas aeruginosa in conditions more relevant to the cystic fibrosis lung. J Vis Exp. 2012: e3857. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKorgaonkar A, Trivedi U, Rumbaugh KP, et al.: Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection. Proc Natl Acad Sci U S A. 2013; 110: 1059–1064. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeekha S, Terrell CL, Edson RS: General principles of antimicrobial therapy. Mayo Clin Proc. 2011; 86: 156–167. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeenaars CH, De Vries RB, Heming A, et al.: Animal models for cystic fibrosis: A systematic search and mapping review of the literature - Part 1: genetic models. Lab Anim. 2020; 54: 330–340. PubMed Abstract | Publisher Full Text\n\nLopes SP, Azevedo NF, Pereira MO: Emergent bacteria in cystic fibrosis: in vitro biofilm formation and resilience under variable oxygen conditions. Biomed Res Int. 2014; 2014: 678301. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLopes SP, Azevedo NF, Pereira MO: Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress. Int J Med Microbiol. 2017; 307: 460–470. PubMed Abstract | Publisher Full Text\n\nLopes SP, Ceri H, Azevedo NF, et al.: Antibiotic resistance of mixed biofilms in cystic fibrosis: impact of emerging microorganisms on treatment of infection. Int J Antimicrob Agents. 2012; 40: 260–263. PubMed Abstract | Publisher Full Text\n\nLubamba B, Dhooghe B, Noel S, et al.: Cystic fibrosis: insight into CFTR pathophysiology and pharmacotherapy. Clin Biochem. 2012; 45: 1132–1144. PubMed Abstract | Publisher Full Text\n\nLyczak JB, Cannon CL, Pier GB: Lung infections associated with cystic fibrosis. Clin Microbiol Rev. 2002; 15: 194–222. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahboubi MA, Carmody LA, Foster BK, et al.: Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens. J Clin Microbiol. 2016; 54: 613–619. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMalhotra S, Hayes D, Wozniak DJ: Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface. Clin Microbiol Rev. 2019; 32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarkussen T, Marvig RL, Gómez-Lozano M, et al.: Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa. mBio. 2014; 5: e01592–e01514. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMashburn LM, Jett AM, Akins DR, et al.: Staphylococcus aureus serves as an iron source for Pseudomonas aeruginosa during in vivo coculture. J Bacteriol. 2005; 187: 554–566. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMastropaolo MD, Evans NP, Byrnes MK, et al.: Synergy in polymicrobial infections in a mouse model of type 2 diabetes. Infect Immun. 2005; 73: 6055–6063. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoser C, Van Gennip M, Bjarnsholt T, et al.: Novel experimental Pseudomonas aeruginosa lung infection model mimicking long-term host-pathogen interactions in cystic fibrosis. APMIS. 2009; 117: 95–107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMowat E, Paterson S, Fothergill JL, et al.: Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. Am J Respir Crit Care Med. 2011; 183: 1674–1679. PubMed Abstract | Publisher Full Text\n\nMunder A, Wölbeling F, Kerber-Momot T, et al.: Acute intratracheal Pseudomonas aeruginosa infection in cystic fibrosis mice is age-independent. Respir Res. 2011; 12: 148. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO’Brien S, Fothergill JL: The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung. FEMS Microbiol Lett. 2017; 364. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO'Brien TJ, Hassan MM, Harrison F, et al.: An in vitro model for the cultivation of polymicrobial biofilms under continuous-flow conditions. Figshare. 2021. Publisher Full Text\n\nO'Brien TJ, Welch M: A Continuous-Flow Model for in vitro Cultivation of Mixed Microbial Populations Associated with Cystic Fibrosis Airway Infections. Front Microbiol. 2019a; 10: 2713. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO'Brien TJ, Welch M: Recapitulation of polymicrobial communities associated with cystic fibrosis airway infections: a perspective. Future Microbiol. 2019b; 14: 1437–1450. PubMed Abstract | Publisher Full Text\n\nPalmer KL, Aye LM, Whiteley M: Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J Bacteriol. 2007; 189: 8079–8087. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPalmer KL, Mashburn LM, Singh PK, et al.: Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology. J Bacteriol. 2005; 187: 5267–5277. PubMed Abstract | Publisher Full Text | Free Full Text\n\nParsek MRASPK: Bacterial Biofilms: An Emerging Link to Disease Pathogenesis. Annu Rev Microbiol. 2003; 57: 677–701. PubMed Abstract | Publisher Full Text\n\nPeters BM, Jabra-Rizk MA, O'May GA, et al.: Polymicrobial interactions: impact on pathogenesis and human disease. Clin Microbiol Rev. 2012; 25: 193–213. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuinn RA, Whiteson K, Lim YW, et al.: A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. ISME J. 2015; 9: 1052. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajan S, Saiman L: Pulmonary infections in patients with cystic fibrosis. Semin Respir Infect. 2002; 17: 47–56. PubMed Abstract | Publisher Full Text\n\nRogers CS, Abraham WM, Brogden KA, et al.: The porcine lung as a potential model for cystic fibrosis. Am J Physiol Lung Cell Mol Physiol. 2008; 295: L240–L263. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRogers GB, Stressmann FA, Walker AW, et al.: Lung infections in cystic fibrosis: deriving clinical insight from microbial complexity. Expert Rev Mol Diagn. 2010; 10: 187–196. PubMed Abstract | Publisher Full Text\n\nSchick A, Kassen R: Rapid diversification of Pseudomonas aeruginosa in cystic fibrosis lung-like conditions. Proc Natl Acad Sci U S A. 2018; 115: 10714–10719. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSibley CD, Rabin H, Surette MG: Cystic fibrosis: a polymicrobial infectious disease. Future Microbiol. 2006; 1: 53–61. PubMed Abstract | Publisher Full Text\n\nSibley CD, Surette MG: The polymicrobial nature of airway infections in cystic fibrosis: Cangene Gold Medal Lecture. Can J Microbiol. 2011; 57: 69–77. PubMed Abstract | Publisher Full Text\n\nSousa AM, Monteiro R, Pereira MO: Unveiling the early events of Pseudomonas aeruginosa adaptation in cystic fibrosis airway environment using a long-term in vitro maintenance. Int J Med Microbiol. 2018; 308: 1053–1064. PubMed Abstract | Publisher Full Text\n\nSriramulu DD, Lünsdorf H, Lam JS, et al.: Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J Med Microbiol. 2005; 54: 667–676. PubMed Abstract | Publisher Full Text\n\nSun X, Sui H, Fisher JT, et al.: Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis. J Clin Invest. 2010; 120: 3149–3160. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSun X, Yi Y, Yan Z, et al.: In utero and postnatal VX-770 administration rescues multiorgan disease in a ferret model of cystic fibrosis. Sci Transl Med. 2019; 11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSweeney E, Harrington NE, Harley Henriques AG, et al.: An ex vivo cystic fibrosis model recapitulates key clinical aspects of chronic Staphylococcus aureus infection. Microbiology (Reading). 2021; 167. PubMed Abstract | Publisher Full Text\n\nThomas P, Sekhar AC, Upreti R, et al.: Optimization of single plate-serial dilution spotting (SP-SDS) with sample anchoring as an assured method for bacterial and yeast cfu enumeration and single colony isolation from diverse samples. Biotechnol Rep (Amst). 2015; 8: 45–55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTreangen TJ, Maybank RA, Enke S, et al.: Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome Announc. 2014; 2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTurner KH, Wessel AK, Palmer GC, et al.: Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum. Proc Natl Acad Sci U S A. 2015; 112: 4110–4115. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVan Heeckeren AM, Schluchter MD, Xue W, et al.: Response to acute lung infection with mucoid Pseudomonas aeruginosa in cystic fibrosis mice. Am J Respir Crit Care Med. 2006; 173: 288–296. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWeimer KE, Armbruster CE, Juneau RA, et al.: Coinfection with Haemophilus influenzae promotes pneumococcal biofilm formation during experimental otitis media and impedes the progression of pneumococcal disease. J Infect Dis. 2010; 202: 1068–1075. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWinstanley C, O'Brien S, Brockhurst MA: Pseudomonas aeruginosa Evolutionary Adaptation and Diversification in Cystic Fibrosis Chronic Lung Infections. Trends Microbiol. 2016; 24: 327–337. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao J, Schloss PD, Kalikin LM, et al.: Decade-long bacterial community dynamics in cystic fibrosis airways. Proc Natl Acad Sci U S A. 2012; 109: 5809–5814. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "91897",
"date": "20 Aug 2021",
"name": "Daniel R. Neill",
"expertise": [
"Reviewer Expertise Referee suggested by the NC3Rs for their scientific expertise and experience in assessing 3Rs impact. My research is focussed on bacterial infections of the respiratory tract",
"including those of the CF lung. I also have interests in development of in vitro and in vivo infection models that reflect respiratory tract environments."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nO’Brien and colleagues describe a novel model system for the study of polymicrobial biofilms, under conditions designed to reflect those of the cystic fibrosis airways. The authors have built on their previous study that described a continuous-flow model for cultivation of mixed microbial populations. The neat addition, described here, is a metal gauze cage that can be loaded with substrata on which microbial biofilm communities can form. In the examples presented, cubes of agar or ex vivo porcine bronchioles are used. Culture in artificial sputum media provides environmental conditions reflective of the CF airways.\nThis is a very well presented manuscript, with a carefully considered introduction and sufficient methodological detail to enable other users to establish the model in their own labs. The discussion describes further applications for the model that all appear realistic. I agree with the authors’ assertion that this model has potential to reduce or replace animal use for study of polymicrobial biofilms in CF and related conditions, albeit dependent upon the experimental question under consideration.\nThis is primarily a methods paper, so the experimental findings are understandably limited. Nonetheless, I thought the observation of steady planktonic microbial density but fluctuating biofilm densities/composition was an interesting one. There is clear potential for further informative science to be undertaken using this model system.\nI have no major criticisms of the work. I thought the study had been well planned, carefully executed and nicely presented. I have no doubt that others with interests in polymicrobial infections of the CF lung will find the model useful, and I can see it being adapted for study of infection in other chronic lung conditions, as the authors suggest.\nBelow, I include a few minor comments that the authors may wish to consider:\nThe introduction mentions the limits of in vitro systems as being the lack of host cells and an immune system. I would add that most fail to capture the spatial heterogeneity of the respiratory tract. Chemical, nutritional, and microbial conditions differ between anatomical sites within the upper and lower airways and between different foci of infection within lungs. These differences may influence the dynamics of infection, the balance of competing pathogens in the airway space and may also contribute to treatment failure.\n\nThe introduction states that “it should be noted that impaired immune clearance of microbes is an inherent feature of CF, which somewhat mitigates the lack of a functional immune system in in vitro models.” I take the authors point on this, but it is an oversimplification. Inefficient immune clearance is not the same as having no immune response at all. There is still potential for interactions between soluble and cellular immune defences and bacterial pathogens to influence microbial phenotypes. The authors do partially address this point in their discussion, but I think this section of the intro is slightly misleading.\n\nFor the presentation of results, I wondered whether CFU/cm2 of substratum might be more informative than per ml? If this is too challenging to quantify, then per gram of agar/EVPL would at least account for differences in preparation between individual cubes.\n\nIn the section on the microbial densities within biofilm, I was interested in whether there was much difference between biological replicates (i.e. between cubes). Does PA outcompete SA every time or does it depend on which gets a foothold first? Do you ever find cubes that are completely dominated by a single pathogen? This information is available within the source data file, but would be easier to digest in a graph presenting the biological replicates for each species side by side.\n\nThe authors postulated explanations for the relative success of PA vs SA on EVPL are intriguing, but this section should acknowledge that only one strain of each species has been tested. PAO1 is fast growing compared to many PA isolates from CF and this may contribute to the observed outcomes.\n\nAlthough clearly beyond the scope of this manuscript, I was interested as to how the authors think the model may need to be adapted to better reflect the environmental conditions of the CF lung now that patients are moving over to CFTR modulator therapies?\nAre a suitable application and appropriate end-users identified? Yes\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\nAre the 3Rs implications of the work described accurately? 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": []
},
{
"id": "91903",
"date": "14 Sep 2021",
"name": "Lindsay R. Kalan",
"expertise": [
"Reviewer Expertise Polymicrobial interactions",
"biofilm",
"chronic infection"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by O'brien et al. describes the development of an in vitro model for the study of polymicrobial biofilm, specifically focused on the CF lung environment. This work is timely as the importance of polymicrobial colonization, biofilm formation, and infection is increasingly recognized as important towards disease outcome. Here, the authors use artificial sputum in a continuous flow culture vessel to cultivate biofilms. They examined biofilm formation using two different substrates, agar or ex vivo porcine lung tissues. This allows the user to evaluate both biofilm growth on the substrate and measure planktonic cell populations in the surrounding media.\nThe manuscript is well written, and the photographs of the apparatus are helpful to the reader who wishes to set this up in their own laboratory. The protocol provided is detailed and thorough although the production of ASM media seems cumbersome with some steps requiring first hand know-how that may introduce variability. For example, the filtration step is stated to take up to 2-3 days with the membrane being rinsed periodically, it is unclear how this might introduce contamination or impact the final media composition.\nI have no major comments, minor comments follow:\nThe protocol states that each species in inoculated at an OD600 of 0.05. This could vary in the final cfu/mL depending on the species, especially fungi. It may be more informative to state the desired final inoculum in cfu/mL or total CFUs.\n\nThe substrates are washed three times after incubation and before final quantification of biofilm. I wonder if these washes are ever quantified. This may be important to determine if the wash step disrupts significant amounts of biofilm for organisms that are loosely adherent or reaching maturity and may dislodge due to sheer pressure. This could possibly be the case with S. aureus.\n\nFigure 4 is not overly informative showing CFUs of overnight cultures. However, if the main point is that the selective media does not impact growth and quantification, the legend should state the selective media used for each species including any antibiotics/antifungals in the media.\n\nThe authors state in the discussion that the model is amenable to longitudinal studies of polymicrobial biofilm for extended periods of time. However, this study only went out to 96 hrs. It is not clear how long or how stable these communities may be over longer periods. If the model allows for study over several days and even weeks this is very powerful. This information must be determined for each community, however the authors could address their experience with the three-member model community reported in this manuscript in the discussion.\nAre a suitable application and appropriate end-users identified?\nYes\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\nAre the 3Rs implications of the work described accurately?\nYes\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/10-801
|
https://f1000research.com/articles/10-799/v1
|
13 Aug 21
|
{
"type": "Research Article",
"title": "Empowering young immigrant girls in Canada through the ‘Girls’ Voices’ Curriculum: A qualitative study",
"authors": [
"Salima Meherali",
"Mehnaz Rehmani",
"Arzoo Rafiq",
"Neelam Punjani",
"Helen Vallianatos",
"Claudia Romeu",
"Mehnaz Rehmani",
"Arzoo Rafiq",
"Neelam Punjani",
"Helen Vallianatos",
"Claudia Romeu"
],
"abstract": "Background: Gender inequality is a global issue. In Canada, 70% of women experience some form of inequality in their lifetime. Immigrant adolescents in Canada make up a substantial proportion of newcomers, and immigrant girls face the threat of subjugation and oppression, which has a significant impact on their health, development, and economic outcomes as well as gender inequality. Research on girls’ empowerment and resilience-building programs and interventions is virtually nonexistent. In this project, we implemented the ‘Girls’ Voices’ Curriculum. The aim of this project was to engage and empower South Asian (SA) immigrant adolescent girls and to promote gender equality in Canada. Methods: This study utilized a qualitative descriptive design. Pre- and post-curriculum implementation focus group discussions were conducted. Results: A total of 16 adolescent girls ranging from 11 to 18 years of age participated in this study. The participants described challenges many young girls face in relation to gender inequality such as gender discrimination, gendered stereotyping, barriers to education, etc. The ‘Girls’ Voices’ Curriculum allowed participants to highlight and reflect on the various problems faced by SA immigrant adolescents in their communities. The participants learned to examine these challenges through a variety of engaging activities to identify their root cause, effects and propose solutions to bring long-lasting change. The curriculum equipped them with useful tools such as decision-makers maps and advocacy skills to educate decision-makers by creating and delivering powerful messages influenced by personal stories and evidence-based literature. Conclusion: The study provided significant insight into understanding the diverse challenges encountered by SA immigrant adolescent girls in Canada and linking them to the effectiveness of the ‘Girls’ Voices’ Curriculum. The girl-focused development programs that emphasize developing self-confidence, communication skills, problem-solving skills, and decision making are effective in empowering the socially deprived adolescent girls locally and in the global context.",
"keywords": [
"Adolescents",
"Girls",
"Empowerment",
"Immigration",
"Girl's Voices curriculum"
],
"content": "Introduction\n\nAdolescent girls make up 16% of the world’s population - equivalent to one in six people.1 Adolescence (aged 10-19 years)2 is a foundational phase when the physical, emotional, cognitive, and social capabilities essential for adult life are established; they form lifelong health behaviors, and future health trajectories take shape. Canada is among the most ethnically diverse regions in the world. Immigrant adolescents make up a substantial proportion of newcomers to Canada; approximately 34% are under 25 years.3 In Canada, a large part of adolescent girls’ development is impacted by migration, but they are a too often overlooked part of the migration phenomenon. Immigrant girls face potential subjugation and oppression, which has a significant impact on their physical and psychological health and development, economic outcomes, and gender inequality. Accounts of the experiences of immigrant adolescent girls show that, despite having more educational and career opportunities than ever, many girls and young women still face sexual violence, harassment, low self-esteem, negative body image, discrimination/exclusion, and so on.4 A nationwide survey reported that immigrant girls, specifically Asian girls, in Canada feel pressure from society to conform to unrealistic expectations of femininity, not only in terms of their appearance but also in terms of their behaviors or which interests they should pursue.5 In many South Asian (SA) cultures, patriarchal values and social norms maintain gender inequities and stereotyping. These disparities deprive young girls of their privileges, autonomy, and decision making8–10 and therefore negatively impact their prospects in life. Despite the large number of immigrant adolescent girls in Canada, research into empowerment and resilience-building programs and interventions are nearly nonexistent.\n\nTo support and enhance gender equality among immigrant girls and young women in Canada there is a need to design and implement strategies that tackle the root causes of gender inequality and reshape unequal power relations. At the Women Deliver Conference 2019, RISE UP and GIRL UP launched the ‘Girls’ Voices’ Curriculum.11 RISE UP is a global movement that activates girls and women to transform their lives, families, and communities by investing in local solutions, strengthening leadership, and building movements. Since 2009, RISE UP has already built a powerful network of over 500 youth leaders and has implemented over 100 laws and sexual and reproductive health (SRH) policies that have impacted 115 million girls and women in Africa, Latin America, South Asia, and the United States. The United Nations Foundation founded GIRL UP in 2010 - a global leadership-development initiative that positions girls to become leaders in the movement for gender equality and works with a global community of partners to achieve gender equality worldwide. RISE UP collaborated with GIRL UP to develop a 10-week curriculum to activate disadvantaged and underprivileged girls in communities worldwide. This curriculum is an important tool for girl-led advocacy that amplifies girls’ voices and enables them to lead change in their communities to build a stronger movement for gender equality. Girl leaders and their allies will use this curriculum to launch girl-centered training programs, establish Girl Up clubs, and bring girls together to create change. This curriculum will not only enable girls to raise their voices for change, but also support adult allies in key partner organizations to create safe spaces for girls to implement their advocacy strategies, help them understand relevant laws and policies related to SRHR, and support them through the advocacy implementation process to improve their SRH and overall well-being. The curriculum can be used as a guide to identify the issues that most deeply affect girls in any community and to develop local strategies to empower girls to raise their voices, identify and develop solutions to effectively approach decision-makers in their communities, and make tangible change. The curriculum is culturally sensitive and is designed for implementation in low-resource settings. Moreover, the curriculum has also been designed to accommodate girls with limited literacy i.e. reading at a fifth-grade reading level, and provides the evaluation tools so the curriculum can be completed in low literacy settings. The main goal of this curriculum is to engage girls, provide a necessary safe space to talk about the issues they face, and work together to develop girl-centered and girl-led advocacy strategies to improve their lives and advance gender equality around the world.11 The specific objectives of this research were:\n\n1. To investigate the impact of Girl’s Voices Curriculum on immigrant adolescent girls’ lives.\n\n2. To explore and identify barriers and challenges in curriculum implementation.\n\n3. To explore the cultural sensitivity of the curriculum.\n\n\nMethods\n\nWe utilized the ‘Girls’ Voices’ Curriculum as a tool to empower immigrant SA adolescent girls to raise their voices against the issues related to gender inequality and become gender equality advocates, activists, and change agents. Pre-and-post-focus group discussions (FGDs) were used to identify the impact of the ‘Girl’s Voices’ Curriculum and areas for improvement to implement the curriculum at a national level.\n\nThe curriculum was divided into four sessions, each four hours long, and delivered over five weeks. Due to COVID-19 restrictions, we conducted these sessions in an open outdoor space from April 24 – May 22, 2021, using all public health measures to prevent the spread of the virus. The curriculum utilized an experiential learning approach by connecting girls to increase knowledge of the new concepts presented in each session. The curriculum was facilitated by female researchers/facilitators (SM & MR). The researchers had no prior relationship with study participants. The participants were informed about the study purpose with a study information letter along with a consent form. No one except the researchers and participants were present during the curriculum implementation and data collection. The facilitators provided a judgment-free zone and a safe space for participants to freely share their personal stories and work effectively within groups by creating group agreements at the beginning of the course. Furthermore, they utilized several interactive, reflective and artistic pedagogical strategies in delivering the curriculum. The activities included role-play, games, writing personal stories and elevator pitches, group discussions, drawing timeline infographics, problem trees, and mapping exercises.11 The full curriculum is available here: https://riseuptogether.org/girls-voices-curriculum-2019/.\n\nWorking with Edmonton’s Indo Canadian Women Association as our major community partner, we recruited 16 SA immigrant adolescent girls. Purposive and convenience sampling approaches were used. Due to COVID-19 restrictions, we recruited 16 participants to ensure health and safety measures were adhered to. Recruitment posters were posted on the Indo Canadian Women Association website and social media platforms. Participants who were interested contacted the research assistant. The first author (SM) followed up with interested participants by telephone. The first and second authors conducted FGDs before and after the curriculum implementation that ranged in length from 40-50 minutes. FGDs were digitally recorded and transcribed verbatim. The participants for FGDs were divided into two groups (11–14 years) and (15–18 years) to ensure that our data captured the voices of girls and women of various ages. At the beginning of pre-FGD, we asked the girls to create visual timelines to help them to better understand their important life events and experiences and how these impacted their health and development.13 Timelines are a graphic, arts-based data-collection strategy that is particularly useful with vulnerable groups such as young girls.12 In participating, the girls creatively reflected on their experiences, which enhanced their trust, ensure meaningful, accountable engagement,12 and foster discussion in FGDs. A semi-structured interview guide was used to identify the unique challenges that SA immigrant girls face before and after the migration (Extended data: FGD Guide).13\n\nWe made the preliminary results of the study available to participants for their validation.\n\nThe data obtained from the demographic survey form were analyzed in Excel to calculate the focus group sample’s descriptive statistics. The first and third authors (SM, AR) coded the data. All quotes were encoded using the qualitative software program NVIVO® version 12 (QDA Miner Lite is a free alternative qualitative analysis software). An inductive thematic approach was used to examine the data (quotes). Recurrent and common concepts were then systematically identified across the data set and grouped through a coding system (content analysis).14 Similar codes were grouped into general concepts classifying them into subcategories and main categories. We maintained an audit trail of our research process to enhance the dependability and validity of our findings. Reporting of this study followed the Consolidated criteria for reporting qualitative research (COREQ) checklist.13\n\nThis study utilized qualitative description.15,16 Pre- and post-curriculum implementation FGDs were conducted. Ethical approval for this study was obtained from the University of Alberta Health Research Ethics Review Board (Pro00097432). Researchers obtained written informed consent for data collection and publication from all participants in this study. A study information letter was provided to all study participants and their parents (Appendix A & B).13 Parental consent was obtained for participants under 16 years of age. All the participants above 16 years signed the consent form.\n\n\nResults\n\nA demographic survey form was used to collect participants’ demographic information (Table 1). A total of 16 adolescent girls ranged from 11 to 18 years of age, with an average age of 15 years, participated in this study. The majority (eight) of participants were born in Pakistan; five were from India, two in Afghanistan, and one in Bangladesh. Besides this, 56% of participants have been in Canada for more than five years; in comparison, 44% of participants have spent 3-5 years, and 18% spent 1-2 years in Canada. Most (n = 10) participants were studying in junior high school, specifically, five in both grade 8 and 9; two participants were in grade 7, three participants were in grade 11, one was in a post-secondary institution. The demographic characteristics of participants are presented in Table 1.\n\nDuring the FGDs and in participants’ individualized timeline infographics, various challenges were highlighted that are commonly faced by SA immigrant adolescent girls within diverse social determinants of health. The analysis revealed four themes: gender inequality, barriers to education, the impact of migration on psychosocial well-being, and the value of social support networks.\n\nTheme 1: Gender inequality\n\nThis theme represents the participants’ experiences of gender inequality within their communities and the larger social context. Mostly, the participants described gender inequality as the unequal treatment of girls and boys or discrimination based on gender, which was evident in one participant’s statement: “We should treat all the genders equally and not put people down for what gender they are”.\n\nGendered stereotyping: The participant’s responses portrayed a common theme of women’s perceived inferiority, subordinate, and weak personality and highlighted gendered stereotypes. The participants reflected on how everyone is conditioned by gender stereotypes, one participant stating:\n\n“I think it’s always assumed that like we’re [girls and women] weak and that we can’t do like things that men would do”.\n\nAnother participant, while sharing stereotyping encountered in school, said:\n\n“Like that we can’t actually do it and that we’re weak and that we’re in this class for like no reason. But like in all honesty, we could probably just do it just as well as them”.\n\nFurthermore, participants were also able to link these gender stereotypes to predefined gender roles and showed understanding of societal segregation of roles based on gender:\n\n“Sometimes how girls are expected to do certain things like stay home and cook. But like in reality they want to … they want to work. They want to go out. But like people are like, ‘No, you [girl] should stay home and cook and stuff’”.\n\nOther participants shared their school experience, stating:\n\n“Like in school a lot of boys would be like, ‘You’re [girls] supposed to be working in like the kitchen’”.\n\n“… sometimes in school, if like the teacher needs any helpers for … lifting chairs or tables … if a girl raises her hand she won’t pick them; she’ll go for the guys because they’re stronger and they can lift the tables better”.\n\nThese responses identify gender stereotypes and stereotyping against females as a significant cause of SA immigrant female adolescents’ challenges compared to males.\n\nDiscrimination: The adolescent girls shared many observations and personal incidents of discrimination and segregation, humiliation, and a lack of freedom of expression that is deeply rooted in patriarchal values and social norms pervasive in the South-Asian countries. Participants drew attention towards gendered occupational segregation based on the social stereotypes against females and its strong influence on their career choices and other adolescents. One participant described this occupational segregation as:\n\n“… like men are given more like, I guess, heavy lifting jobs and like women are doing like more academic like work, basically”.\n\nThe frustration due to this segregation was expressed as:\n\n“So like sometimes we’re presented opportunities, but like since there’s so many stigmas around something, it just puts us down and like we don’t take advantage of the opportunities. Like in careers, some careers are just assumed that they’re made for men, but like when like a female gets an opportunity to like do that career, there’s like the stigma around it just puts us down and we don’t feel like doing it anymore”.\n\nDuring the discussions, participants also highlighted the most common experiences of gender discrimination faced by females during their education and employment. A participant pointed out a gender bias in the distribution of education and shared that:\n\n“I was put in an all-girls school in Panama, and I couldn’t do a lot of the things I wanted to. So that was kind of discouraging”.\n\nSimilarly, the participants also discussed the issue of the wage gap, which was vocalized by one participant:\n\n“And things like employment, both like men and women should be paid equally, especially if like the woman is doing the higher like skilled job”.\n\nFurther insight into the intensity of discrimination was developed as participants highlighted the burning issues of humiliation and the lack of freedom of expression. Many participants raised these issues during the discussion and represented them by a falling drop in their personalized timeline infographic. The humiliation and their right to freedom of expression were compromised within the family system and at school. A participant shared an incident when she was humiliated and bullied by her classmates:\n\n“People tell me that I’m not good at soccer when I joined a sports program at our school, and they said that I wasn’t good because I tried out playing in the field and people made fun of me and mocked me for it”.\n\nAnother participant expressed disappointment with the lack of freedom of choice:\n\n“They have like the ideals that women should be home by ten. Because if they’re out later, something wrong’s going to happen. And that before they leave they should finish their chores. But when it’s guys, they can come and go as they please, and that’s not equality”.\n\nMany participants commented on not being allowed to wear their choice of clothing, and if they did, they faced criticism from their families and communities:\n\n“Um, like when you wear tank tops in school, the teachers are like, ‘It’s distracting’, and stuff like that. But like you should teach guys to not be distracted with that”.\n\nIn summary, the majority of the participants highlighted that as a SA immigrant girl they face gender inequality and stereotyping at their home and in the community.\n\nTheme 2: Barriers to education\n\nThis theme represents the barriers to professional and health education faced by immigrant adolescent females from a SA background. Many participants identified that their access to academic and professional education and their future career choices were mainly influenced and controlled by the gender stereotypes and values of the patriarchal society of their families and immediate community. Participants admitted that societal values responsible for defining gender roles that relegate women primarily to domestic worker and childcare, have hindered access to basic academic education. A participant reflected during the discussion on how she had to fulfill more household responsibilities in order to educate herself compared to her male siblings:\n\n“I think we are empowered to get our education, but with that there’s like things – there’s challenges that we face that men don’t. Like for example, if I have homework and my brother has homework, I’ll have to do – like I’ll have to wash the dishes and he can – like my parents will say, ‘Yeah, you can just go do your homework’. But I’ll be like in charge of doing the dishes, even though we both have homework. So like I’ll have more like challenges to face to get my education than he does”.\n\nDuring the discussion, it was also highlighted that, as a result of gendered occupational segregation, participants were discouraged to choose and acquire education in male-dominated professions despite their passions:\n\n“Um, like I feel like engineering, maybe, because it’s like people just assume it’s like a male job because it’s like a lot of like handwork, right? So, like, like assume that females can’t do engineering, but like in reality we can do anything we want, basically”.\n\nNot only this, one of the participants illustrated how occupational segregation was also evident in the extracurricular clubs offered by schools regardless of expressing their interests:\n\n“One thing I think more girls should have access to is like coding and robotics clubs or camps, because I’ve been trying to get into a few, but they only allow boys to be in them. So it’s – it’s kind of hard for me to find a good club to join”.\n\nTheme 3: Impact of migration on psychosocial well-being\n\nMigrating to a new country raises issues regarding adolescents’ acculturation, including adaptation to social values, language, social integration, and identity development in a new socio-cultural environment. Some participants in this study recognized the adaptational stress in response to migrating to a new country and adjusting to the physical and social environment. Participants displayed the anxiety of migration, starting a new school, and learning a new language (French) by drawing a drop on their personalized timeline at that point. This also shows that immigrant adolescents’ psychosocial well-being is largely affected by their living conditions, educational environment, and the capability to develop new support networks.\n\nTheme 4: Value of social support networks\n\nAdolescence is a period of significant transitional changes, including hormonal development, new independence in decision making, and expanding their social network beyond family with mainly friends and school peers. In this study, many participants positively exhibited a new friend circle in their personal timeline. On the other hand, participants who were struggling to socialize and make friends portrayed feelings of emptiness by a steep drop in their timeline infographic (Extended data: Sample Timelines).13 Typically, females possess a caring role and are more dependent on their family and friends, making them vulnerable to relational stress.17 The group’s vulnerability for relational stress was evident as many participants pointed negatively to losing their immediate family members and good friends due to migration to a new country.\n\nTheme 1: Enhanced knowledge and awareness about girls’ rights\n\nThe curriculum facilitated participants to highlight and reflect on the several problems faced by immigrant SA adolescents in their communities. Through the problem tree activity, participants learned to examine these challenges and identify its root cause, effects and propose solutions to bring long-lasting change. The participants stated a problem tree method, a new and beneficial strategy to identify the relevant resolutions by directly inspecting the root causes. The program also provided girls with an opportunity to enhance their awareness of culturally sensitive issues such as sexual harassment, which are rarely debated and discussed within families and communities due to associated taboos. A participant verbalized the significance of this discussion:\n\n“And it [discussion] also like made them aware of what it [sexual harassment] is, just so they can try to avoid the situation, or if it does happen to them, they know that it’s okay to go to someone and talk about it”.\n\nFurthermore, the participants welcomed group discussions about various challenges faced by SA immigrant adolescents, particularly regarding sensitive issues such as sexual and reproductive health and rights. Learning about the different forms of issues, causes, and actions plays a critical role in preventing and efficiently dealing with these challenges. Participants had to the opportunity to develop awareness about girls’ empowerment and learn about strategies for exercising it within their family units and communities. The curriculum introduces and facilitates the awareness and development of effective communication and presentation skills, useful for program participants in the advocacy of their rights. Initiating dialogue with decision-makers was considered to be extremely challenging by participants in the pre-program survey. Similarly, most participants expressed their desire to learn effective ways to communicate, emphasizing voice training and body language to improve confidence while having a conversation and educating the decision-makers. The stages involved in the advocacy planning process, which includes delegating the various task functions and roles, identifying and arranging meetings with the primary decision-makers, planning and strategizing the activities for educating the decision-makers, effectively communicating their advocacy message, and ensuring it’s understood, were entirely new skills to learn and practice.\n\nParticipants recognized the significance of formulating and delivering effective and robust advocacy messages while putting forward their opinions and demands for serious consideration. A participant expressed this during the post-FGD as:\n\n“I learned that when you’re like discussing a situation with a grown, like the mayor or government, it [message] should be like short and simple, so they can understand it”.\n\nThe participants’ attempted many questions correctly in the post-assessment which was not attempted and left unanswered in the pre-assessment [10, page 104-107]. This highlights that the Girl’s Voices curriculum positively developed participants’ knowledge about the elements of a compelling advocacy message.\n\nThe curriculum positively shaped participants’ perspectives about women’s empowerment from the early years of their lives. The participants demonstrated that young adolescents also face similar challenges and are more vulnerable to gender violence due to a lack of awareness of their rights, confidence, and the skills to raise their voice against gender inequality. The Girl’s Voices curriculum empowerment strategy provided an opportunity and a platform for all ages of adolescents to learn from one another’s experiences, build resilience, new friendships, and expand their social network.\n\nTheme 2: Change in attitude and practice\n\nThe curriculum helped the program participants develop agency and gain practice as a catalyst change agent against gender inequality and its detrimental effects on adolescents within their communities. Participants were equipped with useful tools like decision-makers maps and advocacy skills to educate decision-makers by creating and delivering powerful messages influenced by personal stories and evidence-based literature. A participant stated:\n\n“Actually [Girls’ Voice Curriculum] help promote the change. And I feel like that was really helpful for like everyone because at one point or another we’re probably going to need those skills”.\n\nThe curriculum made them reflect on the significance of role modeling for other adolescent and younger girls in their communities and provoke a desire to raise awareness about girls’ empowerment, be role models, and guide them to supporting organizations and safe spaces dedicated to adolescent girls when needed. A participant expressed the passion of girls empowering other girls:\n\n“I would tell them about like women empowerment, and that there are like things that you can do to get help if you’re in a certain situation. If you ever feel like you need to talk to another girl like there’s like a safe space”.\n\nThe program participants acquired problem-solving skills through the problem tree strategy and learned to set realistic personal life goals by analyzing the meaning of different life events and how they have impacted the participants’ lives. One participant explained the use of these skills in their daily living challenges and said:\n\n“I feel like the [problem] tree that we made has like helped me realize that like there’s an actual physical way to solve a problem. If I had a problem in my life, or even just in school, I could make something similar to the [problem] tree and try solving the problem. And I would know exactly what to do”.\n\nThe significant impact of the Girls’ Voice Curriculum in empowering girls was summarized by one participant as:\n\n“I think the most I took away from it [program] was … how to advocate for ourselves, and if there’s like something [negative] going on, and like we want to change, how we would step up [initiate]”.\n\nTheme 3: Curriculum evaluation and cultural sensitivity\n\nThe researchers comprehensively evaluated the program’s effectiveness through a post-program FGDs and a program evaluation form13 to better understand its role in developing and enhancing girl’s empowerment and the changes needed for its further implementation at a national level. First FGD was conducted in person and then participants completed the program evaluation form. Participants appreciated that the curriculum is easy to understand and useful for all ages of adolescents. All participants enjoyed the problem tree activity and felt confident and accomplished enough to develop and suggest solutions by analyzing the root cause and effects of a problem. Participants were very confident in sharing personal stories and experiences of dealing with the various challenges adolescents face, the engaging activities decreased their fear of society and boosted their confidence in promoted empowerment and has given them the opportunity to learn how to elevate their voices for their rights and to support their actions and decision-making. The participants enjoyed the presentation and elevator speech activities involved in the program and these reduced their anxiety around public speaking and encouraged them to advocate for themselves and other adolescents confidently. The majority of participants (n = 13) confirmed in the FGDs that the topics included in the Girls Voice Curriculum and the pedagogy used to deliver the program were culturally sensitive. The group dynamics were set on respect, freedom of speech, and confidentiality. Participants valued the group discussions on sensitive issues such as sexual harassment because it is essential to be aware of these issues as they are not discussed within families or communities, and adolescents encounter them daily. Overall, participants appreciated the facilitation of life skills including communication, presentation, reflection, advocacy, and debriefing as valuable for becoming empowered adolescents.\n\n\nDiscussion\n\nThe study provided significant insight into understanding the diverse challenges encountered by immigrant SA adolescent girls in Canada and how effective the ‘Girls’ Voices’ Curriculum is in creating change. The study highlighted the main issues around gender inequality resulting from stereotypes that create various pronounced forms of discrimination. Children are socialized from birth to believe that girls and boys have different gender roles in society, which manifests gender inequality in communities. Social norms are defined as the shared expectations or informal set of rules that explain how one should behave within the society.18,19 The social norms based on cultural and religious values often define gender roles in many SA communities.20,21 For example, adolescent girls from Pakistan highlighted that in Islam both men and women are encouraged to seek knowledge. However, the cultural and religious practices intended to maintain women’s domestic role in Islam is often emphasized in Muslim societies and can lead to gender discrimination around seeking higher education. Pakistani girls who participated in the project stated that even though they are not restricted in pursuing higher education, their access to academic and professional education and their future career choices were influenced and controlled by the religious and cultural values of patriarchal society, their families, and immediate community.\n\nAdolescence is a crucial stage of human development due to the rapid physical, cognitive and psychosocial growth that takes place. The development at this stage impacts thinking, decision-making, and interaction with the world.22 During this phase, many adolescent girls are denied access to the resources and skills needed to protect themselves and ensure their bright futures.23 Gender stereotypes and discrimination limit adolescent girls’ capacity to develop their abilities, pursue careers, and make decisions about their lives.18 The result can be a violation of human rights and fundamental freedom.7 The major findings of this study were how the traditional attitudes and gender stereotypes perpetuate widespread practice involving gender-based violence, discrimination, sexual harassment, and humiliation.24 In this study, the SA immigrant adolescent girls in Canada gave various types of evidence for the ways they face gender inequality in their families, schools, and communities such as additional domestic responsibilities at home, limited freedoms, limited choice in sports, no power in decision making in family matters, etc.\n\nSA immigrants in Western countries often continue to retain their traditional values, beliefs, and expectations.20,21,23,25-27 In traditional SA families, adolescent girls are raised in far more protected, controlled and sheltered home settings compared to the majority of adolescents in Canadian society. They face rigid gender norms concerning socialization. Gender segregation is a prominent instrument in socialization that effectively manages the distribution of power and social reward, and also defines gender-specific social roles. For example, men in SA families generally have greater independence, autonomy, and educational opportunities, whereas women are often restrained by domestic responsibilities.21,25 While girls are expected to perform household chores and take care of younger siblings, while boys have more freedom (e.g. going out after school). In addition, SA girls must follow strict family rules regarding respect for elders and male members of the family, and elders’ decisions. These norms discourage girls from voicing their opinions,21,25 which can result in stress-induced psychological disorders and behavioral issues.28 Many girls in the pre-FGDs reported that they lack the skills and knowledge to voice their feelings and fight for their rights.23\n\nWith regards to girls’ participation in sports, the study findings reveal that girls’ participation in sports was greatly influenced by gender stereotypes, especially in masculine-typed sports. Despite the benefits of sports participation on girls’ development and well-being, participation drops dramatically as young girls enter into adolescence.29 Football, soccer, baseball, hockey, wrestling, and basketball were considered masculine-typed sports. However, a recent study’s findings revealed that social support from parents, siblings, and peers positively impacts girls’ participation in masculine-typed sports.30\n\nThe study findings also pointed towards gender inequality in western countries, which is evident in occupational segregation and differences in gender and immigrant wage gaps. According to Statistics Canada, in 2018, employed women aged between 25 to 54 earned $4.13 (13.3%) less per hour than their male counterparts. Gender-related biases are anticipated as one of the accountable factors for the differences in the men’s and women’s wage gap.31 Furthermore, the American Institute for Conservation/Foundation of the American Institute for Conservation’s (AIC/FAIC) compensation surveys (2009; 2014) revealed a large pay gap between males and females.32 According to the conference board of Canada (2015), the immigrant wage gap for females (23%) is higher than for men (19.2%). SA immigrants are also vulnerable to employment discrimination that varies between provinces.33 Most of the students in our study have shared experiences of teachers enforcing gender-stereotypical behavior which was consistent with recent research conducted to explore teachers’ perceptions on gender roles and classroom practices in a comparative manner.6 Immediate families’ and teachers’ attitudes and behavior have significant effects on students, it is through these influences they learn and internalize attitudes and behavior regarding gender roles.8,6,25\n\nMoving forward with the diverse challenges faced by SA immigrant adolescent girls in Canada. The Girls’ Voices Curriculum has focused on developing life skills to raise empowerment and agency. The girl-focused development programs that emphasize self-confidence, communication skills, problem-solving skills, and decision-making are fruitful in empowering vulnerable adolescent girls.23 According to Kabeer, capabilities, and agency are linked; the greater a girl’s capabilities, the more agency she will have to make life goals and choices, and the more agency she has, the further she will develop her capabilities.34\n\n\nStudy strengths and limitations\n\nThis study had various strengths. We gained in-depth insights into young SA immigrant girls’ experiences of gender inequality through a range of tools and techniques. The variety of ages and cultural backgrounds of the respondents resulted in rich information that is critical to address gender inequality and empowerment among SA immigrant girls in Canada. We also note various limitations. The selection criteria for the study participants was purposive; for example, our selection of only SA immigrant girls might have led to information bias and prevented some participants from expressing perspectives that the rest of the group might not accept. The focus-group environment might have introduced social-desirability bias and prevented some participants from expressing perspectives that the rest of the group might not accept.\n\n\nFuture directions and recommendations\n\nThe findings of this study corroborate existing literature about immigrant girls’ empowerment in the Canadian context and contribute new insights into the experiences of SA immigrant girls with regard to gender inequality. The study findings amplify the fact that gender-related norms, values and stereotypes still pose potent barriers to young immigrant girls in Canada. The research findings are valuable for SA immigrants, educators, social workers, counselors, and policymakers in developing empowerment-focused interventions and programs and introducing relevant policies (e.g., anti-discrimination policy). The findings also demonstrate the benefits of counseling services and safe spaces within school campuses which will be useful for school administrators. These developments will support the empowerment and agency of young women and enable them to raise their voices for immigrant adolescent girls. This study has demonstrated young girls are capable of challenging discriminatory norms, dislodging stereotypes, and creating permanent change not only in their local community but also on a larger scale.\n\nYoung women have the potential to transform their communities. Empowering girls and promoting gender equality is crucial to achieving sustainable development goals.11 The goal of our research was to develop local strategies to empower girls to raise their voices, identify and develop solutions, and to approach decision-makers in their communities effectively to make tangible changes. This high-quality, collaborative, practice-oriented research built SA immigrant young girls’ abilities to respond more effectively to their needs through a girl-led advocacy program that amplifies girls’ voices. The development programs like ‘Girl’s Voices’ Curriculum that emphasize developing self-confidence, communication skills, problem-solving skills, and decision making are fruitful in empowering socially deprived adolescent girls locally and in the global context.\n\nThe prospective goal of this line of investigation is eventually to implement the ‘Girls’ Voices’ Curriculum at the national level to empower young adolescent girls in our society.\n\n\nData availability\n\nAs the data underlying this research is identifiable, it cannot be submitted to an online repository. Data will only be available on request by emailing the corresponding author meherali@ualberta.ca.\n\nMendeley Data: “Girls Empowerment Project FGD Guide”. https://doi.org/10.17632/tp585h7nsj.1.\n\nThis project contains the following extended data:\n\n- FGD guide\n\n- Participant timelines images\n\n- Evaluation Form\n\n- Appendix A & B (Consent and parental consent forms)\n\nMendeley Data: COREQ checklist for ‘Empowering young immigrant girls through the ‘Girls’Voices’ Curriculum in Canada: A qualitative study’. https://doi.org/10.17632/tp585h7nsj.1.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAuthors’ contributions\n\nSM conceived and co-designed this study, SM and MR implemented the curriculum, conducted FGDs, led the analysis, and drafted the manuscript. All authors commented on all drafts of the paper. All approved the final draft.",
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}
|
[
{
"id": "148877",
"date": "03 Oct 2022",
"name": "Johanna Ennser-Kananen",
"expertise": [
"Reviewer Expertise Multicultural 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\nIntroduction The introduction is clearly organized and written and offers a helpful definition of the problem. As a reader, I would have been interested to learn more about the research and goals/values/guiding principles that undergird the curriculum. I found it surprising that there was no theoretical framework mentioned - what are some of the theoretical concepts/approaches/stances/lenses the authors used?\n\nMethods The methods are clearly described, the process is made relatively transparent. I would have liked to know what kind of codes were used during the inductive phase. I would have also liked to learn more about the researchers' positionalities and how they may have shaped the research process (not so much in order to understand potential bias, which we all have, but to understand their motivation for doing this study and contextualize the interview situations).\nFindings I understand that the purpose of the study was to evaluate a curriculum, but I would like to encourage the authors to see the interview as a discursive space rather than take what is being said in that situation at face value and mold it more or less directly into findings. For instance, if participants say \"we should treat all genders equally\", researchers could try to understand how they understood gender or equality and which other themes these were connected to, and how this can inform current theory. For that, a theoretical framework would be important. The point here is not at all to doubt or dismiss the participants' experiences, but add an analytical layer to the research process.\n\nDiscussion The discussion section synthesizes the findings well, but I would recommend that the authors also add another level of abstraction to it: What is the meaning of this study for the academic community, for other local communities? What does it help us see/understand beyond the Canadian context?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-799
|
https://f1000research.com/articles/10-624/v1
|
21 Jul 21
|
{
"type": "Method Article",
"title": "Whole genome sequencing of colonies derived from cannabis flowers and the impact of media selection on benchmarking total yeast and mold detection tools",
"authors": [
"Kevin McKernan",
"Yvonne Helbert",
"Liam Kane",
"Nathan Houde",
"Lei Zhang",
"Stephen McLaughlin",
"Yvonne Helbert",
"Liam Kane",
"Nathan Houde",
"Lei Zhang",
"Stephen McLaughlin"
],
"abstract": "Background: Cannabis products are subjected to microbial testing for pathogenic fungi and bacteria. These testing requirements often rely on non-specific colony forming unit (CFU/g) specifications without clarity on which medium, selection or growth times are required. We performed whole genome sequencing to assess the specificity of colony forming units (CFU) derived from three different plating media: Potato Dextrose Agar (PDA), PDA with chloramphenicol and Dichloran Rose Bengal with chloramphenicol (DRBC).\nMethods: Colonies were isolated from each medium type and their whole genomes sequenced to identify the diversity of microbes present on each medium selection. Fungal Internal Transcribed Spacer (ITS3) and Bacterial 16S RNA(16S) quantitative polymerase chain reactions (qPCR) were performed, to correlate these CFUs with fungi- and bacterial- specific qPCR.\nResults: Each plating medium displayed a ten-fold difference in CFU counts. PDA with chloramphenicol showed the highest diversity and the highest concordance with whole genome sequencing. According to ITS3 and 16S qPCR confirmed with whole genome sequencing, DRBC under counted yeast and mold while PDA without chloramphenicol over counted CFUs due to bacterial growth without selection.\nConclusions: Colony Forming Unit regulations lack specificity. Each medium produces significant differences in CFU counts. These are further dependent on subjective interpretation, failure to culture most microbes, and poor selection between bacteria and fungi. Given the most pathogenic microbes found on cannabis are endophytes which culture fails to detect, molecular methods offer a solution to this long-standing quantification problem in the cannabis testing field.",
"keywords": [
"Cannabis",
"Total Yeast and Mold",
"Microbiome",
"Whole Genome Sequencing",
"qPCR"
],
"content": "Introduction\n\nTotal yeast and mold testing are required in many states to test the safety of cannabis, prior to the sale of cannabis flowers and cannabis-infused products. Cannabis is an inhaled product, and cases of cannabis-transmitted Aspergillosis have been reported in the clinical literature (Bal et al., 2010; Gargani et al., 2011; McKernan et al., 2015, 2016; Remington et al., 2015; Ruchlemer et al., 2015). Cannabis is a unique matrix, in that antibiotic cannabinoids can make up to 20% of the flowers’ weight, and many fungi infecting cannabis are endophytes. Endophytes are not easily cultured from the plant without lysing open plant cell walls. The conditions which lyse open plant cells walls also lyse open fungal cell walls, thus impacting the viability of the microbes in the lysis and homogenization processes required for testing. Cannabis flowers contain both bacteria and fungi, further complicating fungal quantification for colony forming units (CFU) that lack speciation. Antibiotic selections are often utilized to reduce background bacteria, but many of these antibiotics (e.g. chloramphenicol) inhibit the growth of the most pathogenic fungi found on cannabis (Fusarium, Pythium and Aspergillus) (Smith & Marchant, 1968; Day et al., 2009; Joseph et al., 2015).\n\nAs part of an AOAC Emergency response validation (ERV) in the State of Michigan, we investigated the impact of medium selection on surveying total yeast and mold on cannabis. Cured cannabis flowers were homogenized and tested on 3 different plating media. These data were compared to ITS3- and 16S-based qPCR and whole genome sequencing. To further complement these cannabis flower samples, organisms were acquired from the American Tissue Culture Collection (ATCC) and plated as pure monocultures on different plating media to confirm the differential growth on each medium.\n\n\nMethods\n\nSamples originated from Steadfast Analytical Laboratories (Hazel Park, MI) and were tested independently at a laboratory within the Michigan Coalition of Independent Cannabis Testing Laboratories. Briefly, 10 grams of dried cannabis flowers were sampled from three lots of homogenized cannabis containing high, medium and low quantities of fungal and bacterial CFUs, as measured using culture-based techniques with chloramphenicol selection. 10 grams of homogenized flower were soaked with 90 ml of Tryptic Soy Broth (TSB, Medicinal Genomics #420205) in a filtered Nasco Whirl-Pak bag (#B01385). Samples were homogenized by hand, and then 0.1 mL of solution plated onto three media (DRBC, PDA with chloramphenicol, PDA, at 1:100 dilution). Two additional dilutions were prepared (10 mL into 90 mL) and the same plating protocol was followed. All plates were incubated for 5 days at 25°C.\n\nITS3 qPCR was performed as described in McKernan et al. with two modifications. Briefly, 1ml of homogenate from a Whirl-Pak bag was collected and briefly micro-centrifuged to enrich for live organisms. This pellet was resuspended in 200 μl ddH2O and lysed with the addition of 12 μl of Thaumatin-like protein (TLP) and incubated at 37°C for 30 minutes. This enzymatic lysis step (glucanase) ensures more complete lysis of fungal cell walls (Medicinal Genomics part #420206, McKernan et al., 2015, 2016). 12.5 μl of MGC Lysis buffer was added, vortexed and incubated for 5 minutes at 25°C. Lysed samples were micro-centrifuged and 200 μl of supernatant was aspirated and added to 250 μl of Medicinal Genomics binding buffer (MGC part# 420001) for magnetic bead isolation. The samples were incubated with the Medicinal Genomics magnetic bead mixture for 10 minutes, magnetically separated and washed two times with 70% ethanol. The beads were dried at 37°C for 5 minutes to remove excess ethanol and eluted with 25 μl of ddH2O. Quantitative PCR was performed using Medicinal Genomics PathoSEEK Total Yeast and Mold detection assay (MGC# 420103) and Medicinal Genomics PathoSEEK Total Aerobic Count Assay (MGC# 420106) according to the manufacturers’ instructions on a BioRad CFX96 thermocycler.\n\nA total of 45 colonies were picked with a pipette tip and introduced into 200 μl of ddH2O with 12.5 μl of MGC TLP (MGC part #420206). TLP is a glucanase active at 37°C. Samples were digested for 30 minutes at 37°C and 12.5 μl of MGC Lysis buffer was added, vortexed and incubated for 5 minutes at 25°C. Lysed sample were micro-centrifuged and 200 μl of supernatant was aspirated and added to 250 μl of MGC binding buffer (MGC part # 420001) for magnetic bead isolation. The samples were incubated with the bead mixture for 10 minutes, magnetically separated and washed 2 times with 70% ethanol. The beads were dried at 37°C for 5 minutes to remove excess ethanol and eluted with 25 μl of ddH2O.\n\nFragmentation\n\nGenomic DNA (gDNA) was quantified with a Qubit (Thermo Fisher Scientific) and normalized to reflect 4-8 ng/μl in 13 μl of TE buffer. Libraries were generated using enzymatic fragmentation with the NEB Ultra II kits (NEB part # E7103). Briefly, 3.5 μl of 5X NEB fragmentation buffer and 1 μl of Ultra II fragmentation enzyme mix are added to 13 μl of DNA. This reaction was tip-mixed 10 times, vortexed, and quickly centrifuged. Fragmentation was performed in a BioRad CFX96 thermocycler at 3.5 minutes at 37°C, 30 minutes at 65°C. The reaction was kept on ice until ready for adaptor ligation.\n\nAdaptor ligation\n\n\n\nThe master mix for ligation was prepared on ice using 0.75 μl of Agilent SureSelect Adaptor Oligo Mix, 0.5 μl of ddH2O, 15 μl of NEB Ultra II Ligation Master Mix, 0.5 μl of Ligation enchancer (New England Biolabs) for a total reaction volume of 16.75 μl.\n\nLigation was performed by the addition of 16.75 μl of ligation master mix to the 17.5 μl Fragmentation/End Prep DNA reaction mixture, incubate for 15 minutes at 20°C. To purify excess adaptors and adaptor dimers, AMPure XP beads (Beckman Coulter #A63881) were vortexed at room temperature for resuspension and16 μl (approximately 0.45X) of resuspended AMPure XP beads were added to the ligation reactions. This was well-mixed by pipetting up and down at least 10 times. The mixture was incubated for 5 minutes at 25°C. The PCR plate was placed on an appropriate magnetic stand (Medicinal Genomics #420202) to separate the beads from the supernatant. After the solution was clear (about 5 minutes), the supernatant was carefully removed and discarded. We were careful not to disturb the beads containing target DNAmolecules. The magnetic beads were washed by adding 200 μl of 70% ethanol to the PCR plate while on the magnetic stand. Followed incubation at room temperature for 30 seconds, and then careful removal and discarding of the supernatant. The ethanol wash was repeated once for a total of 2 washes. Trace amounts of ethanol were removed. The beads were air dried for ~ 7 minutes while the PCR plate was on the magnetic stand with the lid open. The PCR plate was then removed from the magnet and target DNA eluted from the beads into 10 μl of H2O, then 9 μl of cleaned DNA was transferred to a fresh well.\n\nPCR amplification\n\nA volume of 12.5 μl 2x NEBNext Q5 Hot Start Master Mix (New England Biolabs #M0492S) was added to 9 μl ligated DNA, then 3.5 μl of NEB 8bp index primer/universal primer were added to the mix. The reaction ran in a cycling program set at 98°C for 30 seconds as an initial denaturization step; six cycles of denaturation, annealing and extension were performed, cycling between 98°C for 10 seconds and 65°C for 75 seconds. A final 5-minute step at 65°C was performed, with a final 4°C forever step.\n\nPCR reaction cleanup\n\nAMPure XP beads were resuspended at room temperature with a brief vortex. A volume of 15 μl of resuspended AMPure XP beads was added to the PCR reactions (~ 25 μl). To mix well, we pipetted up and down at least 10 times. The mixture was incubated for 5 minutes at room temperature. The PCR plate was put on an appropriate magnetic stand to separate the beads from the supernatant. After the solution was clear (about 5 minutes), the supernatant was carefully removed and discarded. We were careful not to disturb the beads containing the target DNA. A volume of 200 μl of 70% ethanol was added to the PCR plate while on the magnetic stand. The mix was incubatedat room temperature for 30 seconds, and then the supernatant was carefully removed and discarded. The ethanol wash was repeated once more. The beads were air dried fof 7 minutes while the PCR plate was on the magnetic stand with the lid open. The target DNA molecules were eluted from the beads into 15 μl of nuclease-free H2O, and 15 μl were transferred into a fresh well.\n\nSample quality control\n\nLibraries were evaluated on an Agilent Tape Station prior to pooling for Illumina sequencing. Sequencing was performed by GeneWiz, Cambridge MA. A total of 473 million paired reads (2 × 150bp) were generated, averaging over 10 million read pairs per sample and a total sequence of 141Gb.\n\n\nAnalysis\n\nFastq files were uploaded to OneCodex) for Kmer analysis and Simpson’s diversity index analysis for each genome (Extended data: Supplementary Table 1, sheet Summary https://doi.org/10.5281/zenodo.4759883). Reads were also assembled with MegaHit v.1.2.9 (Li et al., 2015, 2016). The Nextflow mapping and assembly pipeline is published on GitHub. Quast 5.0 was used to calculate the assembly quality statistics (Gurevich et al., 2013). Sequencing data is deposited in NCBI under Project ID PRJNA725256.\n\n\nResults\n\nEach colony which was imaged on plates and chosen for whole genome sequencing and OneCodex analysis is displayed in Figure 1 (DRBC), Figure 2 (PDA-chloramphenicol) and Figure 3 (PDA no chloramphenicol). A link to each OneCodex analysis and its respective NCBI submission ID is available in Supplementary Table 1 - Sheet Summary (Extended data, McKernan et al., 2021). Some of the colonies from the plate merged with other colonies producing mixtures of genomes as evident in the OneCodex pie charts. These merged colonies were further evidenced by the display of bimodal sequence coverage (clusters of contigs at 1000X and 10X coverage) and compared with the plating images (Figure 4). A heatmap of sequencing read speciation and purity is seen in Figure 5. While merged colonies can be difficult to resolve visually, whole genome sequencing can resolve simple metagenomes and still extract additional diversity information from the samples. Colonies that were noticeably mixed according to sequence analysis and colony visual inspection were more prevalent with the PDA without selection colonies (Table 1).\n\nColony Image (Left), Assembly sequence coverage (Y) compared with contig Length (X) where the contigs are sorted largest to smallest from left to right (Mid-Left). Assembly statistics calculated with Quast 5.0 (Mid Right). OneCodex speciated Kmer count (Right).\n\nColony Image (Left), Assembly sequence coverage (Y) compared with contig Length (X) where the contigs are sorted largest to smallest from left to right (Mid-Left). Assembly statistics calculated with Quast 5.0 (Mid Right). OneCodex speciated Kmer count (Right).\n\nColony Image (Left), Assembly sequence coverage (Y) compared with contig Length (X) where the contigs are sorted largest to smallest from left to right (Mid-Left). Assembly statistics calculated with Quast 5.0 (Mid Right). OneCodex speciated Kmer count (Right).\n\nDichloran Rose Bengal (Top). Potato Dextrose Agar with chloramphenicol (PDA – CAMP, Middle). PDA without CAMP (Bottom).\n\nA Simpson’s diversity index analysis demonstrated PDA with CAMP provides the highest diversity score (Figure 6) While the DRBC had 100-fold lower CFU counts than PDA without selection, it predominantly displayed fungal colonies (80%) while PDA without selection was biased toward bacteria (22%). PDA with chloramphenicol displayed more fungi (55%) than bacteria and also produced a half log more fungal colonies than DRBC with chloramphenicol (Table 2).\n\nSimpson’s diversity index (https://geographyfieldwork.com/Simpson%27sDiversityIndex.htm) is used to quantify the biodiversity of a habitat on a 0 to 1 scale. It takes into account the number of species present, as well as the relative abundance of each species. A diversity index of 1 represent infinite diversity where 0 reflects no diversity. Dichloran Rose Bengal (DRBC) plating demonstrates the lowest diversity. This is not surprising given DRBC contains 3 different selection agents. While this limits bacterial contamination it also limits yeast and mold growth.\n\nPlating on different media demonstrates a LOG scale difference in Colony Forming Units (CFU) with each plating medium. Sequencing can attribute only half of the colonies as bacteria on Potato Dextrose Agar (PDA) with chloramphenicol. This implies a 5-fold under counting of yeast and mold on Dichloran Rose Bengal (DRBC).\n\nOne fungal sample (Cladosporum) presented delayed Ct (31.79) with PathoSEEK Total Yeast and Mold (ITS3-TYM) qPCR primers. Scrutiny of the primer sequences against the Cladosporum genome shows proper primer binding locations but missing probe sequences. This genome has low coverage (10X) and the repetitive ITS qPCR target regions are often poorly assembled in low coverage-genomes. This may explain the missing probe sequence in the low coverage fragmented assembly. Additionally, some significantly delayed PathoSEEK Total Aerobic Count (TAC) signal was observed in fungal colonies. This is the result of the use of the lytic enzyme (TLP) which is cloned and expressed in E. coli and contains some background E.coli DNA. This background TLP expression in E. coli produces signals that can be seen in blank preparations. In some cases, this signal is elevated due to mixed colonies observed in the sequencing data.\n\nThe qPCR method represents an increased selectivity in assessing fungal and bacterial CFU compared to DRBC, where only -92% of the colonies were fungal colonies. Quantitative PCR identified all fungi and never mistook one for bacteria. In a minority of cases we had visually mixed colonies. Even if we discount the mixed colonies and count, only the single bacterial colony out of 13 on DRBC, we obtain 92% (1/13) fungal colonies on DRBC where qPCR delivered perfect results. As a comparison, quantitative PCR demonstrated over 10 Cts (1024 fold) differences between the TYM and TAC signals on fungal colonies. The majority of the residual TAC signal being observed in fungi can be normalized and discounted with the background E. coli TLP DNA signal measured in blank preparations.\n\nTo confirm these observations several Aspergillus species and Botrytis cinerea were ordered from ATCC and plated on various plating medias in absence of background cannabis matrix (Table 3 and Figure 7). In all cases DRBC showed reduced CFU counts.\n\nCultures were plated on Potato Dextrose Agar (PDA), PDA with selection (chloramphenicol or Tartaric acid), and Dichloran Rose Bengal (DRBC). Fewer colonies are consistently found on DRBC.\n\nFungi species were ordered from American Tissue Culture Collection (ATCC) and plated on 2 different medias (PDA and DRBC) to assess growth performance of the organisms in absence of cannabis background bacteria and matrix.\n\n\nDiscussion\n\nMicrobial media and their selection have a significant impact on the Simpson’s diversity index of microbes observed with whole genome sequencing. This has been noted in prior microbiome surveys in cannabis, in which culturing the microbes changes the representation of the microbiome as measured by qPCR and sequencing performed directly off of the flower (McKernan et al., 2015, 2016). In this study the DRBC selection reduced bacterial growth more than PDA with chloramphenicol, but also reduced the fungal CFU 5-fold in the process. This has important implications for chloramphenicol-sensitive cannabis endophytes like Aspergillus, Pythium and Fusarium. Both media types (PDA and DRBC) are referenced in the FDA Bacteriological Analytical Manual. States exclusively considering DRBC for ease of colony visualization should be aware of the species-specific sensitivities of using a single medium type, and consider species-specific testing for such pathogenic organisms, to complement a partial yeast and mold test offered from a single selection-based medium. PCR-based techniques can identify more organisms than DRBC alone as no selection is occurring given thorough cell lysis is achieved for qPCR analysis.\n\nPlating also suffers from having a very limited dynamic range. Since it is difficult to count colonies when more than 100 colonies are present on a plate, multiple dilutions are often required to understand the full range of CFU counts one may encounter with a test which is attempting to quantify 10,000 CFUs/gram. This results in multiplying diluted CFUs 10, 100 and even a 1,000 fold to back-estimate the total CFU count. In this scenario a single colony can swing the CFU count from passing to failing (9 colonies x 1,000 fold dilution vs 10 colonies at 1,000 fold dilution). Quantitative PCR has a linear dynamic range over 5-6 orders of magnitude and no such multiplication is required. Thus, qPCR provides a more accurate itemization of actual CFUs counts.\n\nIn-vitro inclusion and exclusion testing with ITS3 qPCR on ATCC-sourced organisms demonstrated over 96% inclusion (50 yeast and mold) and zero bacterial cross reactivity (30 bacteria) (Extended data: Supplementary Table 1- Sheet TYM Inclusion & TYM Exclusion). In-silico analysis of ITS3 primer sequences, predicts over 1400 yeast and mold should amplify with the described ITS3 primer sequences. All plating media, even with three different forms of selection (DRBC), had bacterial contamination and each level of selection reduced fungal CFU counts.\n\n\nData availability\n\nNCBI Bioproject: Under Counting of Total Yeast and Mold on Cannabis using DRBC, Accession number PRJNA725256, https://www.ncbi.nlm.nih.gov/bioproject?term=PRJNA725256.\n\nZenodo: Whole genome sequencing of colonies derived from cannabis flowers and the impact of media selection on benchmarking total yeast and mold detection tools, https://doi.org/10.5281/zenodo.4759883 (McKernan et al., 2021).\n\nThis project contains the following extended data:\n\nSummary Table 1: OneCodex URLs and NCBI BioSample IDs for every sample.\n\nTYM Inclusion: ATCC organisms tested for inclusion criteria\n\nTYM Exclusion: ATCC organisms tested for exclusion criteria\n\nSequencing: Number of reads, Read Pairs and Total Gigabases sequenced for each sample.\n\nAssembly: Complete Assembly statistics for each sample generated by QUAST\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nBal A, Agarwal AN, Das A, et al.: Chronic necrotising pulmonary aspergillosis in a marijuana addict: a new cause of amyloidosis. Pathology . 2010; 42: 197–200. PubMed Abstract | Publisher Full Text\n\nDay S, Lalitha P, Haug S, et al.: Activity of antibiotics against Fusarium and Aspergillus. Br J Ophthalmol . 2009; 93: 116–119. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGargani Y, Bishop P, Denning DW: Too many mouldy joints - marijuana and chronic pulmonary aspergillosis. Mediterr J Hematol Infect Dis . 2011; 3: e2011005. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGurevich A, Saveliev V, Vyahhi N, et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics . 2013; 29: 1072–1075. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJoseph MR, Al-Hakami AM, Assiry MM, et al.: In vitro anti-yeast activity of chloramphenicol: A preliminary report. J Mycol Med . 2015; 25: 17–22. PubMed Abstract | Publisher Full Text\n\nLi D, Liu CM, Luo R, et al.: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics . 2015; 31: 1674–1676. PubMed Abstract | Publisher Full Text\n\nLi D, Luo R, Liu CM, et al.: MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods . 2016; 102: 3–11. PubMed Abstract | Publisher Full Text\n\nMcKernan K, Spangler J, Helbert Y, et al.: Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests. F1000Res . 2016; 5: 2471. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcKernan K, Spangler J, Zhang L, et al.: Cannabis microbiome sequencing reveals several mycotoxic fungi native to dispensary grade Cannabis flowers. F1000Res . 2015; 4: 1422. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcKernan KJ, Helbert Y, Kane LT, et al.: Whole genome sequencing of colonies derived from cannabis flowers and the impact of media selection on benchmarking total yeast and mold detection tools (Version 1). Zenodo. 2021, May 14. Publisher Full Text\n\nRemington TL, Fuller J, Chiu I: Chronic necrotizing pulmonary aspergillosis in a patient with diabetes and marijuana use. CMAJ . 2015; 187: 1305–1308. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRuchlemer R, Amit-Kohn M, Raveh D, et al.: Inhaled medicinal cannabis and the immunocompromised patient. Support Care Cancer . 2015; 23: 819–822. PubMed Abstract | Publisher Full Text\n\nSmith DG, Marchant R: Chloramphenicol inhibition of Pythium ultimum and Rhodotorula glutinis. Arch Mikrobiol . 1968; 60: 262–274. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "90094",
"date": "28 Jul 2021",
"name": "Cindy Orser",
"expertise": [
"Reviewer Expertise plant microbiology",
"cannabis analytical testing",
"diagnostics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 well-executed study of considerable breath and size to further solidify the argument against State regulatory bodies requiring agar plating to evaluate microbial load on cannabis flower in lieu of proven superiority of molecular assays. In addition, this study demonstrates confirmation of chloramphenicol's ability to knock down Fusarium and Aspergillus growth when plating on DRBC at relatively low chloramphenicol levels [~0.1 mg/mL], not sure of the concentration in PDA agar. Nonetheless, this study should finally put to rest the issue of which method is most accurate at representing microbial load on cured cannabis flower. With qPCR assays shown to be fundamentally superior to culturing and plating, the discussion should now move over to \"sampling\" and how inadequate the normal sample size per batch size is to give a glimpse into the microbiome of the cannabis flower and the intrigue of how cultivation methods influence the cannabis microbiome.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "7020",
"date": "13 Aug 2021",
"name": "Kevin McKernan",
"role": "Author Response",
"response": "Thank you for this feedback. The sampling comment is very pertinent. We were not in control of this aspect of the study so opted to save this topic for another manuscript. AOAC communicated to us that many different cannabis samples were mixed to normalize chemotype affects on culture. This is a very good idea as we have seen chemotype specific effects on cannabis microbiology and its published to occur in Trema orientalis (https://pubmed.ncbi.nlm.nih.gov/34035994/). One of the concerns with plating, is that the antibiotic cannabinoids and terpenes may get liberated from trichomes in the aggressive lab homogenization and media saturation process. This may influence the viability of some of the microbes. This aggressive homogenization and fluid saturation is not what a consumer experiences. Many publications demonstrate the antibiotic nature of cannabinoids and how different cannabinoids exhibit different antibiotic properties thus we should expect different chemotypes to plate differently given there is no purification step prior to plating (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105690/). Molecular methods lyse open cells and purify the DNA away from such potential growth inhibitors with Ethanol extractions. To confirm these samples were indeed a mixture of different cannabis samples, we were sent DNA from these mixtures and performed 10Mb SureSelect capture and deep Illumina Sequencing on these samples to under stand how well they were mixed and how diverse they where. The read genotypes indeed suggested more than a single cannabis sample was present and likely more than 4 in each High, Medium and Low Categories. We put these data public for anyone who is interested but felt it would bloat this manuscript with confirmatory data and distract from the core focus of the study. https://www.kannapedia.net/strains/rsp11748/ https://www.kannapedia.net/strains/rsp11749/ https://www.kannapedia.net/strains/rsp11750/ https://www.kannapedia.net/strains/rsp11752/ https://www.kannapedia.net/strains/rsp11753/ https://www.kannapedia.net/strains/rsp11754/ https://www.kannapedia.net/strains/rsp11755/ https://www.kannapedia.net/strains/rsp11756/ https://www.kannapedia.net/strains/rsp11757/ https://www.kannapedia.net/strains/rsp11758/ https://www.kannapedia.net/strains/rsp11759/ https://www.kannapedia.net/strains/rsp11760/ https://www.kannapedia.net/strains/rsp11761/ https://www.kannapedia.net/strains/rsp11762/"
}
]
},
{
"id": "90093",
"date": "04 Aug 2021",
"name": "Zamir K. Punja",
"expertise": [
"Reviewer Expertise microbiology",
"plant pathology",
"plant biology",
"cannabis pathogens",
"post-harvest quality"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAdd “human pathogenic” where pathogenic is mentioned as the concern is with these particular microbes and not those potentially that could be affecting the plant as plant pathogens.\n\nThe inclusion of the 3 selection media should be elaborated on. Why were these particular 3 media selected? Provide references to show where, or in what capacity, they may have been used in previously published work. There is abundant published work on the use of PDA with antibiotics to isolate fungi in the plant pathology literature. In fact, it is a standard medium used for isolation in labs worldwide. The addition of dichloran and rose bengal have also been used to restrict the growth of certain groups of fungi and bacteria as a semi-selective medium for isolation in particular from soil samples. Therefore, it would not be expected to provide a broad spectrum of recovery of fungi and yeasts. It is surprising that this medium would be used to assess total yeast and mold counts in cannabis.\n\nThe comparison of the 3 media in this study sheds light on the differences in levels of recovery of fungi and yeasts. This is an important finding – not all media behave in the same manner. To observe a 10-fold difference in recovery between these media is quite significant as it illustrates the potential for under-representation in the recovery process.\n\nThe use of whole genome sequencing to apply to the identification of colony-forming units is a definite plus for this work. It shows the ability to rapidly identify what is present on the culture media with regard to molds that originated from the samples.\n\nThere are several prior reports of authors having recovered a range of fungi from cannabis buds and identified them using the ITS region. Please include these as a reference by which to compare the fungi and yeasts identified in the present study. It is important to build a body of knowledge on the exact identity of the general and species found on cannabis and how prevalent they are.\n\nThe report of endophytes in cannabis should be accompanied by a reference citation. These particular microbes are more difficult to recover in culture media and therefore a molecular approach has merit.\n\nThe inclusion of confirmed ATCC culture specimens to demonstrate differences in growth on the 3 media is a good confirmatory experiment.\n\nThe cannabis samples that originated from Steadfast Analytical Laboratories would have had an analysis of total yeast and mold conducted on them. Is it possible to have these results compared to those from the present study to show how the commercial lab testing may differ from the current study? Or was that not an objective of the current study?\n\nDuring the preparation of samples for the ITS3 qPCR procedure, was there a subset of samples included that did not contain the TLP lysis step to show that it made a difference? Or is that included in prior published work?\n\nFor the 45 colonies that were selected for whole genome sequencing, could the identified genus and species be presented in a separate table? Perhaps in accordance with the media from which they were derived from? These would be a summary of what is shown in Figures 1, 2, 3. This is in addition to the OneCodex analysis and the NCBI submission ID available in Supplementary Table 1 It also helps clarify the data shown in Figure 5.\n\nThe Simpson’s diversity index analysis shown in Figure 6 is extremely helpful to show the differences between the 3 media types in recovery.\n\nThe results from qPCR of the homogenate that was collected from the Whirl-Pak bags and subjected to PathoSEEK. How did this compare with the colony identification of the same sample plated on the 3 different media with regards to the identification of the genus and species present? Can this be shown in a Table?\n\nThe use of DRBC, if conducted by testing laboratories, is worrisome. It is known that the addition of dichloran and rose bengal is specifically used to discourage certain types of microbes from growing when used for recovery of specific types of fungi from soil samples. The inclusion of DRBC in a testing laboratory for cannabis TYM counts should be discouraged, as shown in the present work where total CFU’s recovered were significantly lower compared to PDA with chloramphenicol. DRBC would significantly under-estimate the TYM counts as shown in Figure 4.\n\nIn Table 2, the headings seem incorrect as there are two with “PDA with chloramphenicol” and one should be “PDA w/o chloramphenicol”\n\nTable 3 and Figure 7 clearly show how DRBC provides reduced growth compared to PDA.\n\nOverall, this is an informative study and the results merit publication. Once the items identified by the reviewer are addressed, this study will be a good addition to the slowly expanding studies showing how complex the assessment of total yeast and mold levels in cannabis is. The information from these types of studies should guide government agencies on the pitfalls of certain methods used to assess TYMC.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "7002",
"date": "12 Aug 2021",
"name": "Kevin McKernan",
"role": "Author Response",
"response": "Thank you for this valuable feedback. I have interweaved our responses below and will update the manuscript accordingly: Add “human pathogenic” where pathogenic is mentioned as the concern is with these particular microbes and not those potentially that could be affecting the plant as plant pathogens. Response: Agree. Done The inclusion of the 3 selection media should be elaborated on. Why were these particular 3 media selected? Provide references to show where, or in what capacity, they may have been used in previously published work. There is abundant published work on the use of PDA with antibiotics to isolate fungi in the plant pathology literature. In fact, it is a standard medium used for isolation in labs worldwide. The addition of dichloran and rose bengal have also been used to restrict the growth of certain groups of fungi and bacteria as a semi-selective medium for isolation in particular from soil samples. Therefore, it would not be expected to provide a broad spectrum of recovery of fungi and yeasts. It is surprising that this medium would be used to assess total yeast and mold counts in cannabis. Response: We were not involved in the selection of these media types. The study was initiated on PDA in Michigan. After we completed the PDA study, the organizers informed us they were switching to DRBC based on Steadfast having used chloramphenicol based culture platforms to categorize the samples before shipping them to other labs in Michigan. We suspect the 3 media types were chosen due to their presence in the FDA BAM. We have added a sentence to clarify this. The comparison of the 3 media in this study sheds light on the differences in levels of recovery of fungi and yeasts. This is an important finding – not all media behave in the same manner. To observe a 10-fold difference in recovery between these media is quite significant as it illustrates the potential for under-representation in the recovery process. The use of whole genome sequencing to apply to the identification of colony-forming units is a definite plus for this work. It shows the ability to rapidly identify what is present on the culture media with regard to molds that originated from the samples. There are several prior reports of authors having recovered a range of fungi from cannabis buds and identified them using the ITS region. Please include these as a reference by which to compare the fungi and yeasts identified in the present study. It is important to build a body of knowledge on the exact identity of the general and species found on cannabis and how prevalent they are. Response: Very good point. We have added a paragraph to describe the substantial prior art here. The report of endophytes in cannabis should be accompanied by a reference citation. These particular microbes are more difficult to recover in culture media and therefore a molecular approach has merit. Response: Very good point. We have added references to emphasize Dichlorans inhibitory nature. The inclusion of confirmed ATCC culture specimens to demonstrate differences in growth on the 3 media is a good confirmatory experiment. Response: This is an important control but it should be known by people in the field that AOAC certification doesn’t require the inclusion or exclusion testing to be performed in the presence of matrix and this inclusion and exclusion criteria can be obtained using a different media than DRBC. We believe this provides a false sense of safety. This is challenging to perform in the presence of matrix as there is no supplier of sterilized cannabis that ship across state lines and inclusion and exclusion testing can be impacted by background microbial content. Further legalization will improve this. The cannabis samples that originated from Steadfast Analytical Laboratories would have had an analysis of total yeast and mold conducted on them. Is it possible to have these results compared to those from the present study to show how the commercial lab testing may differ from the current study? Or was that not an objective of the current study? Response: As part of the AOAC study, we were blinded from these data. We do know that the high, medium and low categories were allocated according to culture-based methods that used CAMP and that quantitative PCR over estimated microbial burden on the low DRBC samples. During the preparation of samples for the ITS3 qPCR procedure, was there a subset of samples included that did not contain the TLP lysis step to show that it made a difference? Or is that included in prior published work? Response: We did not include TLP lysis versus no TLP as the study required we settle on a single method for evaluation. We are in the process of writing up that comparison for another publication. For the 45 colonies that were selected for whole genome sequencing, could the identified genus and species be presented in a separate table? Perhaps in accordance with the media from which they were derived from? These would be a summary of what is shown in Figures 1, 2, 3. This is in addition to the OneCodex analysis and the NCBI submission ID available in Supplementary Table 1 It also helps clarify the data shown in Figure 5. Response: This is an important point. This does exist in Figure 5 but we failed to clarify the sample nomenclature that clarifies this. We have added a sample key to describe which samples are DRBC, PDA-CAMP, PDA-no-CAMP. The Simpson’s diversity index analysis shown in Figure 6 is extremely helpful to show the differences between the 3 media types in recovery.The results from qPCR of the homogenate that was collected from the Whirl-Pak bags and subjected to PathoSEEK. How did this compare with the colony identification of the same sample plated on the 3 different media with regards to the identification of the genus and species present? Can this be shown in a Table? The use of DRBC, if conducted by testing laboratories, is worrisome. It is known that the addition of dichloran and rose bengal is specifically used to discourage certain types of microbes from growing when used for recovery of specific types of fungi from soil samples. The inclusion of DRBC in a testing laboratory for cannabis TYM counts should be discouraged, as shown in the present work where total CFU’s recovered were significantly lower compared to PDA with chloramphenicol. DRBC would significantly under-estimate the TYM counts as shown in Figure 4. Response: We were only allowed to ship cultures on plates across state lines. As a result, we have Cq scores for the colonies that were picked and isolated in Figures 1,2,3 under the TYM and TAC Cq columns on the right. This only informs on inclusion and exclusion capabilities of the primers for the colonies harvested but loses quantitative information. We were not allowed to ship homogenized matrix in the mail to assess the Cq prior to plating. Labs local to Michigan have performed this comparison and are free to publish those results. The summary of the results communicated to us were that the qPCR had better concordance with PDA with CAMP and over estimated CFUs on the DRBC Low samples. This significantly differs from Michigans stated intentions with the ERV where they voiced concerns about molecular methods undercounting risk (https://help.medicinalgenomics.com/hubfs/Regulatory%20Info%20for%20Sales/Michigan%20MRA%20Notification%20of%20additional%20validation%20requirements%20August%202020.pdf). The opposite turned out to be true. DRBC is undercounting risk compared to qPCR. The MRA was also led to believe that Klebsiella was not an appropriate validation organism as it was not commonly found on cannabis despite it having been published by Thompson et al previously. Candida albicans (which we have never seen documented on Cannabis) was prioritized as a CRM. We have added some language to address this to the best of our ability. In Table 2, the headings seem incorrect as there are two with “PDA with chloramphenicol” and one should be “PDA w/o chloramphenicol”Table 3 and Figure 7 clearly show how DRBC provides reduced growth compared to PDA. Response: Thank you!. Good catch. We have updated that."
}
]
}
] | 1
|
https://f1000research.com/articles/10-624
|
https://f1000research.com/articles/10-794/v1
|
11 Aug 21
|
{
"type": "Research Article",
"title": "The effects of government policy on organizational performance of provincial administration organization: mediating role of public entrepreneurship",
"authors": [
"Panitee Karnsomdee"
],
"abstract": "Background: The new paradigm of government management has stimulated public organizations to establish innovative and competitive management policies through public entrepreneurship in order to provide excellent public service and to enhance public organizational performance. This research study aims to investigate the effects of government policy on organizational performance through the mediating role of public entrepreneurship of provincial administration organization in the upper northeastern region 2 in Thailand. Methods: This research employs a cross-sectional questionnaire study. Data were collected from 216 government officials through five-point Likert scale questionnaires with validity and reliability analyses. Data were analyzed by descriptive statistics and inferential statistics toward path analysis. Results: The research results reveal that government policy has a significant direct influence on organizational performance with a standardized coefficient of 0.655. Government policy has a significant indirect effect on organizational performance through the mediating role of public entrepreneurship with a standardized coefficient of 0.566. The total effects can be described with a standardized coefficient of 0.733 at a 0.05 significance level. Conclusions: The government should establish innovative and competitive public policies to support a rapid change of entrepreneurial orientation, and transform policies into action. As public entrepreneurship has a significant mediating role in enhancing organizational performance, conventional public structures of performance management are being replaced by more innovative, adaptive, and competitive public entrepreneurship in order to get the desired and effective public outcomes for a provincial administration organization.",
"keywords": [
"government policy",
"public policy",
"organizational performance",
"public outcome",
"entrepreneurship",
"public entrepreneurship",
"mediating role",
"provincial administration"
],
"content": "Introduction\n\nThe concept of public entrepreneurship has recently been established based on new public management, which focuses on developing competitiveness to drive innovative public work processes and provide excellent public service. Proactive and competitive government management policies on enhancing public entrepreneurship transformation have been determined as key success factors to support the achievement of organizational performance, especially for provincial administration organization as a local government agency in Thailand (Oyebanji & Olanrewaju, 2020). The decentralization of public power and budget to build public entrepreneurs is considered one of the major turning points of the bureaucratic system towards the Thailand 4.0 development model. Thailand 4.0 is a new economic agenda to boost economic development in Thailand based on creativity, innovation, digital technology, and high public service quality as well as to transform labor intensive industry into knowledge orientation towards value-based economy (Jones & Pimdee, 2017). Public entrepreneurship focuses on creating work innovation in order to improve public service quality and to meet public requirements with an appropriately flexible working system, achieving high performance, accepting specified risk, and finally resulting in the achievement of public goals. Many transformational projects have been launched to pivot government agencies toward public entrepreneurship such as establishing digital communities, supporting digital innovative start-up networks, and promoting digital parks for small and medium-sized enterprises (SMEs) (Sangwanna & Pupat, 2014). Although the influence of government policy on organizational performance is well explored (Rodrigo et al., 2019; Kareem & Haseeni, 2015), the mediating role of public entrepreneurship in the context of provincial administration organization as local government agency in Thailand remains in question. Therefore, this research study aims to address this question and explore it in further detail. The objective of this research study is to investigate the effects of government policy on organizational performance through the mediating role of public entrepreneurship, in the context of provincial administration organization in the upper northeastern region 2 in Thailand. The results of this research study could be applied as strategic guidelines for local government organizations to enhance organizational performance. The paper begins with a review of the concepts and theories related to government policy, organizational performance, and public entrepreneurship in order to conceptualize the research conceptual framework and hypotheses development. The research methodology, data collection, analysis of data and the research results are later presented. Next, the proposed recommendation on public entrepreneurship transformation and public organizational performance enhancement as well as managerial implications and government suggestions are discussed. Finally, conclusion of the research findings and recommendations for future researches are documented.\n\nA policy can be defined as a plan of action established by an organization or a political party to determine the scope of operations; a policy is also a principle or set of plans used as a basis for making decisions (Akinyemi & Adejumo, 2018). Government policies include political activities, plans, and a scope of principles to be achieved by government and political actors in order to recognize public issues and make public decisions for the country’s development. Recently, government agencies are continuously implementing change through transforming public policies into actions and supporting the growth of innovation capacity in the government organization, as government policies have an influence on organizational performance (Ismanu & Kusmintarti, 2019; Karungani & Ochiri, 2017). As the challenges for public services become more complex, the concept of innovative and competitive management policies is being increasingly revisited and replaced by more adaptive and effective policies such as public entrepreneurship policies. It can be seen that an essential and appropriate government policy can enhance the concept of public entrepreneurship within an organization (Akinyemi & Adejumo, 2018; Obaji & Olugu, 2014). The role of government is perceived to be establishing innovative and proactive public policy to serve new public service demands and to motivate entrepreneurial orientation in various public organizations. Consequently, public entrepreneurship, as a government tool, seems to rapidly enhance public organizational performance and outcomes (Kareem & Haseeni, 2015; Sandfort, Selden, & Sowa, 2008). Therefore, this research study focuses on the entrepreneurship policies made by the government in order to build an innovative and effective public working system in the organization, and finally to increase organizational performance.\n\nThe concept of entrepreneurship in public organizations is highly incorporated into the mind-set of government officials (Kim, 2010; Kearney, Hisrich, & Roche, 2009) and can be used to change the orientation of public staff to be more innovative, creative, anticipatory, have higher risk acceptance, and be able to predict opportunities (Fahim, 2018; Banda & Kazonga, 2018). Public entrepreneurship can be defined as an activity that integrates or blends two different managerial roles: that of a public servant, and that of private entrepreneur (Syam, Lamangida, Madubun, Norwawati, & Akib, 2018). In emerging countries, and especially in Thailand, entrepreneurship development in the public sector seems to be of particular importance for driving the improvement of the economy. The government can implement various policies that change social and economic behaviors in order to influence the country’s growth and sustainability (Nikolov & Botseva, 2018; Wahyuni, 2004). It is thought that the recent government policy development on public entrepreneurship, consisting of building competitiveness, innovation, and digitalization, will bring the necessary change for the country (Svensson, 2019; Sarfat, 2012). Future government services will increasingly need to rethink and react like an entrepreneur, including innovative-orientation, risk acceptance, competitive service, and public digitalization (Kim, 2010; Zerbinati & Souitaris, 2005). The need for public entrepreneurship policies and programs has been recognized and programs have been established to promote entrepreneurial activities, stimulate innovative systematic thinking, and form collaborative relationships across government agencies, private sectors, and civil society in order to rapidly increase change and particularly to enhance public performance and outcomes (Rezaeikar & Azadehdel, 2015; Kim, 2010). Currently, the managerial and administrative organizational reforms of public organization toward public entrepreneurship have been established in the public sector with critical key functions to improve organizational performance (Fahim, 2018; Karinda et al., 2016). Therefore, this research study focuses on public entrepreneurship as having a mediating role in government policy and organizational performance in provincial administration organizations in Thailand.\n\nOrganizational performance has become a significant indicator to measure ultimate outcomes compared to desired outcomes, especially in government organizations. Organizational performance has been defined as the process or action of performing a task towards the ultimate result of operations (Kearney, Hisrich, & Roche, 2008; Antoncic & Scarlat, 2005). It can be seen that public organizational performance seems to be directly influenced by government policy implementation (Akinyemi & Adejumo, 2018; Peters, 2015). Currently, a public entrepreneurship policy has been launched by the government to increase innovative and competitive public outcomes, and consequently enhance public organizational performance. Importantly, public organizations have established various modern performance determinant methods in order to measure outcome achievement. One of the various measurement instruments indicated a balanced scorecard, an organizational performance measurement system to reach the desired outcome, which provided a general outline for government organizations to achieve (Zastempowski, 2015; Greatbanks & Tapp, 2007). A balanced scorecard has gained widespread acceptance due to its use as a practical and a multi-dimensional performance measurement tool for public organizations. The performance management of a balanced scorecard applied in the public sector consists of four perspective dimensions: innovation and learning; efficiency of internal processes; public service quality; and effectiveness of goal achievement (Northcott & Taulapapa, 2012). The public performance will ultimately be driven by establishing the innovative and proactive government management policy and implementing public entrepreneurship in public organizations, in order to achieve desired organizational outcomes according to the rapid change of the external environment (Rodrigo et al., 2019). It can be seen that the concept of entrepreneurship within the public sector establishes a vital impact on public sector organizational performance including growth, development and productivity (Oyebanji & Olanrewaju, 2020; Kearney, Hisrich, & Roche, 2008). Therefore, this research study focuses on the effects of government policy on organizational performance in order to investigate the direct and indirect effects of such relationships.\n\nTo conclude, from the literature reviews of three variables of government policy, organizational performance, and public entrepreneurship, as discussed above, it can be seen that there are some relationships among the three specified variables to further explore and conceptualize in the model of this research study. The conceptual framework explaining such relationships was intensively investigated with hypotheses development.\n\nFrom the literature review, the conceptual framework of this research study was built and is presented in Figure 1. It describes the effects of government policy on organizational performance through the mediating role of public entrepreneurship in provincial administration organizations in the upper northeastern region 2 of Thailand. The conceptual framework has been developed for hypotheses testing based on the three bodies of knowledge (government policy, organizational performance, and public entrepreneurship) cited in the theoretical framework, as well as the researcher’s exploration about the relationship among the specified three variables.\n\nBased on the literature reviews of the constructs with the conceptualization of the relationships among the specified three variables, the hypotheses development proposed by the above conceptual framework can be described as follows:\n\nH1. Government policy has a direct effect on organizational performance of the provincial administration organization in the upper northeastern region 2 of Thailand.\n\nH2. Government policy has an indirect effect on organizational performance through the mediating role of public entrepreneurship in a provincial administration organization in the upper northeastern region 2 of Thailand.\n\nIn addition, the research hypotheses can be described in the forms of structural equations in order to explain the relationship between the independent variable and the dependent variable, as well as to predict the dependent variable according to the causal model analysis. The symbols used to represent the specified three variables stated as follows:\n\nGOVP = Government policy\n\nPUBE = Public entrepreneurship\n\nORGP = Organizational performance\n\nThe structural equations can be described as follows:\n\nThe parameters of β1, β2, and β3 in the equations refer to path coefficients, and they quantify the causal effects of the independent variable on the dependent variable (Pearl, 2010).\n\n\nMethods\n\nEthical approval was waived for this study as it is a survey research with no sensitive questions, as well as having no impact on respondents as the results are not specific. Additionally, the encode-recording of information ensures confidentiality as individual persons cannot be identified. The research had voluntary participation in the form of a consent statement in the questionnaire, with privacy and confidentiality protection. Finally, the data was collected through research assistants for education only and the research results do not identify the functional department of organizations, merely the organizations overall.\n\nThis research study aimed to investigate the effects of government policy on organizational performance through the mediating role of public entrepreneurship in provincial administration organizations in the upper northeastern region 2 of Thailand. This research study used a quantitative research method. A sample of 216 government officials of provincial administration organizations in the upper northeastern region 2 of Thailand was collected from the Office of the Permanent Secretary database as of June 2019; this number was determined using simple random sampling based on Taro Yamane’s formula (Yamane, 1973). Yamane explains a simplified formula to calculate the sample size from the population size with 95% confident level. Data were collected using five-point Likert scale questionnaire surveys. Printed questionnaires were created and distributed to the participants during the period of August–September 2019 via research assistants who are responsible for explaining the purpose of this research and the data usage, and gaining voluntary consent from participants. The respondents were asked to rate the questions using the five-point rating scale indications (5 = most agree, 1 = least agree). This research study was a cross-sectional construct as the data were collected at a single point in time from the specified key respondents with 100% response rate. For validity and reliability analysis, content validity was applied to ensure the accuracy of the research instrument. Content validation employs a primary role in assessing the degree to which the instrument measures the targeted constructed (Rusticus, 2014). Overall, the scale content validity index for the questionnaire was 1.00, demonstrating absolute agreement among content qualified experts. In addition, this research study employed the Cronbach’s alpha to test for reliability. The Cronbach’s alpha coefficient of all variables were calculated as follows: reliability values of government policy, organizational performance, and public entrepreneurship were at 0.904, 0.941, and 0.936, respectively, as shown in Table 1. The Cronbach’s alpha value for all variables is greater than 0.700, so it shows that the survey has very good reliability. The research results can be analyzed for significance with 95% confidence interval.\n\nThe research results were analyzed using SPSS version 26. Data were analyzed by using descriptive statistics. Frequency and percentage were used to describe the demographic information of respondents and mean and standard deviation were used for levels of respondents’ opinions on government policy, organizational performance, and public entrepreneurship. In addition, data were analyzed using inferential statistics stated as follows: Pearson’s product-moment correlation was applied to test the relationship among variables; path analysis was applied for hypotheses testing on direct and indirect effects of government policy on organizational performance through the mediating role of public entrepreneurship. Bias in research was considered and can be minimized through implementing a structured survey design and ensuring questions are well constucted, as this helps to ensure participants’ responses are more accurate and autonomous.\n\n\nResults\n\nThe research findings from the respondents, hypotheses testing, discussion of results and implications for the study of the effects of government policy on organizational performance through the mediating role of public entrepreneurship on provincial administration organizations in the upper northeastern region 2 of Thailand are presented as follows.\n\n216 questionnaire surveys were distributed to participants during the period of August-September, 2019. All were completed and correctly filled out, giving a 100% response rate. The research findings revealed that of 216 government officials from the upper northeastern region 2 in Thailand who took the surveys, 59.30% were female. The most common age group of government officials was that of 21-30 years, and this made up 36.10% of respondents. For the respondents’ education, most of the government officials had earned a Bachelor’s degree (77.80%). In addition, the most common position was that of government official (63.00%), with 6-10 years’ experience (33.30%). Most of the government officials worked for the Sakon Nakhon Provincial Administration Organization (43.10%). Lastly, the most common monthly income of the respondents was in between 10,001-20,000 Baht (52.30%), as shown in Table 2.\n\nFor descriptive statistics, the collected data from five-point Likert scale questionnaire surveys specifying the rating scale indications (5 = most agree, 1 = least agree) were calculated as average scores and standard deviations. The mean scores of government officials’ opinion on government policy, public entrepreneurship, and organizational performance were high, with average scores on Likert scale of 3.65, 3.70, and 3.68, respectively. In addition, the standard deviations on Likert scales of these measures were 0.69, 0.74, and 0.70, respectively.\n\nFor inferential statistics, the analysis of the correlation coefficient among the two independent variables and the dependent variable was investigated. Pearson's product-moment correlation was used to determine the relationship of the independent variables. The objective of correlation analysis was to find the magnitude of correlation among the variables and to test for multi-collinearity. Correlation analysis between the independent variables of government policy and public entrepreneurship is shown in Table 3.\n\n** Correlation is significant at the 0.01 level (two-tailed).\n\nTable 3 demonstrates that for the relationship between the independent variables, the correlation coefficients (r) do not exceed 0.800. As Hair et al. (2010) described, the relationship between the variables must be less than 0.800 otherwise it may cause multi-collinearity problems (Hair, Black, Babin, & Anderson, 2010). As this research study found that the relationship between the independent variables with the highest coefficient value was 0.756, and so a multi-collinearity problem was not found in this relationship. Therefore, the research study can be tested for hypotheses by applying path analysis using a linear model structure, in order to investigate direct and indirect effects of government policy on organizational performance through the mediating role of public entrepreneurship at a 0.05 significance level.\n\nThe research results from hypotheses testing are presented in Table 4.\n\n*** Predictor is significant at the 0.00 level (two-tailed).\n\n** Predictor is significant at the 0.05 level (two-tailed).\n\nTable 4 shows the results of hypotheses testing, which are that government policy and public entrepreneurship can causally predict in organizational performance of provincial administration organizations in the upper northeastern region 2 in Thailand up to 57.60% (adjusted R-Square 0.576) at a 0.05 significance level. In terms of the effects, government policy has a significant direct effect on organizational performance with a standardized coefficient of 0.655. The government policy has a significant direct effect on public entrepreneurship with a standardized coefficient of 0.756. Public entrepreneurship has a significant effect affected on organizational performance with a standardized coefficient of 0.749. In addition, government policy has a significant indirect effect on organizational performance through the mediating role of public entrepreneurship with a standardized coefficient of 0.566. The total effects can be described with a standardized coefficient of 0.773 at a 0.05 significance level. The research results have significant effects with 95% confidence intervals.\n\n\nDiscussion\n\nAccording to the results of hypotheses testing by applying path analysis, government policy has a significant direct and indirect effect on organizational performance through the mediating role of public entrepreneurship in provincial administration organizations in the upper northeastern region 2 of Thailand. In general, the research results from this study are aligned with other previous literatures that investigated this topic in other organizations and in other countries (Oyebanji & Olanrewaju, 2020; Rodrigo et al., 2019; Akinyemi & Adejumo, 2018; Karinda et al., 2016; Kareem & Haseeni, 2015). Specifically, the research results recommend that modern government policies on driving public entrepreneurship are significant to organizational performance achievement in public sector. Despite the contributions this research study intensely provided, nominal limitations still need to be discussed. Firstly, the scope of data collection is only limited to the provincial administration organizations in the upper northeastern region 2 of Thailand. The limited sample coverage could impact the degree to which the research results can be generalized to the larger population. Secondly, the use of self-administered questionnaire surveys for data collection could lead to some subjective bias in the data. However, the proposed proactive policies for public entrepreneurship transformation and public performance enhancement of provincial administration organizations are discussed as follows.\n\nFirstly, the government should establish innovative and competitive public policies to support the rapid change of entrepreneurial orientation for provincial administration organizations. As government policies on public entrepreneurship can encourage public organizations to take risks, and boost creativity, innovation, flexibility and adaptation as well as utilization of opportunities, the government should intensely consider these issues.\n\nSecondly, government organizations should drive radical change to public entrepreneurship in order to efficiently manage public resources, innovatively provide excellent public services, strategically facilitate risk, continually sustain public interests, and effectively achieve organizational performance in the long run. The government should predominantly transform important policies into action.\n\nThirdly, government agencies should build public capacity as the role of public entrepreneurship will be critical in continuing to support the potential of government officials to deliver excellent public services and achieve better performance and outcomes. Conventional public structures of performance management are being replaced by more innovative, adaptive, and competitive public entrepreneurship strategies in order to get the desired and more effective public outcomes.\n\nIn conclusion, it can be seen that the essential proposed recommendations on public entrepreneurship transformation and public organizational performance enhancement as well as managerial implications and government suggestions are significant to all public organizations. The research results can be generalized to local government agencies to transform proactive government policies into actions, through establishing innovative strategy, implementing proactive working system, and incorporating digital technology for public service provision in order to enhance organizational performance.\n\n\nConclusion\n\nThe general inference drawn from this research study on the effects of government policy on organizational performance through the mediating role of public entrepreneurship in provincial administration organizations in the upper northeastern region 2 of Thailand concludes that government policies are important guidelines to implement entrepreneurial activities and to enhance government organizational performance, especially for some local government organizations that plan to transform themselves into public entrepreneurship. Public entrepreneurship is favourable in promoting innovation, increasing risk-taking orientation and boosting public organizational performance and outcomes for local government organizations in Thailand. However, this research study eagerly calls for more studies on other antecedent factors influencing public entrepreneurship in various levels of government organizations as future research.\n\n\nData availability\n\nFigshare: Input-SaNooK_Scopus (English). https://doi.org/10.6084/m9.figshare.15050787.v1.\n\nThis research contains the following underlying data:\n\n- Input-SaNooK_Scopus (English).sav (raw data sheet).\n\nFigshare: Data Key for Questionnaire Responses. https://doi.org/10.6084/m9.figshare.15098556.v1.\n\nFigshare: Questionnaires-Sanook-Scopus. https://doi.org/10.6084/m9.figshare.14993541.v1.\n\nFigshare: Questionnaires-Sanook-Scopus (English) https://doi.org/10.6084/m9.figshare.15050643.v1.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAkinyemi FO, Adejumo OO: Government policies and entreprenuership phases in emerging economies: Nigeria and South Africa. J Entrepr Res. 2018: 1–18. Publisher Full Text\n\nAntoncic B, Scarlat C: Corporate entrepreneurship and organizational performance: A comparison between Slovenia and Romania. In: Proceedings of the 6th international conference of the faculty of management Koper Congress Centre Bernardin. Slovenia; November 2005. 71–89.\n\nBanda P, Kazonga E: The effect of public sector corporate entrepreneurship on organizational performance in the health sector: A case of selected public hospitals in Lusaka, Zambia. IOSR J Business Management (IOSR-JBM). 2018; 20(4): 8–18.\n\nFahim MA: The impact of entrepreneurship on performance in public sector organizations with application to the Egyptian electricity holding company. Arab J Admin. 2018; 38(2): 227–256. Publisher Full Text\n\nGreatbanks R, Tapp D: The impact of balanced scorecard in a public sector environment: Empirical evidence. Int J Operations Production Management. 2007; 27(8): 846–873. Publisher Full Text\n\nHair JF, Black WC, Babin BJ, et al.: Multivariate Data Analysis. 7th ed Prentice Hall: Englewood Cliffs; 2010.\n\nIsmanu S, Kusmintarti A: Government policies and firm size as a moderating effect of innovation on business performance. Adv Economics, Business Management Res. 2019; 136: 123–128. Publisher Full Text\n\nJones C, Pimdee P: Innovative ideas: Thailand 4.0 and the fourth industrial revolution. Asian Int J Soc Sci. 2017; 17(1): 4–32. Publisher Full Text\n\nKareem MA, Haseeni ZJ: E-Government and its impact on organizational performance. Int J Management Commerce Innovations. 2015; 3(1): 664–672.\n\nKarinda JM, Noermijati, Armanu, et al.: The effect of organizational culture, and entrepreneurship characteristics of knowledge management on company performance (Study on contruction services company first small qualification Papua in Jayapura). South East Asia J Contemporary Business, Economics Law. 2016; 11 (2), 80–86.\n\nKarnsomdee P: Input-SaNooK_Scopus (English). figshare. Dataset. 2021. Publisher Full Text\n\nKarnsomdee P: Questionnaires-Sanook-Scopus. figshare. Dataset. 2021. Publisher Full Text\n\nKarnsomdee P: Questionnaires-Sanook-Scopus (English). figshare. Dataset. 2021. Publisher Full Text\n\nKarnsomdee P: Data Key for Questionnaire Responses. figshare. Dataset. 2021. Publisher Full Text\n\nKarungani WP, Ochiri G: Effect of policy and regulatory framework on organizational performance: A case of Nairobi country, Kenya. Int J Economics, Commerce Management. 2017; 5(6): 565–573.\n\nKearney C, Hisrich R, Roche F: A conceptual model of public sector corporate entrepreneurship. Int Entrep Manag J. 2008; 4: 295–313. Publisher Full Text\n\nKearney C, Hisrich R, Roche F: Public and private sector entrepreneurship: similarities, differences or a combination? J Small Business Enterprise Devel. 2009; 16(1): 26–46. Publisher Full Text\n\nKim Y: Stimulating entrepreneurial practices in the public Sector: The roles of organizational characteristics. Admin Society. 2010; 42(7): 780–814. Publisher Full Text\n\nNikolov GB, Botseva D: Role and importance of government policies and strategies for long-term economic development. Synthesis of Science and Society in Solving Global Problems Conference, Shioda GmbH, Steyr, Austria. 2018; 2018: 34–38.\n\nNorthcott D, Taulapapa TM: Using the balanced scorecard to manage performance in public sector organization: Issues and challenges. Int J Public Sector Management. 2012; 25(3): 166–191. Publisher Full Text\n\nObaji NO, Olugu MU: The role of government policy in entrepreneurship development. Sci J Business Management. 2014; 2(4): 109–115. Publisher Full Text\n\nOyebanji AS, Olanrewaju FK: Fostering corporate entrepreneurial culture through performance appraisal in organizations. IOSR J Business Management (IOSR-JBM). 2020; 22(7): 43–48. Publisher Full Text\n\nPearl J: An introduction to causal inference. Int J Biostat. 2010; 6(2). PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeters BG: Policy capacity in public administration. Policy Society. 2015; 34: 219–228. Publisher Full Text\n\nRezaeikar EM, Azadehdel MR: Relationship between entrepreneurship and organizational performance in executive organization in Guilan. Science J (CSJ). 2015; 36(3): 3425–3431. Publisher Full Text\n\nRodrigo MR, Victor J, M G, et al.: Technological antecedents of entrepreneurship and its consequences for organizational performance. Technological Forecasting Social Change. 2019; 147: 22–35. Publisher Full Text\n\nRusticus S: Content validity. In: Michalos AC (eds) Encyclopedia of Quality of Life and Well-Being Research. Dordrecht: Springer; 2014. Publisher Full Text\n\nSandfort J, Selden SC, Sowa JE: Do government tools influence organizational performance? Examining their implementation in early childhood education. Am Rev Public Admin. 2008; 38(4): 412–438. Publisher Full Text\n\nSangwanna S, Pupat P: Thai industrial cluster promotion model development for Region 8: Rajamangala University of Technology and Suvarnabhumi Airport. Asian Int J Soc Sci. 2014; 14(2): 84–103. Publisher Full Text\n\nSarfat G: Do public policies for entrepreneurship make a difference? Prospective scenarios for Canada, Ireland, and Italy. Future Studies Res J. 2012; 4(1): 114–139. Publisher Full Text\n\nSvensson P: Formalized policy entreprenuership as a governance tool for policy integration. Int J Public Admin. 2019; 42(14): 1212–1221. Publisher Full Text\n\nSyam H, Lamangida T, Madubun J: Public entreprenuership perspective in management of the Limboto Lake in Gorontalo Regency, Indonesia. Acad Entreprenuership J. 2018; 24(4): 1528–2686.\n\nWahyuni H: The role of government in economic growth: Evidence from Asia and Pacific countries. Jurnal Ekonomi dan Bisnis Indonesia. 2004; 19(1): 71–81. Publisher Full Text\n\nYamane T: Statistics an Introduction Analysis. 2nd ed New York: Harper and Row; 1973.\n\nZastempowski M: The balanced scorecard in the public sector organization. Managing Public Organizations in Theory and Practice. 2015: 53–64.\n\nZerbinati S, Souitaris V: Entrepreneurship in the public sector: a framework of analysis in European local governments. Entrepreneurship Regional Devel. 2005; 17: 43–64. Publisher Full Text"
}
|
[
{
"id": "142113",
"date": "28 Jun 2022",
"name": "Kittisak Jermsittiparsert",
"expertise": [
"Reviewer Expertise Political Science",
"Public & Private Management",
"International Political Economy",
"Social Research"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn fact, the issues the author set out to study are important and interesting. However, it has so many flaws that it is unsuitable for indexing in this format.\nStart from the title of the article. It has a few interesting points. The first question is what does the term \"government policy\" mean here? What is the direction of that policy? However, when looking at the attached questionnaire, the author call it the external factors. And almost all the questions try to repeatedly ask whether various government policies contribute to promoting entrepreneurship of government agencies or not. And how is it possible that by summing and averaging the opinions of these respondents, it will lead to a link to the results that the author tries to say that these \"government policies\" are what caused them? However, it must be considered in terms of logic, rationality, not just the results of numerical analysis.\nIn terms of improvements, the author should change the term \"provincial administrative organization\" to \"local government\" to make this research clearer, more international, and better linked to other research and the bigger picture. The picture that will emerge from such revisions is that federal policies, which should have a clearer and more rational direction such as decentralization and budgets to local governments, will lead to better performance of local governments. However, if the author still wishes to clearly specify that it is a PAO (provincial administration organization), it can be done by stating in the research method that the local government organizations in this research are PAOs in the upper northeastern region of Thailand.\nThe Introduction is very short, it still needs to be expanded accordingly. The author needs to have a clearer direction in highlighting the importance of the subject to be studied. The author may make it clear that government organizations here refer to local government organizations. With this clarity, the author will be able to begin clearly that local governments are critical in providing public services to the people. The most basic explanation is that it is the agency closest to the people. Therefore, its performance means something that will benefit the people. Subsequently, the author should point out that the performance of local government organizations differs from country to country. Anyway, what factors are involved? These issues should be cited by a number of research papers to give a brief overview without going into details but to show that they are of great academic importance and have been studied extensively. In this Introduction, the author may also mention the situation in Thailand. There are related reports suggesting that the performance of local governments in the country is still poor. There are many reasons for this. The question of this research is, what factors will improve the performance of these local government organizations?\nLiterature reviews need to be updated to a higher standard than they are. A synthesis of really relevant research needs to be produced in order to develop hypotheses and form a research conceptual framework accordingly. The big problem with this research paper is citations. The sources the author refer to are not mentioned, as the author tries to say they do. It becomes a problem that, in fact, what the author is trying to bring up, to convince readers, is information that does not exist. For example, it is said that Oyebanji & Olanrewaju (2020) is referring to local government organizations in Thailand, but it is actually a general organization and is conducted in Nigeria. Or saying that government policy affects organizational performance is based on two studies that looked at the underlying variables: technology and e-government, not government policy.\nIn the Research methods, the author did not mention the population size. Indeed, the biggest problem and at the heart of the matter that render the results of this article's analysis useless is the questionnaire. It is clear that the author did not actually design the questionnaire for research on this issue, but on another issue. Attempting to convert an issue from the original questionnaire to a new issue that the content of the questionnaire could not reflect, would cause problems that could not be resolved.\nAs for the results of the research, the author must be aware that the demographic data of the samples are not the results of the research. Because it is not an answer to a research question, and no one cares about what gender or monthly income the respondents are in the sample.\nThe conclusions and discussions were not very good. Author need to point out the findings of the research, what it means, and discuss other research, especially overseas, which is the big picture. However, since the questions in this questionnaire are problematic from the beginning. When examined in detail to describe the results of statistical analysis and their origins, there are large gaps or discrepancies in the matter.\nThe number of references used is relatively small. And as I said, they were incorrectly referenced.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-794
|
https://f1000research.com/articles/10-790/v1
|
11 Aug 21
|
{
"type": "Research Article",
"title": "Prevalence and determinants of contraception use in Pakistan: trend analysis from the Pakistan Demographic and Health Surveys (PDHS) dataset from 1990 to 2018",
"authors": [
"Salima Meherali",
"Anna Ali",
"Asif Khaliq",
"Zohra S. Lassi",
"Anna Ali",
"Asif Khaliq",
"Zohra S. Lassi"
],
"abstract": "Background: In developing countries, pregnancy and childbirth are the leading causes of death among women. In this context, family planning and access to contraceptives are crucial for reducing pregnancy-related morbidity and mortality. Therefore, we aimed to look into the trends of contraception and determinants of contraceptive use in Pakistan. Methods: This study used data for women of reproductive age from four Pakistan Demographic and Health Surveys datasets. Contraception was the outcome variable, whereas, women’s and partner’s education, occupation, wealth quintile, region, place of residence, and exposure to family planning messages were the explanatory variables. Pooled prevalence was estimated using SUMARI and regression analysis was undertaken using SPSS to produce an adjusted prevalence ratio with 95% confidence intervals. Results: Data of 40,259 ever-married women of reproductive age (EMWRA) was analysed. Of the total EMWRA, 30% were using contraception. Of these, 26% were using traditional methods and 74% were using modern methods. The most common method of contraception was condoms (30.5%). The pooled prevalence of contraception used was 29.5% (95% CI 29.1 to 30.0). Through multivariate analysis, women's age, place of residence, region, wealth index, women’s education, their working status, and exposure to family planning messages were found to be significant determinants of contraception usage. Conclusions: There is a noticeable gap regarding awareness and uptake of contraception leading to low contraceptive use among women in Pakistan. In the light of our results, it is important to highlight the importance of girl’s education for building awareness and empowerment.",
"keywords": [
"Pakistan",
"contraception",
"demographic and health survey"
],
"content": "Introduction\n\nPregnancy and childbirth are the leading causes of death among girls and women aged 15 to 49 years in many low and middle-income countries (LMICs) (World Health Organization [WHO], 2017). In this context, family planning and access to contraceptives are crucial for reducing pregnancy-related morbidity and mortality, improving the health outcomes of young girls and women and their children, and reducing the related social and economic costs of early pregnancy (Chandra-Mouli et al., 2017). Although significant progress has been made in improving coverage of family planning services worldwide (Cahill et al., 2018; MacQuarrie, 2014) there is still a large gap in relation to effectively meeting the contraceptive needs and family planning goals in LMICs (Chandra-Mouli et al., 2017; MacQuarrie, 2014; Dennis et al., 2017; Ewerling et al., 2018).\n\nPakistan is an LMIC situated in the South Asian region and shares the highest population growth rate i.e. 2% per year in South Asia (The World Bank, 2019). Progress towards accomplishing the United Nations’ Sustainable Development Goals (SDG) to increase the contraceptive prevalence rate (CPR) to 55% by 2015 remained unachievable for Pakistan. One of the pivotal reasons for the high population growth rate of Pakistan is the unmet need for family planning (Nyoni, 2018). The government of Pakistan and private health sectors have been continuously struggling to bring down population growth by improving the availability of family planning services. Although progress has been made to reduce the fertility rate from seven children per woman in 1970 (Shah et al., 1986) to 3.6 children per woman in 2020, the acceptability and use of contraceptives in the country are low (A. Mahmood & Sultan, 2006). According to the World Bank report (2015), the average CPR in South Asian countries is 53%, and Pakistan has the lowest rate of 35%. Many potential barriers exist to contraceptive use among women of reproductive age (WRA) in Pakistan such as the social, cultural, and perceived religious unacceptability of contraception, lack of knowledge and awareness of contraception, cost of contraceptives, and access to contraceptive services (Asif and Pervaiz, 2019; Memon & Jonker, 2018; N.Z. Shah et al., 2020; Dasgupta et al., 2019).\n\nLow CPR increases the risk of unplanned pregnancies, teenage pregnancies, abortions, and thereby resulting in poor maternal and child health outcomes (Wulifan et al., 2017). Moreover, the low CPR also produces a drastic effect on the economy of a nation. Currently, Pakistan is facing issues related to inflation, poverty, unemployment, and other related economic crises (Nyoni, 2018). Under such conditions, it is essential to know about the trends and determinants of CPR in Pakistan from the nationally available datasets. Knowing the trends and determinants of contraceptive prevalence among WRA will aid in understanding and planning appropriate interventions and policies for the promotion of contraceptive use. This in turn helps the nation to control the population outgrowth and other economic issues.\n\nThe objectives of this study were:\n\n• To determine the prevalence of contraception among WRA in Pakistan\n\n• To identify the factors leading to low CPR among WRA in Pakistan\n\n\nMethods\n\nDatasets from the Pakistan Demographic and Health Surveys (PDHS) were used in this study (NIPS, 2019). These surveys include information on the health, demographic and socioeconomic characteristics of the representative sample of Pakistan. From 1990 until 2018 Pakistan has implemented four Demographic and Health Surveys (DHS) under the AEGIS of the National Institute of Population Studies (NIPS) and Pakistan Bureau of Statistics (PBS) (National Institute of Population Studies, 1992). For the current study, we have used secondary data of all the DHS conducted in Pakistan regarding the use of contraception by ever-married women of reproductive age (EMWRA) aged between 15 to 49 years.\n\nA multistage stratified cluster systematic sampling technique was used in these surveys. After stratification of all provinces on the urban and rural population, Enumeration Blocks (EB) (the cluster of 200 to 250 households (HH)) were selected followed by random selection of 20-30 HH from each EB. The total number of EMWRA was 40,259; 6,611 in 1990-91 PDHS; 9,177 in 2006-07 PDHS; 11,763 in 2012-13 PDHS; and 12,708 in 2017-18 PDHS.\n\nThe outcome variable of this study was the use of contraception both modern (such as a pill, intrauterine device, injection, condom, female sterilization, implant) and traditional (such as withdrawal, and lactation) methods. Use of contraception was defined by using the information of current methods of contraception used by study participants at the time of the interview. Women using any modern or traditional methods of contraception were grouped. The information regarding the use of contraception was collected verbally by the interviewers in the PDHS. Information on types and methods of contraception were also collected verbally and this information is included in the analyses. Data on the decision of using contraception were available for two years only 2012-13 and 2017-18 and data regarding the decision of not using contraception were available for the year 2017-18 only. Respondent’s age was available in seven categories which were merged into four categories as 15-24, 25-34, 35-44, and 45 and above. Respondent’s and partner’s education were coded into four categories: no education, primary, secondary, and higher. Both respondent’s and their partner’s occupations were coded as: not working, professional, services/sales, agricultural, skilled, and unskilled. To avoid a small cell count, occupation categories for respondents were merged into working and not working; while for their partner was merged into: not working, unskilled, skilled, and professional categories for the partner. The place of residence was coded as urban or rural; the region was coded into Punjab, Sindh, Khyber Pakhtunkhwa (KPK), Baluchistan, and Islamabad Capital Territory (ICT). Wealth index was constructed using principal component analysis on assets-ownership including land and livestock with a range of socio-economic factors including income, type of flooring, availability of electricity, radio, television, telephone and refrigerator, type of vehicle, persons sleeping per room, household construction, utilities, source of drinking water and sanitation facilities, ownership of agricultural land, domestic servants. and categorized as five wealth quintiles: poorest, poorer, middle, richer, and richest; and exposure to family planning messages via radio, TV, and newspaper were merged and categorised as yes and no to avoid small cell counts.\n\nAll analysis was done in SPSS version 26 (Jiang & Hardee, 2014) and pooled prevalence was estimated from Joanna Briggs Institute’s SUMARI (Babalola, 2014). Frequency and percentage of categorical variables and mean with standard deviation (SD) of continuous variables were reported. The use of contraception was defined by using the information of current methods used by study participants. Women using any method (traditional or modern) of contraception were grouped. The rate of contraception usage was determined for each year (1990-91, 2007-08, 2012-13, and 2017-18) separately, and later pooled prevalence was estimated. Prevalence ratios were estimated for socio-demographics, media exposure, and use of contraception using cox regression. All variables with borderline statistical significance (p < 0.25) were considered as potential confounding variables. The determinant of contraception usage is reported as prevalence ratio (PR) with a 95% confidence interval (CI). Multivariable regression models were used to produce covariate-adjusted PR (APR) and 95% CIs. R is an open access software that could also be used for performing this analysis.\n\n\nResults\n\nData of 40,259 EMWRA was analysed. In total, 29.4% were in the age group 25-29 years and 23.4% were between 30-34 years. More than half (57.4%) were from rural areas of Pakistan and around one-third were from Punjab and Sindh (29.8% and 22.8%), respectively. Around half of the women (44.7%) were from the poorest and poor wealth quantile. More than half were not educated (60.7%) and 80.8% were not working. With respect to their partner, almost one-third (33.6%) were not educated, and almost (97%) all were working in some capacity. Of all the women, a quarter heard about family planning on the TV (25.3%), and a small percentage on the radio (7.6%) and newspaper (3.7%) (Table 1).\n\n* Data not available for the year 1990-91.\n\n** Data not available for 1990-91 and 2007-08.\n\nOf the total 12,078 women who were using contraception, more than half were of age 25-34 and were from urban areas of Pakistan (53.2%). Around one-third of the province of Punjab (35.2%) followed by Sindh (19.6%) and Baluchistan (18.8%) and half of them were from richer and richest wealth quintile (50.2%) (Table 1).\n\nOf the total EMWRA, 30% were using contraception. Of these, 26% were using traditional methods and 74% were using modern methods. With respect to the individual methods, the most common method of contraception was condom (30.5%) followed by withdrawal (20.4%), female sterilization (12.0%), injections (12.1%), pills (8.0%), intrauterine device (IUD) (7.5%), periodic abstinence (5.1%), lactation amenorrhea (2.8%), Norplant (0.9%) and other methods (0.7%) (Figure 1). With respect to the decision-making for using or not using contraception, most of them reported that it is the joint decision (86.0% vs 62.2%, respectively). However, when it is one-sided, the husband decides not to use contraception (22.9%) (Figure 2).\n\n*Data on the decision of using contraception were available for two years only 2012-13 and 2017-18 and data regarding the decision of not using contraception were available for the year 2017-18 only.\n\nThe rate of contraception use was 13.0% (95% CI 12.2 to 13.8) in 1990-91 and since then the rates increased to 27.7% (95% CI 26.7 to 28.6) in 2006-07, 36.4% (95% CI 35.6 to 37.3) in 2012-13, and slightly declined to 34.6% (95% CI 33.8 to 35.5) in 2017-18. The overall pooled prevalence of contraception used was determined as 29.5% (95% CI 29.1 to 30.0) (Figure 3).\n\nThrough multivariate analysis, it was found that women's age, place of residence, region, wealth index, education, working status, and exposure to family planning messages were significant determinants of contraception usage. The APR was significantly higher among women who were aged 45 years and above (APR 1.59; 95% CI 1.32 to 1.91) followed by women aged 35-44 years (APR 1.47; 95% CI 1.37 to 1.58) and women aged 25-34 years (APR 1.26; 95% CI 1.19-1.33) compared to women aged 15-24 years. The APR was significantly higher among women who were from urban areas (APR 1.08; 95% CI 1.02 to 1.13) compared to those who were living in rural areas. However, the APR was significantly lower among women who were from the province of Sindh (APR 0.83; 95% CI 0.72 to 0.86), KPK (APR 0.78; 95% CI 0.71 to 0.84), and Baluchistan (APR 0.58; 95% CI 0.52 to 0.65) compared to those living in ICT. The APR of contraception usage was significantly higher among women who were from the richest quantile (APR 2.10; 95% CI 1.91 to 2.32) followed by richer quantile (APR 2.02; 95% CI 1.85 to 2.21), middle quantile (APR 1.77; 95% CI 1.63 to 1.92) and poorer quantile (APR 1.43; 95% CI 1.32 to 1.55) compared to women who were from poorest quantile. The APR was higher for women who were highly educated (APR 1.08; 95% CI 1.00 to 1.16) and (APR 1.13; 95% CI 1.07 to 1.19) for those who had primary or secondary education compared to women who were not educated. With respect to women's occupation, APR was significantly higher among women who were working (APR 1.22; 95% CI 1.16 to 1.30) compared to not working women. Lastly, women who had exposure to family planning messages had significantly higher APR of contraception usage (APR 1.21; 95% CI 1.15 to 1.27) (Table 2).\n\n\nDiscussion\n\nFamily planning and planned pregnancies are crucial to the health and development of a child as well as their mothers, thereby reducing maternal and child mortality, and rates of unsafe abortions. Besides health benefits, family planning offers a range of non-health benefits that entails women empowerment, sustainable population growth, and economic development of the country. Despite major family planning initiatives by the government in Pakistan and being one of the first countries in South Asia to start a national family-planning programme (Fikree et al., 2001), the total fertility rate remains high with relatively low contraception usage (Shah et al., 2020; Cham et al., 2005).\n\nThe results of the study highlight the key contextual factors that are associated with the high prevalence of contraceptive use among EMWRA. Some of the factors that increase the likelihood of contraceptive use include the education level of mothers, their employment status, exposure to family planning messages, and overall socio-economic status. Firstly, our multivariate analysis reveals that the use of contraception was significantly higher among educated women and those who belonged to the working class.\n\nThese findings mirror the results from other studies where mainly the completion of primary and secondary school education of women was strongly correlated to lower desire for fertility (Jiang & Hardee, 2014), the greater number of antenatal visits (Babalola, 2014), higher use of contraception and the higher probability of using family planning practices (Jiang & Hardee, 2014). Similarly, studies from India and Bangladesh show that consultation with doctors particularly about family planning was more common among working women than the unemployed ones (Jiang & Hardee, 2014; Islam et al., 2016). This could be attributed to the impact of education which leads to women empowerment through employment that further influences their health-seeking behaviour (Jamali et al., 2018). Another explanation could be the improved decision-making ability among educated women that leads to improved insight about health problems, resulting in enhanced health-seeking behaviour (Jamali et al., 2018). Furthermore, formal education exposes women to the outside world, generates awareness, and empowers them to make independent choices about family making (United Nations Educational, Scientific and Cultural Organization [UNESCO], 2014). In contrast, illiteracy greatly reduces the modes of communication available to reach women, prohibits access to a world of ideas, and allows them access to information only through their husbands and other relatives (León et al., 2014), hence influencing their freedom for using contraceptive methods.\n\nSecondly, it was noted that the use of contraceptive or family planning methods was highly prevalent among women who heard about family planning on the TV or greatly aware of it. The most common sources of information that remained vital in promoting contraceptive usage, as highlighted in previous studies include TV, radio, printed material, and health facilities (Qazi et al., 2010). Particularly, media due to its enhanced access and availability provides more opportunities for women to communicate with their friends and relatives for information regarding contraception, hence educating the community through media will increase the contraception practice rate (Jaffery et al., 2019).\n\nThirdly, the use of contraception was reported to be higher among women living in urban areas of Pakistan. The average distance to a reproductive health facility in rural areas is larger than that to urban areas, hence access to family health services is difficult for rural women, especially without transportation or funds (Mustafa et al., 2015). On the other hand, in urban areas, the proximity to health facilities and more reproductive and family planning services increases the odds of receiving more information related to family planning methods which reflects more usage of contraceptives (Qazi et al., 2010).\n\nFurthermore, the prevalence of contraception use was noted to be higher among older age women as compared to women aged between 15 to 24 years. This could be linked with the number of births per woman that influences their decisions regarding contraceptive usage. In one study conducted in Pakistan, women having three or more children were more inclined to using family planning methods compared to those who had two or fewer children (Qazi et al., 2010). In addition, women’s independence, choice, and decision-making capacity increase with their increased age that may be attributed to the cultural norm whereby a newly married woman is expected to perform household chores under the supervision of her husband or mother-in-law, who is the primary decision-maker (Hameed et al., 2014). Hence, such cultural factors combined with the impact of childbearing age and the high risk of mortality associated with pregnancies can potentially lead to early parenthood, unintended pregnancies among teenagers, and greater maternal and child mortality (Patton et al., 2009; Nishtar et al., 2013).\n\nLastly, our findings show that using family planning methods is a conjoint decision that is strongly related to the communication between the spouses, however, disapproval for its usage mainly relies on the decision of husbands which impacts the practice of contraception among couples. Previous literature on Pakistan also underlines the role of the husband as an obstacle to family planning use by their wives (National Institute of Population Studies, 1992; N. Mahmood & Ringheim, 1996; Agha, 2010). Such a situation might arise due to the patriarchal and patrilocal family structure in Pakistan where marriages are mostly contracted between relatives’ families and women exercise less autonomy in the extended households (N. Mahmood & Ringheim, 1996). Whereas, a man is considered the prime decision-maker and holds the financial power to implement their decisions. Therefore, generating awareness and clarifying misconceptions about family planning among men can significantly improve the use of contraception among couples. Similarly, accessibility of services and information on male methods can potentially enhance its usage, because many women, especially in rural areas, have limited mobility; and require money and permission from the husband to leave the household for traveling alone to a clinic or service outlet (Kiani, 2003).\n\nDespite national representation of study findings, the cross-sectional nature of the study caused biases related to the respondents. Moreover, the question asked related to the contraceptive prevalence were not timebound and due to this reason, there can be some recall biases. Moreover, some variables were available from a certain time period for example wealth index was not available for the year 1990-91. Information on hearing family planning information from the newspaper was not collected in the year 1990-91 and 2007-08. Likewise, information on the decision of using contraception was available for two years and information on the decision of not using contraception was available for one year only. The secondary nature of the data also limits the assessment of certain factors, such as the influence of family members, family structure, socio-cultural norms, and beliefs relate to the use of contraceptives. Further studies are needed which could explore the socio-cultural beliefs and the reasons for the low contraceptive prevalence rate among the women of Pakistan.\n\n\nConclusion\n\nThe PDHS data analysis demonstrates that there is a noticeable gap regarding awareness and uptake of contraception leading to low contraceptive use among women in Pakistan. This study has identified some important determinants that significantly impact the use of contraceptives among EMWRA in Pakistan. Contraceptive use is significantly influenced by women's age, education, place of residence, region, wealth index, educational and working status of women, and exposure to family planning information on social/mass media. In the light of our results, it is important to highlight the importance of girl’s education for building awareness and empowerment for contraception through media, particularly social media.\n\n\nData availability\n\nData used in this study are from the individual recode data file of the Paskitan 2019 Demographic and Health Survey, available from the Demographic and Health Survey (DHS) website. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.",
"appendix": "Acknowledgements\n\nThe authors would like to acknowledge the DHS program for providing access to the datasets.\n\n\nReferences\n\nAgha S: Intentions to use contraceptives in Pakistan: implications for behavior change campaigns. BMC Public Health. 2010; 10(1): 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsif MF, Pervaiz Z: Socio-demographic determinants of unmet need for family planning among married women in Pakistan. BMC Public Health. 2019; 19(1): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBabalola S: Women's education level, antenatal visits and the quality of skilled antenatal care: a study of three African countries. J Health Care Poor Underserved. 2014; 25(1): 161–179. PubMed Abstract | Publisher Full Text\n\nCahill N, Sonneveldt E, Stover J, et al.: Modern contraceptive use, unmet need, and demand satisfied among women of reproductive age who are married or in a union in the focus countries of the Family Planning 2020 initiative: a systematic analysis using the Family Planning Estimation Tool. Lancet. 2018; 391(10123): 870–882. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCham M, Sundby J, Vangen S: Maternal mortality in the rural Gambia, a qualitative study on access to emergency obstetric care. Reprod Health. 2005; 2(1): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChandra-Mouli V, Parameshwar PS, Parry M, et al.: A never-before opportunity to strengthen investment and action on adolescent contraception, and what we must do to make full use of it. Reprod Health. 2017; 14(1): 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDasgupta ANZ, Wheldon M, Kantorova V, et al.: Progress in Family Planning: Did the Millennium Development Goals Make a Difference? Population Association of America; 2019, April 11. Reference Source\n\nDennis ML, Radovich E, Wong KLM, et al.: Pathways to increased coverage: an analysis of time trends in contraceptive need and use among adolescents and young women in Kenya, Rwanda, Tanzania, and Uganda. Reprod Health. 2017; 14(130): 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEwerling F, Victora CG, Raj A, et al.: Demand for family planning satisfied with modern methods among sexually active women in low- and middle-income countries: who is lagging behind? Reprod Health. 2018; 15(42): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFikree FF, Khan A, Kadir MM, et al.: What influences contraceptive use among young women in urban squatter settlements of Karachi, Pakistan? Int Family Planning Perspectives. 2001; 27(3): 130–136. Publisher Full Text\n\nHameed W, Azmat SK, Ali M, et al.: Women’s Empowerment and Contraceptive Use: The Role of Independent versus Couples’ Decision-Making, from a Lower Middle Income Country Perspective. Plos One. 2014; 9(8): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIslam AZ, Mondal MNI, Khatun ML, et al.: Prevalence and determinants of contraceptive use among employed and unemployed women in Bangladesh. Int J MCH AIDS. 2016; 5(2): 92. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJaffery HO, Tufail S, Aslam P, et al.: Knowledge, Attitude and Practice of Family Planning Among Pakistani Women Attending a Tertiary Care Hospital. Pak Armed Forces Med J. 2019; 69(SUPPL 2): S329–S333. Reference Source\n\nJamali T, Tanzil S, Ali SS: Influence of Education on Reproductive Health Indicators Among Women in Sindh, Pakistan. Ann Jinnah Sindh Med Uni. 2018; 4(1): 23–29. Reference Source\n\nKiani MFK: Motivation and involvement of men in family planning in Pakistan. Pak Development Rev. 2003; 42(3): 197–217. Reference Source\n\nLeón FR, Lundgren R, Sinai I, et al.: Increasing literate and illiterate women’s met need for contraception via empowerment: a quasi-experiment in rural India. Reprod Health. 2014; 11(1): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMacQuarrie K: Unmet need for family planning among young women: levels and trends. ICF International; 2014.\n\nMahmood A, Sultan M: National Institute of Population Studies (NIPS)(Pakistan), and Macro International Inc. Pak Demographic Health Survey. June, 2008; 2006-07(7): 123–145. Reference Source\n\nMahmood N, Ringheim K: Factors affecting contraceptive use in Pakistan. Pak Development Rev. 1996; 35(1): 1–22. Reference Source\n\nMemon F, Jonker L: Educational level and family planning among Pakistani women: A prospective explorative knowledge, attitude and practice study. Middle East Fertility Soc J. 2018; 23(4): 464–467. Publisher Full Text\n\nMustafa G, Khurram AS, Hameed W, et al.: Family Planning Knowledge, Attitudes, and Practices among Married Men and Women in Rural Areas of Pakistan: Findings from a Qualitative Need Assessment Study. Int J Reprod Med. 2015. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNational Institute of Population Studies (Pakistan), Institute for Resource Development/Westing house: Pakistan Demographic and Health Survey 1990/1991. National Institute of Population Studies; July, 1992. Reference Source\n\nNational Institute of Population Studies, ICF International: Pakistan Demographic Health Survey 2017-18 [Internet]. Islamabad, Pakistan and Calverton, Maryland, USA; 2019. Reference Source\n\nNishtar NA, Sami N, Alim S, et al.: Determinants of contraceptives use amongst youth: an exploratory study with family planning service providers in Karachi Pakistan. Glob J Health Sci. 2013; 5(3): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNyoni T: Determinants of population growth: empirical evidence from Pakistan (1960-2017). MPRA Paper; 2018. Reference Source\n\nPatton GC, Coffey C, Sawyer SM, et al.: Global patterns of mortality in young people: a systematic analysis of population health data. Lancet. 2009; 374(9693): 881–892. PubMed Abstract | Publisher Full Text\n\nQazi HA, Hashmi A, Raza SA, et al.: Contraceptive methods and factors associated with modern contraceptive in use. J Family Reprod Health. 2010; 4(1): 41–46.\n\nShah IH, Pullum TW, Irfan M: Fertility in Pakistan during the 1970s. J Biosoc Sci. 1986; 18(2): 215–229. PubMed Abstract | Publisher Full Text\n\nShah NZ, Ali T, Jehan I, et al.: Struggling with long-time low uptake of modern contraceptives in Pakistan. East Mediterr Health J. 2020; 26(3): 297–303. PubMed Abstract | Publisher Full Text\n\nUNESCO Institute for Life Long Learning: Gender equality matters: empowering women through literacy programmes. United Nations Education, Scientific, and Cultural Organisation; 2014. Reference Source\n\nWorld Bank: The little data book 2015. The World Bank; 2015. Reference Source\n\nWorld Bank: World development indicators. The World Bank; 2019. Reference Source\n\nWorld Health Organization: Global accelerated action for the health of adolescents (AA-HA!): guidance to support country implementation. 2017. Reference Source\n\nWulifan JK, Mazalale J, Jahn A, et al.: Factors Associated with Contraceptive Use among Women of Reproductive Age in Rural Districts of Burkina Faso. J Health Care Poor Underserved. 2017; 28(1): 228–247. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "91664",
"date": "19 Aug 2021",
"name": "Adeel Khoja",
"expertise": [
"Reviewer Expertise Women and Children Health",
"mobile Health",
"electronic Health",
"e-Learning",
"Cardiology",
"Stroke",
"Non-Communicable Diseases"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nOverall, a very nicely written manuscript capturing and highlighting data on contraceptive use among the Pakistani population. I guess this study fills a good research gap in regard to LMICs.\nI personally feel, interviewing some women of reproductive age group from remote regions of Pakistan would have added some scientific rigour to this study and I foresee some sort of triangulation of results/findings from qualitative and quantitative study designs.\nRegarding the use of the PDHS dataset, was it obtained as a clean version, or do the authors have to undertake the cleaning and editing of the dataset, kindly mention this in the method section and also if relevant permissions were obtained for using the PDHS dataset from the relevant authorities.\nWere the seven categories of age mered into four categories based on the distribution of the data, kindly explain\nPlease remove the last line from the method section regarding R software. It is not needed.\nI would encourage the authors to draw line graphs to show the trends of contraceptive use (which is increasing) with time (years) on x-ais.\nThe wealth index was divided into five categories, can the authors please state the reason why it was divided into five, have the authors used any resource or literature backing to support these categories\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7052",
"date": "20 Aug 2021",
"name": "Zohra Lassi",
"role": "Author Response",
"response": "Overall, a very nicely written manuscript capturing and highlighting data on contraceptive use among the Pakistani population. I guess this study fills a good research gap in regard to LMICs. Author's comment: Thank you. I personally feel, interviewing some women of reproductive age group from remote regions of Pakistan would have added some scientific rigour to this study and I foresee some sort of triangulation of results/findings from qualitative and quantitative study designs. Author's comment: This is a secondary analysis of the PDHS dataset and it involved no interaction or actual data collection in the field. Regarding the use of the PDHS dataset, was it obtained as a clean version, or do the authors have to undertake the cleaning and editing of the dataset, kindly mention this in the method section and also if relevant permissions were obtained for using the PDHS dataset from the relevant authorities. Author's comment: It has been mentioned in the data availability section at the very end. Were the seven categories of age mered into four categories based on the distribution of the data, kindly explain Author's comment: It was merged into 4 categories because of small cell counts for some of the categories. Please remove the last line from the method section regarding R software. It is not needed. Author's comment: We were asked to mention this by the editor of the journal. I would encourage the authors to draw line graphs to show the trends of contraceptive use (which is increasing) with time (years) on x-ais. Author's comment: We do not think this is required as we have indicated and reported in the meta-analysis figure 3. The wealth index was divided into five categories, can the authors please state the reason why it was divided into five, have the authors used any resource or literature backing to support these categories Author's comment: This is how DHS generally categories wealth index and is uniform across all country that collects DHS data."
}
]
},
{
"id": "91662",
"date": "01 Sep 2021",
"name": "Nida Zahid",
"expertise": [
"Reviewer Expertise Mental Health",
"Public Health",
"Oncology",
"Male Infertility"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n'In developing countries, pregnancy and childbirth are the leading causes of death among women. In this context, family planning and access to contraceptives are crucial for reducing pregnancy-related morbidity and mortality. The study aims to look into the trends of contraception and determinants of contraceptive use in Pakistan. The source of data is PDHS. The outcome variable is Contraception. The methodology of the study is robust and is described nicely by the authors. The statistical techniques applied by the authors are appropriate. The graphs nicely depict the results of the study\nStatistical analysis :\nPlease mention the inferential tests that were used for assessing the association of categorical variables such as the chi-square/ Fisher exact test.\n\nSince the authors have mentioned that SPSS was used to analyze data, please remove the R software\n\nResults:\nTable1: Please recheck the p-value of work status.\n\nPlease give a footnote and mention the significant variables and the test that was applied.\n\nIt would be better to report the trend from 1990 to 2018 as a line graph instead of a table.\n\nTable 2: Please give footnotes indicating the significant variables and the test that was used\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre 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": "7116",
"date": "03 Sep 2021",
"name": "Zohra Lassi",
"role": "Author Response",
"response": "'In developing countries, pregnancy and childbirth are the leading causes of death among women. In this context, family planning and access to contraceptives are crucial for reducing pregnancy-related morbidity and mortality. The study aims to look into the trends of contraception and determinants of contraceptive use in Pakistan. The source of data is PDHS. The outcome variable is Contraception. The methodology of the study is robust and is described nicely by the authors. The statistical techniques applied by the authors are appropriate. The graphs nicely depict the results of the study Author's comment: Thank you for acknowledging the efforts and work Statistical analysis : Please mention the inferential tests that were used for assessing the association of categorical variables such as the chi-square/ Fisher exact test. Author's comment: Chi-square was used as the cell counts were sufficient Since the authors have mentioned that SPSS was used to analyze data, please remove the R software Author's comment: It was a journal's requirement to mention R. Results: Table1: Please recheck the p-value of work status. Author's comment: Respondent occupation p value: 0.012 Please give a footnote and mention the significant variables and the test that was applied. Author's comment: Table 1 footnotes: Significant p values on chi-square: age, place of residence, regions, wealth index, education, Partner’s education, occupation(both), Heard family planning on TV, Heard family planning on Newspaper, Year of data collection. It would be better to report the trend from 1990 to 2018 as a line graph instead of a table. Author's comment: If it is required, we can add it. Table 2: Please give footnotes indicating the significant variables and the test that was used Author's comment: Cox regression: At univariate: p-value <0.25: age, place of residence regions, wealth index, education, partner’s education, occupation (both), and heard family planning on social media. At multivariate: p-value<0.05: age, place of residence regions, wealth index, education, respondent occupation, heard family planning on social media."
}
]
}
] | 1
|
https://f1000research.com/articles/10-790
|
https://f1000research.com/articles/10-312/v1
|
22 Apr 21
|
{
"type": "Study Protocol",
"title": "Teaching and learning how to make informed health choices: Protocol for a context analysis in Spanish primary schools",
"authors": [
"Laura Martínez García",
"Laura Samsó Jofra",
"Pablo Alonso-Coello",
"Eukane Ansuategi",
"Laia Asso Mistral",
"Monica Ballesteros",
"Carlos Canelo-Aybar",
"Gonzalo Casino",
"Ana Gallego Iborra",
"Ena Pery Niño de Guzmán Quispe",
"Carolina Requeijo",
"Marta Roqué i Figuls",
"Karla Salas",
"Mar Ubeda",
"Iratxe Urreta",
"Sarah Rosenbaum",
"Laura Samsó Jofra",
"Pablo Alonso-Coello",
"Eukane Ansuategi",
"Laia Asso Mistral",
"Monica Ballesteros",
"Carlos Canelo-Aybar",
"Gonzalo Casino",
"Ana Gallego Iborra",
"Ena Pery Niño de Guzmán Quispe",
"Carolina Requeijo",
"Marta Roqué i Figuls",
"Karla Salas",
"Mar Ubeda",
"Iratxe Urreta",
"Sarah Rosenbaum"
],
"abstract": "Introduction The Informed Health Choices (IHC) project developed learning resources to teach primary school children (10 to 12-year-olds) to assess treatment claims and make informed health choices. The aim of our study is to explore the educational context for teaching and learning critical thinking about health in Spanish primary schools.\nMethods During the 2020-2021 school year, we will conduct 1) a systematic assessment of educational documents and resources, and 2) semi-structured interviews with key education and health stakeholders. In the systematic assessment of educational documents and resources, we will include state and autonomous communities’ curriculums, school educational projects, and commonly used textbooks and other health teaching materials. In the semi-structured interviews, we will involve education and health policy makers, developers of learning resources, developers of health promotion and educational interventions, head teachers, teachers, families, and paediatric primary care providers. We will design and pilot a data extraction form and a semi-structured interview guide to collect the data. We will perform a quantitative and a qualitative analysis of the data to explore how critical thinking about health is being taught and learned in Spanish primary schools.\nConclusion We will identify opportunities for and barriers to teaching and learning critical thinking about health in Spanish primary schools. We will formulate recommendations—for both practice and research purposes—on how to use, adapt (if needed), and implement the IHC resources in this context.",
"keywords": [
"Children’s health",
"critical thinking",
"evidence-based medicine",
"health education",
"health promotion",
"public health."
],
"content": "Introduction\n\nPeople are constantly exposed to information about health. When people use unreliable information, they may harm their health or not consume their resources efficiently.1 For this reason, people need to acquire health literacy (obtain, process, and understand health information) and think critically about health (use appropriate criteria to make judgements about health information).2-4 Therefore, they can assess the trustworthiness of health claims and make informed health decisions.\n\nThe Informed Health Choices (IHC) project aims to teach people to assess treatment claims and make informed health decisions.5 As part of the IHC project, the IHC Working Group developed: 1) the IHC Key Concepts (list of concepts that individuals need to understand and apply when assessing claims about treatment effects and making health choices),6 2) the IHC resources (learning resources to teach children and their families to understand and apply some of the IHC key concepts),7-9 and 3) the CLAIM Evaluation Tools (database with questions to assess people’s understanding and ability to apply the IHC key concepts).10\n\nThe IHC Working Group evaluated the effect of the IHC resources in a cluster randomised trial in Ugandan primary schools.11 The study showed that the children (10 to 12-year-olds) who used the IHC resources improved their ability to assess treatment claims and retained this knowledge one year later.11,12\n\nThe IHC project has acquired greater relevance during the ongoing COVID-19 pandemic, considering that the current health situation is aggravated by an infodemic. The World Health Organization (WHO) defines “infodemic” as an excessive amount of information, in some cases correct and in others not, which makes it difficult for people to find reliable sources and guidance when they need them.13 In this context, it is vital to teach people to critically assess health information (e.g., prolonged use of mask causes hypoxia) and to make informed health decisions (e.g., vaccination against COVID-19).\n\nSpain is organized territorially into self-governing communities (17 autonomous communities and two autonomous cities), provinces, and municipalities. The Spanish education system follows a decentralised model where educational responsibilities are shared among all levels of government: state general authority (Ministry of Education), autonomous communities (Departments of Education), local authorities (Education Councils), and educational institutions (Table 1).14,15\n\n- General organisation of the education system\n\n- Regulation of academic and professional titles, and basic rules for the development of the right to education\n\n- Establishment of the general plan for education\n\n- Evaluation and innovation of the learning integrated into the education system\n\n- Educational inspection\n\n- Design, planning and management of scholarships and financial support\n\n- Promotion of equality, non-discrimination, and universal accessibility policies within the scope of its powers\n\n- Management of the teaching staff policy and development of the foundations for the legal regime of public teaching service\n\n- Exercise of the functions of National Authority for the Erasmus+ Programme of the European Commission\n\n\n\n- Establish the common contents and assessable learning standards of core subjects\n\n- Establish the minimum number of hours for core subjects (not be less than 50% of the total number of teaching hours generally established by each education authority)\n\n- Establish the assessable learning standards of specific subjects\n\n- Design the final evaluation for primary education, compulsory secondary education, and upper secondary education\n\n- Recognise the certificates awarded corresponding to regulated studies\n\n- Establish mixed curricula of the Spanish education system and other education systems\n\n- Promote actions to enhance the quality of educational institutions\n\n\n\n- Assume the regulations developed by the State rules\n\n- Assume the executive and administrative competences for managing the education system in the territory\n\n- Promote and strengthen education school autonomy\n\n- Evaluate school results and implement action plans\n\n\n\n- Complement the contents of core subjects\n\n- Establish the contents of specific subjects and freely-structured subjects\n\n- Conduct methodological recommendations to educational institutions within the territory\n\n- Establish the teaching hours for all the subjects, with the exception of core subjects\n\n- Complement the evaluation criteria for the stage assessment\n\n- Establish assessment criteria and learning standards of the free subjects for the stage assessment\n\n- Expedite the certificates awarded corresponding to regulated studies\n\n- Promote actions to enhance the quality of education educational institutions\n\n\n\n- Assume functions in areas that have a direct local impact\n\n\n\n- Autonomy to develop, approve, and execute school educational projects, management projects, and organizational and functioning rules of the school.\n\n\n\n- Complement the contents of all subjects on the basis of educational provision\n\n- Design and implement their own teaching and learning methods\n\n- Establish the number of hours for the different subjects\n\nThe legislative framework governing the Spanish education system is based on the Organic Law of Education, of 2006 (Ley Orgánica de Educación - LOE), and the Organic Law for the Improvement of the Educational Quality, of 2013 (Ley Orgánica para la Mejora de la Calidad Educativa - LOMCE).16,17 Currently there is a new Draft Organic Law of Modification of the LOE, of 2020 (Ley Orgánica de modificación de la LOE - LOMLOE).18 The Royal Decrees regulate the core curriculum of primary education, compulsory secondary education (Educación Secundaria Obligatoria, ESO), and upper secondary education (Bachillerato).19,20\n\nThe Spanish education system is divided into four levels: 1) pre-primary education, organised into two cycles of three years (0-3 and 3-6 years old); 2) primary education (6-12 years old); 3) secondary education, organised into two cycles: compulsory secondary education (12-16 years old), and upper secondary education (16-18 years old) or vocational training; and 4) higher education, comprised of university or professional studies.21 Basic education (primary and compulsory secondary education) is mandatory and free in schools supported with public funds.14\n\nIn Spain there are three different types of schools according to their ownership and source of funding: 1) public schools, owned by the education authority and publicly-funded (Department of Education); 2) publicly-funded private schools, privately owned (educational institution) but publicly-funded (Departments of Education) through a regime of agreements; and 3) private schools, privately owned and privately-funded (educational institution).14 In the school year 2020-2021, there are 14,151 schools that provide primary education; 75% public schools, 21% publicly-funded private schools, and 4% private schools.22\n\nThe public educational expenditure in 2018 was 4.23% of the GDP (Gross Domestic Product), which was below the EU average (4.6%).23,24 The distribution of public expenditure was mainly among pre-primary and primary education (35%), and secondary education and vocational training (29.3%).24\n\nHealth promotion interventions (interventions to enable people to increase control over and to improve their health) and health education interventions (interventions to improve people's health literacy) in schools have shown to improve the health of children and young people.25-28\n\nHealth promotion and education in schools requires intersectoral collaboration and partnerships between educational and health institutions.29 In 1989, the Spanish Ministry of Education and the Ministry of Health signed a collaboration agreement to encourage the integration of health promotion and education in schools.30-33 In 1993, the country joined to European Network of Health Promoting Schools (ENHPS), which aims to integrate health promotion into every aspect of the curriculum, introduce healthy programmes and practices into schools’ daily routines, improve working conditions, and foster better relations both within the schools and between them and their local communities.33,34\n\nThe Spanish LOE educational law of 2006 defined two competences, “Knowledge and interaction with the physical world” and “Social and citizenship” that included health promotion and education (essential knowledge, skills, and attitudes for participating in society) directly and indirectly, respectively.35 However, the current Spanish LOMCE educational law of 2013 includes health competencies in a transversal way, and its contents are distributed among several knowledge areas (Biology, Physical Education, and Ethical values/Education for citizenship).35\n\nIn Spain, the schools have the ultimate responsibility to integrate health promotion and educational interventions into their educational projects.32 This means to foster the value of health among all different members of the school community, throughout the school year, in order to facilitate healthy behaviours, promote autonomous decision-making and personal choices of healthy lifestyles, and establish long-term positive attitudes towards health care.32\n\nThe contextualization of the IHC resources comprises activities to explore how these resources can be used in a different context from the one that they were originally designed for (primary schools in Uganda). These activities may include, for example: 1) context analysis to explore conditions for teaching critical thinking about health, 2) translation of the IHC resources, 3) pilot testing of the IHC resources, 4) adaptation of the IHC resources (if needed), 5) assessment of the effects of using the IHC resources, or 6) translation and validation of the CLAIM Evaluation Tools.36-38\n\nThe IHC resources have already been translated into Spanish (Figure 1), and a pilot study is being conducted in schools in Barcelona to explore the students and teachers’ experience when using the IHC resources.39-42 The next step is to analyse the educational context to ensure the relevance and appropriateness of the IHC primary school resources for Spanish primary schools.\n\n\nObjectives\n\nTo explore the educational context for teaching and learning critical thinking about health in Spanish primary schools.\n\nSecondary objectives\n\n\n\n• To identify and describe relevant educational documents and resources that support teaching and learning of critical thinking about health, and that are available in Spanish primary schools.\n\n• To explore the experience and perspective of key education and health stakeholders regarding teaching and learning critical thinking about health in Spanish primary schools.\n\n• To identify factors that can potentially impact the implementation of the IHC resources in Spanish primary schools.\n\n\nMethods\n\nDuring the 2020-2021 school year, we will conduct 1) a systematic assessment of educational documents and resources, and 2) semi-structured interviews with key education and health stakeholders; based on methods proposed by the IHC Working Group.43 Table 2 describes the different steps of the study. We will report qualitative findings using the COREQ (Consolidated criteria for reporting qualitative research) checklist.44\n\nEligibility criteria\n\nWe will include educational documents and resources (state and autonomous communities curriculums, school educational projects, textbooks and other health teaching materials) that cover aspects related to critical thinking about health (critical thinking in general, health in general, and critical thinking specifically about health), focused on primary education, available in the Spanish context, written in any official or co-official language of the country (Spanish, Catalan, Galician, Valencian, or Basque), and currently used during 2020-2021 school year.\n\nInformation sources and search strategy\n\nTo identify the state and autonomous communities’ curriculums, we will conduct a manual search on the website of the Spanish Ministry of Education and Vocational Training,45 as well as on the websites of the corresponding departments of the autonomous communities.\n\nTo identify school educational projects, we will select a convenience sample of schools from the Spanish Ministry of Education registry.22 We will aim for representativeness of schools based on geographic area (autonomous communities), and source of funding of schools (public, publicly-funded private, or private) (Table 3). We expect to include a sample of approximately 34 schools. We will contact, inform, and invite head teachers from selected schools (invitation e-mail, first e-mail reminder, second e-mail reminder, and telephone reminder) (Extended data 146). If a school does not respond or does not agree to participate, we will select the next eligible school from the registry.\n\n* We will consider strata 2 only for head teachers, teachers, and families’ profiles.\n\nTo identify commonly used textbooks and other health teaching materials, we will ask head teachers and teachers from the participating schools for suggestions.\n\nDocument selection\n\nOne author will screen titles and full texts to identify potentially eligible documents for inclusion. A second author will cross-check the selection. The two authors will resolve potential disagreements by discussion, and if necessary, by consulting a third author.\n\nData collection\n\nWe will design, pilot and refine a data extraction form that will include the following information: 1) document identification, 2) description of the document, 3) description of the content related to critical thinking, health, and critical thinking about health, and 4) mapping of the content with IHC Key Concepts (if applicable) (Extended data 246).\n\nOne author will perform the data collection, and a second author will cross-check the data. The two authors will resolve potential disagreements by discussion, and if necessary, by consulting a third author.\n\nParticipants\n\nTo cover key education and health stakeholders, we will involve education and health policy makers, developers of learning resources, developers of health promotion and educational interventions, head teachers, teachers, families, and paediatric primary care providers (physicians and nurse practitioners). We will identify participants from 1) articles included in the systematic assessment of educational documents and resources, 2) participating schools included in the systematic assessment, and 3) expert colleagues. We will aim for representativeness of participants based on geographic area (autonomous communities), source of funding of schools (public, publicly-funded private, or private), and profile of participants (education and health policy makers, developers of learning resources, developers of health promotion and educational interventions, head teachers, teachers, families, physicians, and nurse practitioners) (Table 3). We expect to include a sample of approximately 36 participants, although we will continue recruiting and collecting data until information becomes repetitive and no new information emerges (sampling saturation).47,48\n\nWe will contact, inform, and invite potential participants (invitation e-mail, first e-mail reminder, second e-mail reminder, and telephone reminder) (Extended data 146). Those who agree to participate will be asked to complete a written informed consent (Extended data 346) and declare potential conflicts of interest.49\n\nData collection\n\nWe will design, pilot and refine a semi-structured interview guide that will include the following information: 1) participant identification, 2) description of the participant (age, gender, profile, working institution, and autonomous community), 3) participant’s experience on how critical thinking about health is being taught and learned in Spanish primary schools (curriculum, subjects, educational documents and resources, and evaluation), 4) participant’s perspective on the relevance of teaching and learning critical thinking about health in Spanish primary schools (relevance in the educational context), 5) participant’s perspective on how to implement IHC resources in Spanish primary schools (potential facilitators and barriers50) (Extended data 446).\n\nBefore each interview, we will introduce the participants to the IHC project, the IHC resources, and the pilot study in Barcelona with a training video.5,7-9,42 After that, one trained researcher will conduct the interviews face to face or via teleconference. Each interview will last approximately one hour and will be audio recorded and transcribed. The interview transcripts will be sent to participants for approval before conducting the data analysis.\n\nQuantitative analysis\n\nWe will perform a descriptive analysis of the categorical variables (absolute and relative frequencies), and the continuous variables (median and range) (Extended data 546).\n\nQualitative analysis\n\nWe will register in an Excel sheet quotes from: 1) educational documents and resources, and 2) semi-structured interviews. We will identify themes related to the educational context applying a three-step descriptive thematic synthesis: 1) codifying extracted quotes, 2) proposing descriptive themes, and 3) identifying main themes based on conceptual similarities within and across quotes.51 If applicable, we will map the extent to which the educational documents and resources overlap with the IHC Key Concepts through a data matrix, including documents as rows and the IHC Key Concepts as columns. One author will conduct the analysis, and a second author will cross-check it. The two authors will resolve potential disagreements by discussion, and if necessary, by consulting a third author.\n\nFinally, using the summarised data, we will explore the nature of the phenomena (how critical thinking about health is being taught and learned in Spanish primary schools), and the possible explanations for the findings. Furthermore, we will deepen our understanding of the opportunities for and barriers to teaching and learning critical thinking in general, about health in general, and critical thinking specifically about health.\n\nThe dissemination activities of the study results will include: 1) publication in a peer-reviewed journal; 2) online communication via related websites, electronic bulletins, and social media; and 3) tailored presentations for key education and health stakeholders.\n\nThe study protocol has obtained an approval exemption (does not include patients, biological specimens, or clinical data) from the Ethics Committee of the Hospital de la Santa Creu i Sant Pau (Barcelona, Spain).\n\nWe will inform participants about the study and request their written informed consent and declaration of potential conflicts of interest. We will not collect any sensitive personal data (racial or ethnic origin, political opinions, religious or philosophical beliefs, trade-union membership, genetic data, biometric data, health-related data, or data concerning a person’s sex life or sexual orientation).52 We will anonymise personal data, coding the name of the participants and the institutions. Only researchers will have access to the identifier list (with the code linked to personal data). Personal data will be deleted five years after the study has concluded.\n\nFigure 2 is a Gantt chart illustrating the schedule of the context analysis. To date, we started the systematic assessment of relevant education documents and resources.\n\n\nDiscussion\n\nPeople need to learn to think critically about health and make informed health decisions. The IHC project proposed to start this challenge by teaching children and using the IHC resources, which were specifically designed and evaluated to achieve this goal. The next step is to support the dissemination of the IHC resources, thus help to empower people around the world to make well-informed decisions.\n\nThe context analysis is an important step to complete before developing innovative health promotion and educational interventions in schools, such as the IHC resources. This analysis can identify factors that might affect scaling up at a stage that is early enough to inform the development of the interventions.\n\nDuring the trial to evaluate the effects of the IHC resources in primary schools in Uganda, the IHC Working Group conducted a process evaluation to identify factors affecting their implementation.11,49 This study showed that participants valued the IHC resources, although they highlighted the need to incorporate the lessons into the national curriculum to scale up their use.49 They also found that the cost of the IHC resources was a critical barrier to scale up their use.49 After this experience, they conducted a context analysis before developing the IHC resources for secondary schools.43 Therefore, they are designing the resources considering relevant factors from the context of reference.53\n\nLund et al. 2018 conducted a market analysis to explore the demand, adequacy for the curriculum, and market conditions for introducing the IHC resources in Norwegian primary and secondary schools.54 They analysed key documents and interviewed teachers and other key stakeholders.54 One of the primary findings was that teaching critical thinking about health fits into the curriculum and should be prioritised; however, classroom time is limited and critical thinking about health cuts across subjects.54 The teachers who participated pointed out that they are empowered to decide what to teach, how, and with what learning resources.54 Further work is needed to adapt the IHC resources (e.g., use as little classroom time as possible, facilitate collaboration across subjects and grades, and engage teachers in the design) and scale up its use in Norwegian primary and secondary schools.\n\nOur proposal has several strengths. We are building on previous studies and using multiple methods and triangulation to ensure the trustworthiness of our findings.43,54 Furthermore, this study is part of a comprehensive project of contextualization activities that we have completed (translation of the IHC resources) or that are ongoing (pilot study) to explore how Spanish primary schools can benefit from the IHC resources.39-42\n\nOur proposal also has some limitations. We will face numerous challenges, as we will have to consider different educational contexts and languages (autonomous communities) within the same country (Spain). In addition, the ongoing COVID-19 pandemic may be a significant barrier for the recruitment of participants.\n\nWe will formulate recommendations—for both practice and research purposes—on how to use, adapt (if needed), and implement the IHC resources in Spanish primary schools. The findings of the contextualization activities will inform the design of a cluster randomised trial to determine the effectiveness of the IHC resources in this context prior to scaling up their use.\n\n\nData availability\n\nNo data are associated with this article.\n\nFigshare: IHC@BCNContextAnalysis. https://doi.org/10.6084/m9.figshare.14152880.46\n\nThis project contains the following extended data:\n\n- Extended data 1 – Information for schools and participants (documents available in Spanish)\n\n- Extended data 2 – Data extraction form for educational documents and resources\n\n- Extended data 3 – Written informed consent form for participants\n\n- Extended data 4 – Guide for the semi-structured interviews\n\n- Extended data 5 – Descriptive-quantitative variables of the study\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nLaura Samsó Jofra is a doctoral candidate at the Paediatrics, Obstetrics and Gynaecology and Preventive Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain.\n\nWe would like to thank Dr Andrew Oxman (Centre for Informed Health Choices, Norwegian Institute of Public Health, Oslo, Norway) for his advice and feedback on an earlier version of this protocol.\n\n\nReferences\n\nAustvoll-Dahlgren A, Oxman AD, Chalmers I, et al.: Key concepts that people need to understand to assess claims about treatment effects. J Evid Based Med. 2015; 8(3): 112–25. PubMed Abstract | Publisher Full Text\n\nOxman AD, Martínez García L: Comparison of the Informed Health Choices Key Concepts Framework to other frameworks relevant to teaching and learning how to think critically about health claims and choices: a systematic review [version 1; peer review: awaiting peer review]. F1000Res. 2020; 9: 164. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSørensen K, Van den Broucke S, Fullam J, et al.: Health literacy and public health: a systematic review and integration of definitions and models. BMC Public Health. 2012; 12: 80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Health literacy. The solid facts. Geneva:World Health Organization;2013.\n\nInformed Health Choices, Learning To Think Critically About Health Choices.2020. [Accessed 1 January 2021] Reference Source\n\nOxman AD, Chalmers I, Austvoll-Dahlgren A, et al.: Key Concepts for assessing claims about treatment effects and making well-informed treatment choices [version 2; peer review: 3 approved]. F1000Res. 2019; 7: 1784. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe Informed Health Choices Group: The Health Choices Book: Learning to think carefully about treatments. A health science book for primary school children. Oslo: Norwegian Institute of Public Health; 2016. PubMed Abstract | Publisher Full Text\n\nThe Informed Health Choices Group: The Health Choices Book: Learning to think carefully about treatments. A health science book for primary school children. EXERCISE BOOK. Oslo: Norwegian Institute of Public Health2016.\n\nThe Informed Health Choices Group: Teachers’ Guide for The Health Choices Book: Learning to think carefully about treatments. A health science book for primary school children.Oslo: Norwegian Institute of Public Health2016.\n\nAustvoll-Dahlgren A, Semakula D, Nsangi A, et al.: Measuring ability to assess claims about treatment effects: the development of the ‘Claim Evaluation Tools’. BMJ Open. 2017; 7(5): e013184. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects: a cluster-randomised controlled trial. Lancet. 2017; 390(10092): 374–388. PubMed Abstract | Publisher Full Text\n\nNsangi A, Semakula D, Oxman AD, et al.: Effects of the Informed Health Choices primary school intervention on the ability of children in Uganda to assess the reliability of claims about treatment effects, 1-year follow-up: a cluster randomised trial. Trials. 2020; 21(1): 27. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: An ad hoc WHO technical consultation managing the COVID-19 infodemic: call for action, 7-8 April 2020.Geneva: World Health Organization; 2020. Licence: CC BY-NC-SA 3.0 IGO.\n\nEuropean Commission - Eurydice: National Education Systems.2020. [Accessed 1 January 2021]. Reference Source\n\nNational Institute of Educational Evaluation: Organization for Economic Cooperation and Development (OECD) Review of Policies to Improve the Effectiveness of Resource Use in Schools.Madrid: Country Report - Spain; 2016.\n\nBoletín Oficial del Estado: Ley Orgánica 2/2006, de 3 de mayo, de Educación. BOE. 2006: 106.\n\nBoletín Oficial del Estado: Ley Orgánica 8/2013, de 9 de diciembre, para la mejora de la calidad educativa. BOE. 2013: 295.\n\nMinisterio de Educación y Formación Profesional: Una educación para el siglo XXI. [Accessed 1 January 2021].Reference Source\n\nReal Decreto 126/2014, de 28 de febrero, por el que se establece el currículo básico de la Educación Primaria. BOE. 2014; 52: 19349–19420.\n\nReal Decreto 1105/2014, de 26 de diciembre, por el que se establece el currículo básico de la Educación Secundaria Obligatoria y del Bachillerato. BOE. 2015; 3: 169–546.\n\nMinisterio de Educación y Formación Profesional: Itinerarios Sistema Educativo LOMCE. [Accessed 1 January 2021].Reference Source\n\nMinisterio de Educación y Formación Profesional: Registro Estatal de Centros Docentes no Universitarios. [Accessed 1 January 2021].Reference Source\n\nEuropean Commission - EuroStat: Government expenditure on education.2020. [Accessed 1 January 2021]. Reference Source\n\nMinisterio de Educación y Formación Profesional: Estadísticas de la Educación.2018. [Accessed 1 January 2021]. Reference Source\n\nWorld Health Organization: Health Promotion Glossary.Geneva: World Health Organization; 1998.\n\nBonell C, Wells H, Harden A, et al.: The effect on student health of interventions modifying the school environment: systematic review. J Epidemiol Community. 2013; 67: 677–81. PubMed Abstract | Publisher Full Text\n\nLangford R, Bonell CP, Jones HE, et al.: The WHO Health Promoting School framework for improving the health and well-being of students and their academic achievement. Cochrane Database Syst Rev. 2014; (4): CD008958. PubMed Abstract | Publisher Full Text\n\nWhat is the evidence on school health promotion in improving health or preventing disease and, specifically, what is the effectiveness of the health promoting schools approach?Geneva: World Health Organization; 2006.\n\nBada E, Darlington E, Masson J, et al.: European Standards and Indicators for Health Promoting Schools. Schools for Health in Europe Network Foundation. 2019.\n\nSalvador Llivina T, Suelves Joanxich JM: Ganar salud en la escuela; guía para conseguirlo.Madrid: Ministerio de Educación, Ministerio de Sanidad y Política Social; 2009.\n\nSalvador Llivina T, Suelves Joanxich JM, Puigdollers Muns E, et al.: Informe. Diagnóstico de situación sobre avances conseguidos, necesidades y retos en promoción y educación para la salud en la escuela en España.Madrid: Ministerio de Educación Política Social y Deporte, Centro de Innovación y Documentación Educativa (CIDE) y Ministerio de Sanidad y Consumo, Dirección General de Salud Pública; 2008.\n\nSalvador Llivina T, Suelves Joanxich JM, Puigdollers Muns E: Criterios de calidad para el desarrollo de proyectos y actuaciones de promoción y educación para la salud en el Sistema educativo. Guía para las Administraciones educativas y sanitarias.Madrid: Ministerio de Educación, Política Social y Deporte, Centro de Innovación y Documentación Educativa (CIDE) y Ministerio de Sanidad y Consumo, Dirección General de Salud Pública; 2008.\n\nAnia Palacio JM: Guía para el diseño y la mejora de proyectos pedagógicos de educación y promoción de la salud.Madrid: Secretaría general Técnica del MEC; 2007.\n\nEuropean Commission, the WHO Regional Office for Europe, and the Council of Europe.European Network of Health Promoting Schools: the alliance of education and health.1999.\n\nMontero-Pau J, Tuzón P, Gavidia V: La Educación para la Salud en las leyes de Educación españolas: comparativa entre la LOE y la LOMCE [Health Education in the Spanish Education Laws: comparative analysis between LOE and LOMCE]. Rev Esp Salud Publica. 2018; 92: e201806030.\n\nThe Informed Health Choices Group: Informed Health Choices Newsletter.Norwegian Institute of Public Health; 2019. [Accessed 1 January 2021]. Reference Source\n\nThe Informed Health Choices Group: Informed Health Choices Newsletter.Norwegian Institute of Public Health; 2020. [Accessed 1 January 2021]. Reference Source\n\nThe Informed Health Choices Group: Informed Health Choices Newsletter.Norwegian Institute of Public Health; 2021. [Accessed 1 January 2021]. Reference Source\n\nThe Informed Health Choices Group: Libro de las decisiones en salud: Aprendiendo a reflexionar sobre los tratamientos. Un libro sobre ciencias de la salud para niños en educación primaria. Oslo: Instituto de Salud Pública de Noruega2016. Translation: Iberoamerican Cochrane Centre (CCIb).\n\nThe Informed Health Choices Group: Libro de las decisiones en salud: Aprendiendo a reflexionar sobre los tratamientos. Un libro sobre ciencias de la salud para niños en educación primaria. LIBRO DE EJERCICIOS. Oslo: Instituto de Salud Pública de Noruega2016. Translation: Iberoamerican Cochrane Centre (CCIb).\n\nThe Informed Health Choices Group: Guía para maestros del Libro de las decisiones en salud: Aprendiendo a reflexionar sobre los tratamientos. Un libro sobre ciencias de la salud para niños en educación primaria. Oslo: Instituto de Salud Pública de Noruega; 2016; Translation: Iberoamerican Cochrane Centre (CCIb).\n\nMartínez García L, Alonso-Coello P, Asso Ministral L, et al.: Learning to make informed health choices: Protocol for a pilot study in schools in Barcelona. F1000Res. 2019; 8: 2018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIHC Choice team: Protocol for a context analysis: Exploring the considerations for introducing digital learning resources for critical thinking about health in secondary schools. Norwegian Institute of Public Health. 2020.\n\nTong A, Sainsbury P, Craig J: Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. Int J Qual Health Care. 2007; 19(6): 349–57. PubMed Abstract | Publisher Full Text\n\nSpanish Ministry of Education and Vocational Training: 2020. [Accessed 1 January 2021]. Reference Source\n\nLaura MG: IHC@BCNContextAnalysis. figshare. 2021. Publisher Full Text\n\nGrossoehme DH: Overview of qualitative research. J Health Care Chaplain .2014; 20: 109–22. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuetterman TC: Descriptions of sampling practices within five approaches to qualitative research in education and the health sciences. Forum Qual Soc Res. 2015; 16. Publisher Full Text\n\nConflicts of Interest, International Committee of Medical Journal Editors.2020. [Accessed 1 January 2021]. Reference Source\n\nNsangi A, Semakula D, Glenton C, et al.: Informed health choices intervention to teach primary school children in low-income countries to assess claims about treatment effects: process evaluation. BMJ Open. 2019; 9(9): e030787. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThomas JHA, Synthesis NM: Combining results systematically and appropriately. In: Gough D, Oliver S, Thomas J, editor. An Introduction to Systematic Reviews. London: Sage Publications Ltd; 2012.\n\nEuropean Commission: What personal data is considered sensitive? [Accessed 1 January 2021]. Reference Source\n\nInformed Health Choices, Secondary school resources.2020. [Accessed 1 January 2021]. Reference Source\n\nLund HM, Rekkavik ME, Voll E, et al.: Teaching critical thinking about health claims: market analysis for Norwegian primary and lower secondary school. Informed Health Choices Working Paper. 2018."
}
|
[
{
"id": "84053",
"date": "28 Jun 2021",
"name": "Loai Albarqouni",
"expertise": [
"Reviewer Expertise Evidence-based practice"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThanks for inviting me to review this protocol for an interesting research study. The authors aim to explore the educational context for teaching and learning critical thinking about health in Spanish primary schools. To achieve these aims, the authors plan to conduct a systematic assessment of educational resources and interviews with relevant stakeholders.\nComments:\nAuthors will select a convenience sample of 34 schools. It would be good if authors can put this in context e.g. the total number of schools (population).\n\nI wonder if headteachers are easily identified and if they are the best to address their queries. I also wonder if they should have a unified approach for their request to the documents from the headteachers.\n\nAuthors might consider describing their selection criteria e.g. would they include a document that has just marginally covered a few aspects relevant to critical thinking about health.\n\nAuthors might consider describing their qualitative analysis approach e.g. thematic analysis.\n\nSimilar authors might consider describing their approach of dealing with duplicating or overlapping aspects identified in the educational resources.\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": "7007",
"date": "11 Aug 2021",
"name": "Laura Martínez García",
"role": "Author Response",
"response": "We would like to thank Dr Albarqouni for his time and effort providing feedback on our manuscript. Below we describe how we have addressed each of the comments about the manuscript. Comment 1 – Sample Response 1 The context of the study was described in the Introduction section ‘Spanish education system’. In this section we included the number of schools in the country, the text read: ‘In the school year 2020-2021, there are 14,151 schools that provide primary education; 75% public schools, 21% publicly-funded private schools, and 4% private schools.’ Comment 2 – Head teachers Response 2 The Spanish Ministry of Education registry (https://www.educacion.gob.es/centros/home.do) included the following information for each school: 1) identification (including telephone number, email, and web page), 2) situation, and 3) source of funding (public schools, publicly-funded private schools, and private schools). Based on this information, we will be able to contact the selected schools and their headteachers directly. We described the recruitment strategy in the Methods section, the text read: ‘We will contact, inform, and invite head teachers from selected schools (invitation e-mail, first e-mail reminder, second e-mail reminder, and telephone reminder) (Extended data 1)’. Furthermore, we developed an informative document to introduce the study to head teachers (‘Extended data 1 – Information for schools and participants’, (https://figshare.com/articles/online_resource/IHC_BCNContextAnalysis/14152880). We will have to wait for the findings of the study to assess whether 1) the recruitment strategy is efficient, and 2) the request should be addressed by head teachers. Comment 3 – Document selection criteria Response 3 The selection criteria were described in Methods section ‘Eligibility criteria’, which stated: Educational documents and resources (state and autonomous communities curriculums, school educational projects, textbooks and other health teaching materials) Covered aspects related to critical thinking about health (critical thinking in general, health in general, and critical thinking specifically about health) Focused on primary education Available in the Spanish context Written in any official or co-official language of the country (Spanish, Catalan, Galician, Valencian, or Basque) Currently used during 2020-2021 school year We will have to wait for the findings of the study to describe in depth the aspects covered by identified educational documents and resources. Comment 4 and 5 – Qualitative analysis Response 4 and 5 We amended the text in Methods section ‘Qualitative analysis’ according to the reviewer’s suggestion. The text now reads: ‘We will analyse and synthesise qualitative data using a thematic synthesis. We will register in an Excel sheet quotes from: 1) educational documents and resources, and 2) semi-structured interviews. We will identify themes related to the educational context applying a three-step descriptive thematic synthesis: 1) codifying extracted quotes, 2) proposing descriptive themes, and 3) identifying main themes based on conceptual similarities within and across quotes [51]. We will describe the extent of duplication and overlapping themes within and across documents. If applicable, we will map how themes reflect the IHC Key Concepts framework through a data matrix (including documents as rows and the IHC Key Concepts as columns) [6]. One author will codify extracted quotes and propose descriptive themes. Two authors will select the descriptive themes, identify main themes, and assess the overlap with the IHC Key Concepts guided by iterative discussion, and if necessary, by consulting a third author. The authors' team will approve the final synthesis of findings.’ References 6. Oxman AD, Chalmers I, Austvoll-Dahlgren A, et al.: Key Concepts for assessing claims about treatment effects and making well informed treatment choices [version 2; peer review: 3 approved]. F1000Res. 2019; 7: 1784. 51. Thomas JHA, Synthesis NM: Combining results systematically and appropriately. In: Gough D, Oliver S, Thomas J, editor. An Introduction to Systematic Reviews. London: Sage Publications Ltd; 2012."
}
]
},
{
"id": "88339",
"date": "22 Jul 2021",
"name": "Elaine M. Finucane",
"expertise": [
"Reviewer Expertise Trial Methodology & Evidence Synthesis."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nWell done on a very timely study whose primary aim is to explore the educational context for teaching and learning critical thinking about health in Spanish primary schools. To achieve this, the authors plan to conduct a systematic assessment of educational documents and resources and conduct semi-structured interviews with key education and health stakeholders.\nI have just a few comments:\nIntroduction:\n‘In this context, it is vital to teach people to critically assess health information (e.g., prolonged use of mask causes hypoxia) and to make informed health decisions (e.g., vaccination against COVID-19).' - I feel the context of the examples used in this sentence need to be clearer.\nMethods:\n‘In the semi-structured interviews, we will involve education and health policy makers, developers of learning resources, developers of health promotion and educational interventions, head teachers, teachers, families, and paediatric primary care providers.' - Where the authors state that families will be participants, I think it would be helpful if it were clearly stated if this included children as stakeholders also.\nInvolving stakeholders, including service users, in all stages of a study, from design through to dissemination supports relevance, diversity, and accessibility, which would seem particularly relevant to this study as the authors note it will face challenges as they ‘will have to consider different educational contexts and languages (autonomous communities) within the same country (Spain)’. To this end, I am surprised not to see a PPI group (public and patient involvement in research) actively involved throughout the different study processes.\n\nI wish the authors all the best with their 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": [
{
"c_id": "7008",
"date": "11 Aug 2021",
"name": "Laura Martínez García",
"role": "Author Response",
"response": "We would like to thank Dr Finucane for her time and effort providing feedback on our manuscript. Below we describe how we have addressed each of her comments about the manuscript. Comment 1 – COVID-19 examples Response 1 We amended the text in Introduction section according to the reviewer’s suggestion. The text now reads: ‘In this context, it is vital to teach people to critically assess health information (e.g., how to assess the reliability of the claim ‘If you wear a face mask for a long time, you may have hypoxia’) and to make informed health decisions (e.g., how to decide whether to vaccinate against COVID-19).' Comment 2 – Participants Response 2 The perspective of children is considered in our previous study ‘Learning to make informed health choices: Protocol for a pilot study in schools in Barcelona’ [1]. The aim of this study is to explore both the students’ and teachers’ experience when using the IHC resources in the context of Barcelona (Spain). However, the present study is more related to education and health policies. Therefore, we decided not to include young children as a target stakeholder. To clarify this issue, we amended the text in Methods section according to the reviewer’s suggestion. The text now reads: ‘To cover key education and health stakeholders, we will involve education and health policy makers, developers of learning resources, developers of health promotion and educational interventions, head teachers, teachers, families (without including children), and paediatric primary care providers (physicians and nurse practitioners)’. Comment 3 – Public and Patient Involvement group Response 3 As far as we know, there are no established PPI groups - as in the health area - for the education area. We would be grateful to the reviewer to suggest any interest group for considering in our next studies. References 1. Martínez García L, Alonso-Coello P, Asso Ministral L, et al. Learning to make informed health choices: Protocol for a pilot study in schools in Barcelona. F1000Res. 2019; 8: 2018."
}
]
}
] | 1
|
https://f1000research.com/articles/10-312
|
https://f1000research.com/articles/10-786/v1
|
10 Aug 21
|
{
"type": "Case Report",
"title": "Case Report: Infected primary hydatid cyst of the thigh",
"authors": [
"Myriam Jrad",
"Haifa Zlitni",
"Hakim Zouari",
"Miriam Boumediene",
"Ines Soussi",
"Meriem Bouzrara",
"Myriam Jrad",
"Hakim Zouari",
"Miriam Boumediene",
"Ines Soussi",
"Meriem Bouzrara"
],
"abstract": "Hydatic cyst may occur in many organs such as the liver, lung, brain or heart with radiologic features of liver and lung involvement being well known. The musculo-skeletal site is infrequent accounting for 0.7–3% cases of all cases resulting from direct implantation of oncospheres more often than hematic dissemination. We report the case of an 18-year-old female student who visited our hospital because of a swelling in the posteroexternal aspect of the left thigh that had grown during the previous six months and had become tender in the previous month with setup of fever three days before admission. Superficial ultrasound and magnetic resonance imaging demonstrated a cystic mass of the posterior compartment of the thigh developed within the short chief of the biceps femoris. Serology for hydatid cyst was positive. The diagnosis of an infected hydatid cyst was suspected preoperatively, and the patient was given antibiotics and anthelminthic treatment. The cyst was then completely excised and the histopathologic exam confirmed the hydatic origin. The patient was put on oral anti-helminthics and has been on regular follow up for last twelve months with no evidence of recurrence.\nHydatidosis rarely occurs in the soft tissues and the diagnosis is challenging particularly when it is secondary infected. Hydatid serology provides certainty in the diagnosis of echinococcosis when it is positive. When it’s negative, imaging (Ultrasound, Computed tomography (CT) and Magnetic resonance imaging (MRI)) may be an approach for making the diagnosis revealing the most characteristic features of hydatid cyst.",
"keywords": [
"hydatidosis",
"cyst",
"ultrasound",
"MRI",
"surgery"
],
"content": "Case presentation\n\nAn 18-year-old Tunisian female student presented to the orthopedics department of Charles Nicolle Hospital of Tunis, Tunisia on January 15, 2019 with a lump in the posteroexternal aspect of the left thigh. She had noticed the swelling on her thigh six months before visiting the hospital. She was without history of trauma, surgery or any additional disease. The swelling had become painless during the six months prior to her visit but it had become tender within the previous month with the setup of fever three days prior. On examination, the patient was febrile (38.5° Celsius) with normal vital parameters. There was a tender, indurate, non-moveable lump on the posteroexternal aspect of the middle one-third of the left thigh measuring about 12 cm × 5 cm. The overlying skin was erythematous without any punctum or discharge. The knee and leg movements were normal.\n\nLaboratory investigations on January 15, 2019 showed a biological inflammatory syndrome with elevated white blood cell count (12,000/mm3) and C-reactive protein. Conventional radiography of the left femur showed a thickening of the soft tissues of the middle and posterior region of the thigh with integrity of the bone (Figure 1).\n\nSuperficial Doppler ultrasound performed the second day of hospitalization showed an ill-defined multilocular cystic mass of the middle one-third of the posterior compartment of the left thigh measuring 13 cm × 5.5 cm and containing an echogenic peripheral portion that was finely vascularized on color Doppler (Figure 2). Magnetic resonance imaging (MRI) performed two days later demonstrated a large intramuscular cystic mass of the middle one-third of the posterior compartment of the left thigh (Figure 3) within the biceps femoris muscle measuring 10 cm × 4 cm. This mass was delimited by a discontinuous rim of low T2 and high T1 signal “rim sign” and contained multiple well defined cystic lesions of more intense high T2 and low T1 signal corresponding to daughter cysts with a “cyst within a cyst appearance”. This cystic mass was surrounded by an edematous infiltration of the adjacent muscles with low T1 and high T2 signal and avid enhancement after contrast administration predominant in the posterior compartment. Enhancement of the muscular fascia and of the subcutaneous fat of the posterior aspect of the thigh was noticed. The mass repressed the sciatica nerve without invading it and was distant from the profound and superficial femoral pedicles. A low T1 signal of the spongy bone enhanced after contrast administration was noticed (Figure 4).\n\nAxial TSE T1-weighted images (A1+B1), TSE T2-weighted images (A2+B2) and contrast-enhanced fat-suppressed TSE T1-weighted images demonstrated an intramuscular cystic mass of the middle one-third of the posterior compartment of the left thigh within the biceps femoris muscle. This mass is delimited by a discontinuous rim of low T2 and high T1 signal \"rim sign\"(pink arrow) and contains multiple well defined cystic lesions of more intense high T2 and low T1 signal corresponding to daughter cysts (blue arrow) with a \"cyst within a cyst” appearance. This cystic mass is surrounded by an edematous infiltration of the adjacent muscles with low T1 and high T2 signal and avid enhancement after contrast administration (red arrows). Enhancement of the muscular fascia and of the subcutaneous fat of the posterior aspect of thigh. The mass represses the sciatica nerve without invading it (yellow arrow) and is distant from the profound and superficial femoral pedicles. A low T1 signal of the spongiest bone enhanced after contrast administration was noted (green arrow).\n\nThe enzyme-linked immune-absorbent assay (ELISA) was positive for the Echinococcal granulosis antigens (40 U/ml).\n\nThe diagnosis of an infected hydatid cyst was suspected perioperatively and the patient was given antibiotics and anthelminthic treatment (Albendazole 400 mg Per Os twice daily for 28 days). The patient didn't have any history of hydatidosis and hydatid cysts were not detected in any other organ on preoperative computed tomography (CT) of the abdomen and thorax. The surgical exploration found a firm oblong mass within the short chief of left biceps femoris densely adherent to the surrounding muscles and abutting the femur cortex. The mass was widely excised. The surgeon then performed an irrigation with Povidone iodine and hypertonic saline solutions and closed the wound over a negative suction drain. The macroscopic examination of the lesion revealed multiple daughter cysts and the histopathological exam confirmed the hydatic origin.\n\n\nDiscussion\n\nEchinococcosis is a cosmopolitan helminthic infection caused by the tapeworm Echinococcus granulosus and it affects humans and many mammals.1 This tapeworm species is endemic in the Mediterranean region, Australia, Argentina, Africa, Eastern Europe and the Middle East. The dog is a definitive host, but this situation is shared by the wolf and some species of jackal.2\n\nThe dog infestation is through the digestive track and is believed to be secondary to the consumption of parasite viscera especially the liver and the lungs of the sheep as an intermediate host.3 The latter, constituting the main reservoir of Echinococcus tapeworm, becomes infected by eating grass soiled by the dog’s droppings containing the eggs of the parasite.4 Humans are only an intermediate host and an epidemiological impasse of the parasite. They become infected either through direct contact with parasitized dogs or indirectly through ingestion of contaminated food.3–5\n\nMuscular localization of hydatid cyst is rare varying from 1 to 5.4 % of all hydatid locations.6 It’s the third localization after the lungs and the liver. For some, involvement of the spleen must precede that of muscle since it is estimated at 8%.1,7 Several arguments have been put forward to explain the scarcity of muscle localization: the efficiency of hepatic and pulmonary barriers that opposes the migration of the parasite into the systemic circulation; the muscular environment’s hostility to the growth of hydatid larvae due to the production of lactic acid and the alternation of contraction–relaxation inhibiting uniform vascularization.8,9 The muscle localization of echinococcosis seems to be mostly primary and affects mainly proximal muscles of the lower limbs, very probably due to the importance of irrigation of these.10 Daali and Hssaida reported 10 cases out of 15 of deep muscular location involving the diaphragm and psoas.11\n\nDiagnosis of echinococcosis must be suspected when a patient from a rural area is presenting with slowly growing soft tissue mass and it should be included in the differential diagnosis of limb masses: abscess, malignant or benign tumor, calcified hematoma or lipoma.12 The diagnosis of echinococcosis should be considered before surgical biopsy in order to prevent the risk of anaphylaxis.13\n\nUltrasound is a non-irradiating, accessible, and non-expensive exam, which can be used as a first line approach for making the diagnosis revealing the most characteristic features of hydatid cyst: daughter cysts, detached membranes and double line sign. Cysts may be classified according to the ultrasound criteria of Gharbi.14 Atalar et al. reported a sensitivity of 95%, increasing to 100% in the presence of vesicular fibrils.15 In our case, superficial Doppler ultrasound showed a multilocular cystic mass (type III) of the middle one-third of the posterior compartment of the left thigh. The mass was ill-defined and containing an echogenic peripheral portion finely vascularized on color Doppler probably related to the secondary infection of the cyst. However, in non-endemic areas, ultrasound can be misleading with soft tissue tumors especially in deep locations.16\n\nComputed tomography (CT) radiologic features vary from a unilocular or multilocular cyst, with or without septas, debris or wall calcifications, to a complex or solid mass without enhancement on intravenous contrast.13 The appearance of muscular hydatidosis is unoften typical and the multivesicular form is specific as is reflects multiple daughter cysts within the parent cyst. Since bony invasion and relationship of the cyst with adjacent organs is essential to describe, computed tomography (CT) must be a part of the screening protocol.17\n\nAlthough, magnetic resonance imaging (MRI) characteristics of liver hydatid cyst are detailed in the literature, the diagnosis is challenging in the soft tissue of the musculoskeletal system because the magnetic resonance imaging (MRI) features are not well labelled. Magnetic resonance imaging (MRI) is the gold standard imaging test in the identification of soft-tissue masses including hydatid disease thanks to its capacity to establish most of its features, with the exception of calcifications. Performing magnetic resonance imaging (MRI) requires the use of a surface antenna depending on the concerned part of the body, the use of a large field of view allowing the inclusion of the neighboring joint, a section thickness of 3 to 7 mm, and an inter-cut space of 0 to 2 mm. Acquisitions are performed in the axial plan, sagittal plan for anterior or posterior lesions, and coronal plan for lateral or medial lesions. The sequences must include T1-weighted sequence in the axial plane and T2 and T1-weighted sequences after fat saturation before and after injection of gadolinium in two orthogonal planes.\n\nThe classic magnetic resonance imaging (MRI) findings include a unilocular or multilocular cyst with a low-intensity rim (\"rim sign\") or detached membrane on T2-weighted images without enhancement after contrast injection.18 “The rim sign” corresponds to the pericyst that is a collagen reaction generated by the host. The most pathognomonic sign is that of daughter cysts within a larger cyst.19 The rim sign is a characteristic sign in muscular hydatidosis that is uncommon in hydatic cyst located elsewhere in the body. Magnetic resonance imaging (MRI) of our patient demonstrated a cystic mass containing multiple well-defined cysts corresponding to daughter cysts with a “cyst within a cyst appearance” delimited by a discontinuous “rim sign”.20 This lesion was surrounded by an edematous infiltration with avid enhancement of the muscular environment and the spongy bone in contact after contrast related to the secondary infection of the cyst.19–21\n\nHydatid serology provides certainty in the diagnosis of echinococcosis when it is positive. However, there is a significant proportion of false negatives, variable depending on the location of the cyst. Lamine et al. reported 80% of false negatives.9 The enzyme-linked immune-absorbent assay (ELISA) was positive for the E. granulosis antigens in our case. Hypereosinophilia is not specific and inconstant and is of interest only in the orientation of the diagnosis, ultrasound, and nowadays magnetic resonance imaging (MRI) can confirm the diagnosis.9,19\n\nSurgical excision of the cyst is the treatment of choice. For non-surgical cysts, anthelminthic chemotherapy with or without percutaneous aspiration-injection re-aspiration (PAIR) is an alternative option for the treatment.21,22 Our patient was given antibiotics and anthelminthic treatment (Albendazole 400 mg Per Os twice daily for 28 days). Thereafter, the mass was widely excised, and the patient was put on oral anthelminthics after surgery. Percutaneous drainage echo guided without re-aspiration is simple, easy to apply, low cost, repeatable, and does not require hospitalization.21,22\n\nHydatidosis rarely occurs in the soft tissues and the diagnosis is challenging particularly when it is secondary infected. Hydatid serology provides certainty in the diagnosis of echinococcosis when it is positive. When it’s negative, ultrasound is an accessible way to approach the diagnosis, computed tomography (CT) may help to evaluate the surrounding tissues and find calcifications and magnetic resonance imaging (MRI) provides imaging characteristics of hydatic cyst. Open surgery is the gold standard of the treatment of muscular hydatidosis while ambulatory percutaneous techniques are gaining scale.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of clinical details and clinical images was obtained from the patient.",
"appendix": "References\n\nAbi F, El Fares F, KAIS D: Les localisations inhabituelles du kyste hydatique a propos de 40 cas. J Chir. 1989; 126: 307–12.\n\nMcManus DP, Yang YR: Helminthic Diseases Echinococcosis. In: Reference Module in Biomedical Sciences. 2014.\n\nGougoulias NE, Varitimidis SE, Bargiotas KA, et al.: Skeletal muscle hydatid cysts presenting as soft tissue masses. Hippokratia. 2010; 14(2): 126–30. PubMed Abstract | Free Full Text\n\nMseddi M, Mtaoumi M, Dahmene J, et al.: Kyste hydatique musculaire. Revue de Chirurgie Orthopédique et Réparatrice de l’Appareil Moteur. 2005 May; 91(3): 267–71. Publisher Full Text\n\nHmidi M, Touiheme N, Rbai M, et al.: Isolated hydatid cyst of the neck: An unusual site. Eur Ann Otorhinolaryngol Head Neck Dis. 2012 Apr; 129(2): 108–10. PubMed Abstract | Publisher Full Text\n\nLamine A, Fikry T, Zryouil B: L’hydatidose primitive des muscles périphériques. A propos de 7 cas. Acta Orthop. 1993; 59: 184–7.\n\nBendib A, Bendib S, Benmamar L, et al.: Tomodensitométrie du kyste hydatique du foie: sémiologie et classification à propos de 157 cas dont 146 vérifiés chirurgicalement. J Radiol. 1985; 66: 367–75.\n\nKehila M, Allegue M, Letaief R, et al.: Le kyste hydatique du muscle psoas: A propos d’un cas. J radiol. 1987; 68: 265–8.\n\nEssadki O, Elhajjam M, Kadiri R: Kyste hydatique des parties molles, aspect radiologique. Ann Radiol. 1996; 39: 135–41.\n\nDaali M, Hssaida R: [Muscle hydatidosis. 15 cases]. Presse Med. 2000 Jun 17; 29(21): 1166–9. PubMed Abstract\n\nBourree P: Vers un traitement médical de l’hydatidose. Rev Prat. 1978; 28: 2879–900.\n\nOrhan Z, Kara H, Tuzuner T, et al.: Primary subcutaneous cyst hydatic disease in proximal thigh: an unusual localisation: a case report. BMC Musculoskelet Disord. 2003 Nov 7; 4: 25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTekin R, Avci A, Tekin RC, et al.: Hydatid cysts in muscles: clinical manifestations, diagnosis, and management of this atypical presentation. Revista da Sociedade Brasileira de Medicina Tropical. 2015 Oct; 48(5): 594–8. PubMed Abstract | Publisher Full Text\n\nAtalar MH, Cankorkmaz L, Koyluoglu G, et al.: Imaging characteristics of three primary muscular hydatid cyst cases with various patterns. Kafkas J Med Sci. 2012; 2(2): 74–6. Publisher Full Text\n\nBenhaddoua H, Margib M, Kissrab M, et al.: Le kyste hydatiqueu du muscle trapezius: Une localisation inhabituelle. Archives de pédiatrie. 2012: 263–5.\n\nMughal A, Saeed Minhas M, Bhatti A, et al.: Hydatid Cyst Of Skeletal Muscle Presenting As Soft Tissue Tumour. J Coll Physicians Surg Pak. 2018 Feb 26; 28(3): S51–3. PubMed Abstract | Publisher Full Text\n\nGarcia Diez A, Ros Mondoza L, Villacampa V, et al.: MRI evaluation of soft tissue hydatid disease. Eur J Radiol. 2000; (10): 462–6. PubMed Abstract | Publisher Full Text\n\nAlexiadis G, Lambropoulou M, Deftereos S, et al.: Primary muscular hydatitosis. US, CT and MR findings. Acta Radiol. 2002; 43: 428–30. PubMed Abstract | Publisher Full Text\n\nComert R, Aydingoz U, Ucaner A, et al.: Waterlily sign on MR imaging of primary intramuscular hydatidosis of sartorius muscle. Skel Radiol. 2003; 32: 420–3. PubMed Abstract | Publisher Full Text\n\nBayram M, Sirikci A: Hydatic cyst located intermuscular area of the forearm: MR imaging findings. Eur J Radiol. 2000 Dec; 36(3): 130–2. PubMed Abstract | Publisher Full Text\n\nÖrmeci N, Idilman R, Akyar S, et al.: Hydatid cysts in muscle: a modified percutaneous treatment approach. Int J Infect Dis. 2007 May; 11(3): 204–8. PubMed Abstract | Publisher Full Text\n\nGuillaureau P, Deunier B, Levet Y: Hydatidose musculaire à localisation masseterine. 1986; 1049; 15."
}
|
[
{
"id": "102033",
"date": "23 Dec 2021",
"name": "Hichem Jerraya",
"expertise": [
"Reviewer Expertise hydatid cyst surgery",
"digestive surgery"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI congratulate the authors for the quality of their manuscript. The iconography is rich and of high value.\nI have only two comments to make:\nIn the abstract, one has the impression that hydatid serology represents an indispensable tool in the diagnostic process. I think that currently in endemic countries, serology has been supplemented by imaging and its only interest could be in rare cases of diagnostic doubt after complete morphological assessment.\n\nOnce the diagnosis of infected hydatid cyst has been retained, should the surgery have been indicated earlier? and was intraoperative samples done to confirm the diagnosis of hydatid cyst infection?\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-786
|
https://f1000research.com/articles/10-785/v1
|
10 Aug 21
|
{
"type": "Research Article",
"title": "Self-reported COVID-19 among physicians: An Egyptian online study during the pandemic",
"authors": [
"Hala Samir Abou-ElWafa",
"Abdel-Hady El-Gilany",
"Ahmed A. Albadry",
"Abdel-Hady El-Gilany",
"Ahmed A. Albadry"
],
"abstract": "Abstract: Background: COVID-19 causes a critical occupational risk to frontline healthcare workers (HCWs) who respond to the pandemic, as they are placed in environments with an increased risk of infection exposure. It is a public health priority to understand how transmission occurs to protect this vulnerable group of HCWs. This study was conducted to estimate the incidence of self-reported COVID-19 infection among physicians and its possible associated factors. Methods: An online national survey using Survey Monkey was initiated to collect sociodemographic e.g. age and sex, occupational e.g. place and duration of work, and clinical data e.g. COVID symptoms and laboratory investigations, and to describe affected physicians' diagnoses. Results: The self-reported incidence of COVID-19 infection was found to be 65.4% among studied physicians. The significant independent predictors of COVID-19 infection were smoking, working as a frontline physician, having contact with a COVID-19 case, and working for less than ten years [ARR (95% CI): 3.0(1.6-5.7), 2.3(1.4-3.8), 2.1(1.2-3.6), and 1.8(1.2-2.9); respectively]. Conclusions: The incidence of COVID-19 infection among Egyptian physicians is relatively high. Smoking, being a frontline physician, having contact with a COVID-19 case, and working for less than 10 years are all factors associated with an increased risk of infection. There should be strict application of preventive measures, periodic screening for COVID-19 for early detection and isolation of infected HCWs together with effective vaccination.",
"keywords": [
"COVID-19",
"physicians",
"pandemic",
"incidence",
"Egypt",
"frontline",
"PPE"
],
"content": "Introduction\n\nCOVID-19, has become a universal threat to public health1. Since the beginning of the COVID-19 pandemic, healthcare workers have exhibited tremendous strength and professional loyalty despite the risk of infection and spreading the infection to others2.\n\nDuring the initial wave of the COVID-19 pandemic, overstrained healthcare systems in severely affected countries left healthcare workers fighting with prolonged work hours, intense emotional stress, and fatigue. Speedily declining resources, lockdowns, and a high demand for personal protective equipment (PPE) led to shortages3. Healthcare workers frequently had to care for patients with confirmed or suspected COVID-19 infections with insufficient PPE or improper training. These conditions contributed to a heightened risk to healthcare workforces of contracting the infection throughout the pandemic's early stage4–6.\n\nMost studies reported enhanced risks for health professionals who care for COVID-19 patients5,7,8. The ultimate threat to healthcare professionals may be their contact with colleagues or patients in the early stages of unpredicted infections when viral loads are at a high-level9.\n\nBased on previous respiratory virus experience, consistent PPE use is essential for managing nosocomial transmission10. Strategies from the USA and the UK recommended that healthcare workers wear a surgical mask when providing care for individuals with COVID-1911. However, worldwide deficiencies of masks, face shields, respirators, and gowns, triggered by heavy needs and supply series disturbances, have directed efforts to save PPE throughout prolonged usage or reuse, Disinfection procedures have also been employed, but there is a lack of adequate agreement on best practice12–14.\n\nAccording to the published articles, many healthcare professionals have been infected with COVID-19 internationally and have even died as a result15–17. Consequently, adequate protection for HCWs is of utmost importance18. To the best of our knowledge, there is currently no published work about the incidence of COVID-19 infection among physicians in Egypt. Therefore, this study was performed to estimate the annual incidence, a year before data collection, of self-reported infection among physicians and its possible associated factors including sociodemographic, occupational, medical and preventative factors.\n\n\nMethods\n\nDescriptive longitudinal study with an analytical component.\n\nA national online survey was carried out among Egyptian physicians from December 26, 2020, to January 16, 2021.\n\nEgyptian physicians working anywhere in Egypt that have been on duty for one year or more.The sample size was calculated online using the Open Epi Program., Version 3.01. A pilot study on 100 physicians discovered that 70% reported being infected with COVID-19, whether possible, probable, or confirmed. With a 95% confidence level and 5% precision, the sample size was 323 physicians.\n\nA survey form, developed by the authors, was used to collect the following data: socio-demographics e.g. sex, age, smoking; work profile, medical history; preventive measures at the workplace, e.g. according to the Egyptian guidelines, PPE use, hand sanitization, and diagnostic criteria of cases19. Participants selected the signs and symptoms they experienced during the past year from a list of all possible COVID-19 manifestations. The form allowed participants to choose a final diagnosis, whether suspected, probable, or a confirmed case, guided by their answers on the relevant criteria. Participants were encouraged to respond to understand the problem's magnitude and its risk factors.\n\nParticipants were enrolled via social media (e.g. Facebook and Whatsapp) and invited by the researchers to respond voluntarily to the survey. At enrolment, participants gave consent for the information they provided to be used for research. Consideration of privacy was guaranteed as data were collected anonymously.\n\nData were collected using Survey Monkey, which was launched online, and the survey was open until the required sample size was reached. A copy of the survey can be found here (https://doi.org/10.7910/DVN/BVSLG2)\n\nThe Institutional Research Board (IRB) Approval at Faculty of Medicine, Mansoura University, was obtained. Registration number (R.20.11.1078)\n\nParticipants were asked to voluntarily participate in the study to ensure confidentiality and anonymity of data; the online survey include the first question about informed consent to participate in the research and publication of these results; the question was tick box, if not ticked the survey end automatically.\n\nData were entered/ and statistically analyzed, applying the Statistical Package for Social Sciences (SPSS) version 23. The accompanying dataset is openly available on Harvard Dataverse (https://doi.org/10.7910/DVN/BVSLG2). Categorical variables were portrayed as numbers and percentages. The χ2 test was used to check the significance in bivariate analysis, and crude risk ratios (CRR) and 95% CI were assessed. Variables significantly associated with COVID-19 infection in bivariate analysis were entered into a multivariate logistic regression model using the forward Wald method. Adjusted risk ratios (ARR) and their 95% CI were calculated. \"p-value ≤0.05\" was considered statistically significant. Participants had to complete the whole survey to get their final diagnosis, so missing data were not possible.\n\n\nResults\n\nTable 1 reveals that 65.4% of physicians reported COVID-19 infection. About three-quarters of physicians under 35 years old were infected compared to 57.7% of those aged 35 years and older, with a statistically significant difference between them (p= 0.007). A higher percentage of frontline physicians were infected than those not on the front line with a statistically significant difference (p=0.001). Having contact with a COVID-19 case showed a statistically significant difference (p=0.001), and most smokers (82.3%) and those working for less than ten years (73.1%) were significantly infected.\n\n*Single, widow & divorced **M.D., Ph. D, fellowship & board ***General practitioner, family medicine, public health, laboratory medicine #Primary health care, Family practice, private, insurance ##Obesity, hypertension, diabetes, cardiac diseases RR=risk ratio, CI=Confidence Interval r=reference category\n\nThe incidence of infection does not vary significantly with the use of PPE and hand sanitizers (see Table 2).\n\nRR=risk ratio, CI=Confidence Interval, r=reference category\n\nTable 3 demonstrates that the significant independent predictors of COVID-19 infection were smoking, working as a frontline physician, having contact with a COVID-19 case, and working for less than ten years [ARR (95% CI): 3.0(1.6-5.7), 2.3(1.4-3.8), 2.1(1.2-3.6), and 1.8(1.2-2.9); respectively].\n\nARR=adjusted risk ratio, CI=Confidence Interval, r=reference category\n\nMost of the self-reported COVID-19 cases (about 71%) were probable cases, and confirmed cases represented 23%. A tiny percentage of cases were asymptomatic (2.6%).\n\nAmong symptomatic cases, the most frequent symptoms were fatigue and a sore throat (about 75% each), and the least frequent was mental confusion (7.8%). The health facility was the most frequent possible source of infection (about half the cases), while the least was the general population source (19.4%) (see Table 4).\n\n*cough, expectoration, chest tightness, dyspnea\n\n\nDiscussion\n\nSince its beginning2, COVID-19 has become global health threat.5 Healthcare workers are exposed to the infection to a more considerable extent than other members of society and may be judged to be at an elevated risk of disease20. Throughout the crisis, they were continually caring for patients with confirmed or suspected COVID-19 infection with improper training and/or inadequate protective equipment4–6.\n\nThis study showed that 65.4% of physicians reported having had a COVID-19 infection. This percentage is much higher than the rates reported in other countries. In Brazil, 42.37% of HCWs with symptoms tested positive for COVID-19. In Brazil, over the ten-week study period, the rate of positive testing ranged from 22.2% in the second week to 55.9% in the sixth week, then plateaued to 38–46%21. However, much lower percentages of HCWs who had COVID-19 during the study period were reported in China (33.62%)18 and, in Spain, (11.1%). In Italy, 20% of responding HCWs were infected22. In France, the incidence of COVID-19 positivity was 35% among symptomatic HCWs who were tested23.\n\nA wide variation was found in the prevalence of COVID-19 infection, which fluctuated from 0.4% in Spain24 to 57.06% in New York City25. In Seattle, Washington, the prevalence of COVID-19 amongst frontline HCWs was (5.2%)26.\n\nThe proportion of COVID-19 infection also showed a broad variability. In the early published studies from Wuhan, China, 29% of the cases were HCWs17. A much lower proportion of HCWs (3.8%) was found in another study in China27. A slightly higher frequency was reported in Spain, where the ratio of physicians was 13%22. A much higher frequency was reported in another study from Spain, showing that 22% of COVID-19 cases have been amongst HCWs22. In a meta-analysis and systematic review of the prevalence of COVID-19 in HCWs, among HCWs with positive results, 25% were physicians28.\n\nThe high incidence reported in the current study could be attributed to the self-reported diagnosis that includes all probable, possible, and confirmed infections. Other contributing factors include work overload and shortage of PPE, mainly when dealing with undiagnosed cases, extended use or reuse, or suboptimal use (about two-thirds only of studied physicians used PPE and hand sanitizers) and HCW to HCW transmission may play a role. The environmental factors could contribute to this high incidence as hospital air, surfaces, and devices could be contaminated by aerosol from infected patients. Dual sources of infection could play a role as 47.4% of infected COVID-19 cases and 19.4% of them reported that health facilities and the general community were the possible sources of infection, respectively. About one-third of physicians (33%) were unable to predict the source of infection as asymptomatic carriers, and silent spreaders play an essential role in COVID-19 transmission, which may be among infected work colleagues, patients, household contacts, relatives, or friends.\n\nThe present study showed that smoking was found to be the most important independent predictor of COVID-19 infection [ARR (95% CI): 3.0 (1.6-5.7)]. For COVID-19, data are limited; one review didn't comment on smoking as a risk factor associated with COVID-19 infection but reported an elevated risk of intense disease [relative risk (R.R.) 1.4 (95% CI 0.98–2)] and the requirement for mechanical ventilation or the infection resulting in death [RR 2.4 (1.43–4.04)] for current smokers29. A meta-analysis included 16 studies and revealed that smoking history and active smoking considerably increased the risk for severe COVID-1930. However, a prior study has reported a non-significant correlation between smoking history and COVID-19 severity31.\n\nThere are several ways tobacco smoking might increase the risk of COVID-19 infection and result in worse symptoms for COVID-19. There are the general effects of smoking on host defenses and increased inflammation reactions among smokers, and the specific influences on the ACE2 receptor. Moreover, smoking increases the chronic disease frequently associated with elevated risk for COVID-19 sequalae bad outcomes: coronary heart disease, chronic obstructive pulmonary disease, and type 2 diabetes mellitus. Intensified risk for more severe COVID-19 might be arbitrated through chronic diseases attributed to smoking32.\n\nThe present study showed that being a frontline physician was found to be a predictor of COVID-19 infection [ARR (95% CI): 2.3(1.4-3.8)]. This correlation agrees with results from China, where 23.6% of physicians were diagnosed with COVID-19; amongst them, 35.3% were frontlines first-lines, 21.5% non-first lines. Frontline HCWs may have a higher chance of getting an infection due to close patient contact33. COVID-19 infection prevalence was 2747 cases per 100,000 among frontline HCWs in the study carried out in the UK and USA using self-reported data. Frontline HCWs had a twelvefold increase in the risk of testing positive with multivariate adjustment (adjusted HR 11.61, 95% CI 10.93–12.33)5.\n\nThe present study showed that having contact with a COVID-19 case was found to be a predictor of COVID-19 infection [ARR (95% CI): 2.1(1.2-3.6)]. Similarly, in China, about 60% of the infected HCWs attributed their infection to contact with later diagnosed patients with COVID-1933.\n\nDuration of employment Working for less than ten years was found to be an independent predictor of COVID-19 infection [ARR (95% CI): 1.8(1.2-2.9)] in the present study. Similarly, in China, being younger than 45 years old was correlated with an enhanced risk of getting infected (IRR, 1.9; 95%CI, 1.3-3; p = 0.002)33. This study reported that about three-quarters of physicians below 35 years old were infected compared to 57.7% of those above 35 years, with a statistically significant difference between them. Correspondingly, in a Chinese study, about 71% of the infected HCWs were below 45 years old33. The high incidence in this study could be attributed to the younger age of infected doctors (72.3% were <35 years), their inadequate experience (73.1% worked <10 years) and being resident physicians (72.3%) compared to specialists and consultants/faculty members. Also, younger doctors are in more frequent and prolonged contact with patients and their relatives, which increases their chance of contracting the infection as juniors usually carry most of the workload to gain more experience.\n\nOur findings showed that a high percentage of infection was found among doctors working in governmental hospitals and those working in more than one hospital at the same time. In China, (89.26%) of infected HCWs were general hospital staff, then specialized hospital staff (5.70%), and community hospitals staff (5.05%). The case infection rate (CIR) of community hospitals was markedly lower than the general hospitals (p<0.001 and p<0.001; respectively), while the CIR of community hospitals was lower than specialized hospitals (p<0.001)18. Another study from China showed that working in clinical departments other than fever clinics or wards was correlated with a high risk of getting infected (IRR 3.1; 95%CI, 1.8-5.2, p< 0.001)33.\n\nA non-statistically significant difference was found in infection rates of males and females in this study. Similarly, in China, a non-significant difference was found in the CIR of HCWs, including doctors by gender (p = 0.591)18. Both sexes are exposed to the same potential risks of infection in both the hospital care settings and the community.\n\nDepartment of critical care/emergency specialty did not show a significantly greater incidence of COVID-19 among doctors. Similarly, in the UK, working in ICUs intensive care units were not linked with higher infection risk, probably related to the protection provided by advanced protection by PPE or declining infectivity occurring in subsequent stages of the disease, even amongst seriously ill patients7.\n\nThe incidence of infection in this study does not vary significantly with PPE and hand sanitizers. Similarly, in New Jersey, reported PPE use was positively correlated with the number of confirmed or suspected COVID-19 patients, and HCWs who stated less usage of protective equipment did not seem to be at an increased risk of infection, proposing that use of protective measures was comparative to perceived threats of getting an infection34. Notably, a study of healthcare workers in Wuhan, China, throughout the peak of the pandemic revealed that universal PPE use and other protective measures were extraordinarily successful and entirely protected healthcare workers, evidenced by the negativity of both virus and antibody35. Likewise, in Wuhan, China, utilizing medical masks was significantly associated with an elevated risk of COVID-19 in HCWs than using N95 respirators, even with substantially higher exposure to infected patients among the last group36.\n\nThe health facility (including hospitals and Primary Healthcare units) was the most frequent possible source of infection (about half of the cases). At the same time, in the present study, the minor source of infection was the community (19.4%) which agreed with the studies carried out in Spain37 and the Netherlands38, which offered evidence of a pertinent role of the community as a source of transmission of infection to HCWs. These findings could imply that household contacts could have a substantial role in the COVID-19 disease in HCWs, primarily due to the quick community spread of the virus. The additional explanation might be that the infection from symptomless carriers, considering that nearly half of healthcare workers infected with COVID-19 were symptomless during the screenings28.\n\nIn the current study, most self-reported COVID-19 cases (about 71%) were probable cases, confirmed cases represented about 23%, and a tiny percentage of cases were asymptomatic (2.6%). In COVID-19, the severe cases represent a minority e.g. 14.8% of the cases among healthcare workers in China were categorized as severe or critical27. Severe cases are not adequately reported due to their high mortality.\n\nIn the present study, the most frequent symptoms were fatigue/general weakness (74.1%) and a sore throat (72%), followed by headaches and myalgia, and the least frequent was mental confusion (7.8%). In the systematic review and meta-analysis of COVID-19 infection in HCWs, the frequently reported symptoms were fever (57%) and dry cough (57%), followed by malaise (43%) and myalgia (48%) among symptomatic HCWs28. Similarly, the five most common symptoms among infected HCWs in China were fever (60.9%), myalgia or fatigue (60.0%), cough (56.4%), sore throat (50%), and muscle pain (45.5%)33. Fatigue, ageusia or anosmia, and hoarse voice were persistent symptoms among frontline HCWs in the study carried out in the UK and the USA5.\n\nPositive chest computed tomography scan (C.T scan) findings were found to be 81.5% among the studied COVID-19 cases. This result agrees with that reported in China39, where 86.2% of C.T. scans performed at the time of admission showed abnormal results.\n\n\nStudy limitations\n\nSelection bias was a potential limitation to the study due to non-random sampling of the study population since the use of online surveys as a data collection tool is limited to has selectivity among certain socioeconomic and age groups familiar with this type of online tool. The possibility of overestimation cannot be excluded due to the self-reported nature of the study. The severity of COVID-19 and mortality were not assessed in this study.\n\n\nConclusions\n\nThe self-reported incidence of COVID-19 infection among studied Egyptian physicians is 65.4%. Smoking, being a frontline physician, having contact with a COVID-19 case, and working for less than 10 years are all factors associated with an increased risk of infection. The strict application of preventive measures for all HCWs, including adequate PPE supplies and their proper use in the workplace, enables workers to keep a safe distance to avoid overcrowding and infection transmission. Periodic screening for COVID-19 for early detection and isolation of infected HCWs must be provided together with effective vaccination. Particular attention should be given to smokers, frontline doctors, contacts with COVID-19 cases, and doctors with short working duration. Implementation of an electronic registry for documentation and registration of both general COVID-19 cases and HCW cases will help monitor the magnitude of COVID-19 infection over time and affect different intervention measures.\n\n\nData availability\n\nHarvard Dataverse, V1: Self-reported COVID-19 among physicians: An Egyptian online study during the pandemic https://doi.org/10.7910/DVN/BVSLG240\n\nThe project contains the following underlying data:\n\n- File name: Covid dr incid. short.tab\n\n- File description: 30 Variables, 355 Observations\n\nHarvard Dataverse, V1: Self-reported COVID-19 among physicians: An Egyptian online study during the pandemic: Online Questionnaire 2021 https://doi.org/10.7910/DVN/BVSLG240\n\n- This project contains the following extended data:\n\n- Questionnaire (in English and the introduction in original language)\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\nAnderson RM, Heesterbeek H, Klinkenberg D, et al.: How will country-based mitigation measures influence the course of the COVID-19 epidemic? Lancet. 2020; 395(10228): 931–34. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu Q, Luo D, Haase JE, et al.: The experiences of health-care providers during the COVID-19 crisis in China: a qualitative study. Lancet Glob Health. 2020; 8(6): e790–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurki T: Global shortage of personal protective equipment. Lancet Infect Dis. 2020; 20(7): 785–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKua J, Patel R, Nurmi E, et al.: HealthcareCOVID: a national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers. PeerJ. 2021; 9: e10891. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen LH, Drew DA, Graham MS, et al.: Risk of COVID-19 among front-line health-care workers and the general community: a prospective cohort study. Lancet Public Health. 2020; 5(9): e475–e483. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Z, Liu S, Xiang M, et al.: Protecting healthcare personnel from 2019-nCoV infection risks: lessons and suggestions. Front Med. 2020; 14(2): 229–231. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEyre DW, Lumley SF, O'Donnell D, et al.: Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study. Elife. 2020; 9: e60675. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHunter E, Price DA, Murphy E, et al.: First experience of COVID-19 screening of health-care workers in England. Lancet. 2020; 395(10234): e77–e78. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLucey M, Macori G, Mullane N, et al.: Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks. Clin Infect Dis. 2021; 72(11): e727–e735. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerbeek JH, Rajamaki B, Ijaz S, et al.: Personal protective equipment for preventing highly infectious diseases due to exposure to contaminated body fluids in healthcare staff. Emergencias. Spanish, English. 2021; 33(1): 59–61. PubMed Abstract\n\nCDC COVID-19 Response Team: Characteristics of Health Care Personnel with COVID-19 - United States, February 12-April 9, 2020. MMWR Morb Mortal Wkly Rep. 2020; 69(15): 477–481. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFischer RJ, Morris DH, van Doremalen N, et al.: Assessment of N95 respirator decontamination and re-use for SARS-CoV-2. medRxiv. 2020; 2020.04.11.20062018. Update in: Emerg Infect Dis. 2020 Jun 03; 26(9). PubMed Abstract | Publisher Full Text | Free Full Text\n\nLivingston E, Desai A, Berkwits M: Sourcing personal protective equipment during the COVID-19 pandemic. JAMA. 2020; 323(19): 1912–14. PubMed Abstract | Publisher Full Text\n\nSchwartz A, Stiegel M, Greeson N, et al.: Decontamination and reuse of N95 respirators with hydrogen peroxide vapor to address worldwide personal protective equipment shortages during the SARS-CoV-2 (COVID-19) pandemic. Appl Biosaf. 2020; 25(2): 67–70. Publisher Full Text\n\nUS Centers for Disease Control and Prevention: Interim Additional Guidance for Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed COVID-19 in Outpatient Hemodialysis Facilities. Accessed January 15, 2021. Reference Source\n\nLivingston E, Bucher K: Coronavirus Disease 2019 (COVID-19) in Italy. JAMA. 2020; 323(14): 1335. PubMed Abstract | Publisher Full Text\n\nWang D, Hu B, Hu C, et al.: Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China. JAMA. 2020; 323(11): 1061–1069. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZheng L, Wang X, Zhou C, et al.: Analysis of the Infection Status of Healthcare Workers in Wuhan During the COVID-19 Outbreak: A Cross-sectional Study. Clin Infect Dis. 2020; 71(16): 2109–2113. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMinistry of Health and Population: A provisional definition of the emerging coronavirus (COVID-19) case. 2020.\n\nRudberg AS, Havervall S, Månberg A, et al.: SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden. Nat Commun. 2020; 11(1): 5064. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBuonafine CP, Paiatto BNM, Leal FB, et al.: High prevalence of SARS-CoV-2 infection among symptomatic healthcare workers in a large university tertiary hospital in São Paulo, Brazil. BMC Infect Dis. 2020; 20(1): 917. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSuárez-García I, de Aramayona López MJM, Sáez Vicente A, et al.: SARS-CoV-2 infection among healthcare workers in a hospital in Madrid, Spain. J Hosp Infect. 2020; 106(2): 357–363. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrastinova E, Garrait V, Lecam MT, et al.: Household transmission and incidence of positive SARS-CoV-2 RT-PCR in symptomatic healthcare workers, clinical course and outcome: a French hospital experience. Occup Environ Med. 2020; 78(7): 479–485. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlalla J, Correa AM, Martín-Escalante MD, et al.: Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience. QJM. 2020; hcaa238. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBreazzano MP, Shen J, Abdelhakim AH, et al.: Resident physician exposure to novel coronavirus (2019-nCoV, SARS-CoV-2) within New York City during exponential phase of COVID-19 pandemic: Report of the New York City Residency Program Directors COVID-19 Research Group. medRxiv. 2020; 2020.04.23.20074310. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMani NS, Budak JZ, Lan KF, et al.: Prevalence of Coronavirus Disease 2019 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington. Clin Infect Dis. 2020; 71(10): 2702–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu Z, McGoogan JM: Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020; 323(13): 1239–1242. PubMed Abstract | Publisher Full Text\n\nGómez-Ochoa SA, Franco OH, Rojas LZ, et al.: COVID-19 in Health-Care Workers: A Living Systematic Review and Meta-Analysis of Prevalence, Risk Factors, Clinical Characteristics, and Outcomes. Am J Epidemiol. 2021; 190(1): 161–175. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan Zyl-Smit RN, Richards G, Leone FT: Tobacco smoking and COVID-19 infection. Lancet Respir Med. 2020; 8(7): 664–665. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGülsen A, Yigitbas BA, Uslu B, et al.: The Effect of Smoking on COVID-19 Symptom Severity: Systematic Review and Meta-Analysis. Pulm Med. 2020; 2020: 7590207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang JJ, Dong X, Cao YY, et al.: Clinical characteristics of 140 patients infected with SARS-CoV-2 in Wuhan, China. Allergy. 2020; 75(7): 1730–1741. PubMed Abstract | Publisher Full Text\n\nSamet JM: Tobacco Products and the Risks of SARS-CoV-2 Infection and COVID-19. Nicotine Tob Res. 2020; 22(12 Suppl 2): S93–S95. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLai J, Ma S, Wang Y, et al.: Factors Associated With Mental Health Outcomes Among Health Care Workers Exposed to Coronavirus Disease 2019. JAMA Netw Open. 2020; 3(3): e203976. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarrett ES, Horton DB, Roy J, et al.: Prevalence of SARS-CoV-2 infection in previously undiagnosed health care workers at the onset of the U.S. COVID-19 epidemic. medRxiv. 2020; 2020.04.20.20072470. Update in: BMC Infect Dis. 2020 Nov 16; 20(1): 853. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu M, Cheng SZ, Xu KW, et al.: Use of personal protective equipment against coronavirus disease 2019 by healthcare professionals in Wuhan, China: cross sectional study. BMJ. 2020; 369: m2195. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang X, Pan Z, Cheng Z: Association between 2019-nCoV transmission and N95 respirator use. J Hosp Infect. 2020; 105(1): 104–105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGarcia-Basteiro AL, Moncunill G, Tortajada M, et al.: Seroprevalence of antibodies against SARS-CoV-2 among health care workers in a large Spanish reference hospital. Nat Commun. 2020; 11(1): 3500. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKluytmans-van den Bergh MFQ, Buiting AGM, Pas SD, et al.: Prevalence and Clinical Presentation of Health Care Workers With Symptoms of Coronavirus Disease 2019 in 2 Dutch Hospitals During an Early Phase of the Pandemic. JAMA Netw Open. 2020; 3(5): e209673. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuan WJ, Ni ZY, Hu Y, et al.: Clinical Characteristics of Coronavirus Disease 2019 in China. N Engl J Med. 2020; 382(18): 1708–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlbadry AA, Abou-ElWafa HS, El-Gilany AH: \"Self-reported COVID-19 among physicians: An Egyptian online study during the pandemic\". Harvard Dataverse V1, 2021. UNF:6:zfY8Zi7gZavRl/zmsuxC4Q== [fileUNF]. http://www.doi.org/10.7910/DVN/BVSLG2"
}
|
[
{
"id": "91640",
"date": "15 Sep 2021",
"name": "Indranil Saha",
"expertise": [
"Reviewer Expertise Communicable and non-communicable diseases"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is nicely written but it needs the following clarifications:\nThe study period is written as December to January, but what about the reference period? It has to be mentioned as it is written as a longitudinal study. Again, study subjects responded only once, then how can it be a longitudinal study.\n\nHow the sample size was decided as 323? The assumptions are written, whether these assumptions were put in a formula for longitudinal study? Please clarify.\n\nTable 1, 2, 3, 4: subheading is missing.\n\nTable 1: Please correct the title of the table. Whether incidence would be mentioned or not?\n\nWhat was the operational definition of “probable cases” and “confirmed cases”? Please mention.\n\nHow much variation of dependent variable could be explained by the independent variables from the logistic model? Please clarify.\n\nDiscussion: 1st line – please edit\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the 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": []
},
{
"id": "91602",
"date": "16 Sep 2021",
"name": "Ibrahim Ali Kabbash",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors did not give an operational definition of diagnosis of COVID-19 among studied participants as suspected, probable, or confirmed. It seems that the diagnosis was very subjective. This should be mentioned as one of the limitations of the study.\n\nVolunteer bias is suspected as those who had suspected signs might be more likely to respond to the questionnaire than those who did not.\n\nStatistical analysis and multivariate analysis are of limited value, as the sample was not chosen randomly. This will affect seriously the ability to generalize data.\n\nResults of this study should be considered with caution to the multiple limitations regarding sampling, the sample size that cannot represent national figures, and the subjectivity of self-reported data.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-785
|
https://f1000research.com/articles/9-1399/v1
|
04 Dec 20
|
{
"type": "Research Article",
"title": "Assessment of the performance of the Brazilian Portuguese Nottingham Health Profile in adult growth hormone deficiency and pulmonary hypertension",
"authors": [
"Alice Heaney",
"Rafael W. R. de Oliveira",
"Mariana Bizzi",
"Ricardo Amorim Correa",
"Monica Corso Pereira",
"Suelem Simao Mol",
"Beatriz Santana Soares",
"Stephen P. McKenna",
"Antonio Ribeiro-Oliveira Jr",
"Study Investigators",
"Alice Heaney",
"Rafael W. R. de Oliveira",
"Mariana Bizzi",
"Ricardo Amorim Correa",
"Monica Corso Pereira",
"Suelem Simao Mol",
"Beatriz Santana Soares",
"Stephen P. McKenna"
],
"abstract": "Background: The Nottingham Health Profile (NHP) is a generic measure of perceived distress that has been used widely as an outcome measure in clinical practice and trials. The availability of two Brazilian datasets provided the opportunity to assess the psychometric performance of the NHP in different populations - adult growth hormone deficiency (GHD) and pulmonary hypertension (PH). The purpose of the study was to see how valuable the NHP could be in assessing outcomes in diseases where no disease-specific measures are available. Methods: Secondary analyses were performed with NHP data. Patients diagnosed with adult GHD or PH were administered the NHP during clinic visits on two occasions, two weeks apart. A disease-specific measure of quality of life (QoL) was also administered to the relevant sample of patients on each occasion. Results: The psychometric properties of the NHP were good for both disease groups. As expected, both samples reported high scores on energy level, the PH sample scored high on physical functioning and the GHD sample on emotional reactions. For both samples, most of the NHP sections were able to distinguish between groups of respondents with different ratings of perceived general health. While most sections of the NHP were relatively highly correlated with the QoL measures, pain and sleep did not seem to be important predictors of QoL in either of the samples. Conclusions: The use of the NHP in adult GHD and PH populations in Brazil is not recommended as there are high-quality disease-specific measures available for each disease. However, where no disease-specific measures are available, the NHP can provide good descriptive information of the impact of disease on different patient populations.",
"keywords": [
"health related quality of life",
"Nottingham Health Profile",
"adult growth hormone deficiency",
"pulmonary hypertension",
"CAMPHOR",
"QoL-AGHDA",
"patient-reported outcomes"
],
"content": "Introduction\n\nThe Nottingham Health Profile (NHP) is a generic measure of perceived distress that has been used widely as an outcome measure in clinical practice and trials. It consists of a profile of outcomes assessing different types of distress: physical mobility, pain, sleep, social isolation, emotional reactions, and energy level1. Generic measures are considered valuable as they enable comparison of patient-reported outcomes between different populations and in assessments between healthy and unwell populations2. The NHP has also been widely used as a comparator measure when validating disease-specific patient-reported outcome measures (PROMs). Newer, disease-specific PROMs have the advantage of asking questions that are more relevant to patients, while omitting questions that are less relevant.\n\nAs a result of the lack of responsiveness and age of the generic measures, they are being replaced by disease-specific PROMs. However, in medium and low-income countries, there is a lack of comprehensive information systems, creating methodological obstacles in evaluation studies and limiting the capacity to conduct longitudinal studies3. Healthcare professionals, researchers and pharmaceutical companies are therefore reliant on generic outcome measures to collect information from patients because, theoretically, they can be used with any patient population. However, this means that outcome measures are selected based on availability rather than on quality.\n\nThe NHP has been used in two recent Brazilian studies. The measure was administered to patients with adult growth hormone deficiency (GHD) and pulmonary hypertension (PH) as comparator measures in the evaluation of Brazilian adaptations of the Quality of Life Assessment of Growth Hormone Deficiency in Adults (QoL-AGHDA) for GHD and the Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR) for PH4,5. The availability of these data sets for secondary analysis provided the opportunity to assess the psychometric performance of the NHP in two different Brazilian populations.\n\nAdult GHD results from decreased growth hormone secretion from the anterior pituitary gland. This is characterized by decreased lean body mass and increased fat mass, hyperlipidemia, cardiac dysfunction, decreased fibrinolysis and premature atherosclerosis, decreased muscle strength and exercise capacity, decreased bone mineral density, and decreased insulin resistance6. The most frequent cause of childhood onset is idiopathic and may not necessarily be associated with other pituitary hormone deficiencies. In contrast, adult onset GHD results from hypothalamic-pituitary tumors and/or their treatment7. GHD patients present with lower energy levels and more emotional problems than healthy individuals8.\n\nPulmonary hypertension (PH) is a condition that may occur with a variety of disorders and is characterized by an increase in the pulmonary vascular resistance and in the mean pulmonary arterial pressure (mPAP). PH is currently classified into different groups according to similarities in pathophysiology and the presence of associated conditions9. Group 1 (pulmonary arterial hypertension (PAH)) and Group 4 (PH due to pulmonary artery obstructions) are the most extensively studied and those for which there are approved drugs and/or procedures. Chronic thromboembolic pulmonary hypertension (CPTEH) is the most prevalent of the latter group. Patients with PH present with non-specific symptoms such as shortness of breath, progressive exertional dyspnea, chest pain, fatigue or syncope that progress over time, leading to right ventricular dysfunction and death10. PH presents a significant impact on patients’ social and emotional well-being and on their daily life in general, with restrictions in the ability to perform everyday tasks11.\n\nThe aim of this study was to investigate the psychometric properties of the NHP in adult GHD and PH populations. The purpose of the new analyses was to see how valuable the NHP could be in assessing outcomes in diseases where there is no effective disease-specific measure available.\n\n\nMethods\n\nThe NHP consist of 38 items with ‘yes’ and ‘no’ response alternatives, depending on whether that item fits the individual’s current situation. The possible score for each of the six sections ranges from zero to 100, with a higher score representing greater perceived distress. The NHP has been shown to have good reliability and validity as a generic measure12–14.\n\nThe QoL-AGHDA is the main measure of QoL in adults with GHD15. The measure consists of 25 items with a dichotomous ‘Yes/No’ response format. A score of “1” is given to each item affirmed and these are summed to give a total score. A high score on the QoL-AGHDA indicates poor QoL. It was developed in parallel in the United Kingdom (UK), Sweden, Germany, Italy and Spain and has since been adapted into numerous additional languages.\n\nThe CAMPHOR was the first outcome measure developed specific to PH patients16. This measure consists of two health-related quality of life (HRQL) scales (symptoms and activities) and a QoL scale. The CAMPHOR symptoms and QoL scales each consist of 25 items with a dichotomous response format. A total score is calculated by adding together the number of items affirmed, with a higher score indicating the presence of more symptoms or poorer QoL. The activities scale consists of 15 items that relate to activities described by patients as being affected by PH. Each item is scored according to the extent to which the patient rates themselves as being able to perform each activity, from zero (able to do on own without difficulty) to two (unable to do on own). Scores for each item are summed to give a total score ranging from zero to 30, with a higher score representing worse functioning. The CAMPHOR was originally developed and validated in the UK and has been adapted for use in many countries.\n\nSecondary data analyses were performed using NHP data that had been collected to assess the convergent validity of the Brazilian Portuguese QoL-AGHDA and CAMPHOR4,5. Patients diagnosed with adult GHD or PAH/CTEPH - which will be called PH below - had completed the relevant questionnaires during clinic visits. The adult GHD patients had been diagnosed according to the international criteria17 and were recruited from the following Brazilian endocrinology centres: Federal University of Minas Gerais, Hospital Santa Casa, Belo Horizonte (MG), University of Brasília, Brasília (DF), Federal University of Pernambuco, Recife (PE), SEMPR, the Federal University of Paraná, Curitiba (PR) and Hospital Brigadeiro, São Paulo (SP). These patients were not receiving GH therapy and replacement therapy for other pituitary deficiencies were stable for at least the six months before enrolment. The enrolled PH patients were recruited from the pulmonology centres at the Hospital das Clínicas, Federal University of Minas Gerais in Belo Horizonte, and Hospital das Clínicas of the University of Campinas, São Paulo. These participants were receiving PH-specific treatments18. All patients were at least 18 years of age at enrolment.\n\nFor each patient sample, the NHP was administered on two occasions, two weeks apart. The QoL-AGHDA and CAMPHOR were also administered to the respective sample of patients on each occasion. Demographic and disease information were collected at both time points including age, gender, marital status, employment status, disease duration and perceived general health.\n\nPermission to use the NHP, QoL-AGHDA and CAMPHOR was granted by the copyright holders of the three measures.\n\nThe study was approved by the Brazilian National Ethics Committee – Comite Nacional de Etica em Pesquisa (CONEP) and by the Local Ethics Committees from each participating institution for both adult GHD (CONEP 350/2008) and PH patients (CONEP 2857600). The study was conducted in accordance with the Helsinki declaration and all study participants provided written informed consent.\n\nDescriptive statistical analyses were conducted to examine the distributional properties of the NHP. The median and interquartile range were calculated due to the ordinal level of the data collected. The magnitude of floor and ceiling effects (% of patients scoring the minimum and maximum possible scores, respectively) were also assessed. A threshold of 15% was applied to indicate the presence of floor and ceiling effects19.\n\nThe internal consistency of the NHP sections in adult GHD and PH samples was assessed through Cronbach’s alpha coefficients. These coefficients measure the extent to which the items in a scale are inter-related. A low alpha (below 0.7) indicates that the items do not work together to form a scale20.\n\nThe test-retest reliability of the NHP sections was calculated as an estimate of their reproducibility over time when no change in condition is expected to have taken place. This was assessed by correlating scores obtained on the NHP sections on two different occasions using Spearman’s rank correlation coefficients. A minimum value of 0.85 is generally required to demonstrate that a PROM has low random measurement error21.\n\nKnown group validity was assessed by testing the ability of the NHP sections to distinguish between groups of patients that differed by a known factor, considered likely to affect scores on the measure. The factor used for the present investigation was perceived general health (excellent / good / fair / poor / very poor). Non-parametric tests for independent samples (Mann-Whitney U-Test for two groups) were employed to test for differences in NHP section scores between groups. For this analysis, perceived general health was grouped into ‘Excellent / Good’ and ‘Fair / Poor / Very poor’. This was due to the small number of participants in the ‘Poor’ and ‘Very poor’ groups. Differences in NHP section scores according to demographic factors (age, gender) were also explored using the Mann-Whitney U-test. To produce groups of equal size, the sample was divided by the median age.\n\nTotal scores for each NHP section were correlated with total scores on the QoL-AGHDA and CAMPHOR QoL scale using Spearman’s rank correlation coefficients to explore which symptoms and functional limitations influence QoL in adult GHD and PH, respectively.\n\nAll statistical analyses were conducted using the Statistical Package for Social Sciences (SPSS) version 25.0. A value of p <.05 was considered statistically significant.\n\n\nResults\n\nDemographic information for the GHD and PH samples is presented in Table 1. The GHD study population comprised primarily of patients with adult onset GHD. The PH sample consisted of patients who had been diagnosed as Group 1 PAH (n = 62) and Group 4 CTEPH (n = 40). Although the disease groups were not matched, the groups were similar in age. Similarly, both samples consisted of more females than males. Most of the respondents in both samples were married or living as married. However, considerably more GHD patients were employed and fewer were retired, compared to PH patients.\n\n* Includes Pulmonary Arterial Hypertension and Chronic thromboembolic pulmonary hypertension patients.\n\nDescriptive statistics for the NHP sections are shown in Table 2. The distribution of scores for each section suggest that the patient groups experienced similar levels of distress. GHD patients reported marginally worse scores on the pain, emotional reactions and social isolation sections, compared to PH patients. However, PH patients scored higher on the physical mobility section. Major ceiling effects were observed for the energy section in both samples. Substantial floor effects were observed for all NHP sections with the exceptions of emotional reactions in the GHD sample and physical mobility in the PH sample. Raw NHP data for each participant are available as Underlying data22.\n\n* Includes Pulmonary Arterial Hypertension and Chronic thromboembolic pulmonary hypertension patients.\n\nCronbach’s alpha coefficients for the NHP sections are presented in Table 3. Coefficients above the minimum acceptable level of 0.7 were obtained for all sections in both samples. Spearman’s rank correlation coefficients between scores obtained on Time 1 and Time 2 for the NHP sections are shown in Table 4. All correlations were significant at the p<.01 level.\n\n* Includes pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension patients.\n\n* Includes pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension patients.\n\nDisease duration and perceived general health are presented in Table 5. A Mann-Whitney U-test revealed that the PH sample had significantly worse ratings of general health than the GHD sample (U = 5070.5, p < .05).\n\n* Includes pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension patients.\n\nTable 6a and Table 6b show NHP section scores grouped by perceived general health in the GHD and PH samples, respectively. For both samples, most of the NHP sections were able to distinguish between groups of respondents that differed according to their perceived general health. For these NHP sections, individuals who considered their general health to be ‘Excellent / Good’ had significantly better scores on the NHP sections than those who rated their health less favourably. The exceptions were the sleep section in the GHD sample and the social isolation section in the PH sample.\n\n* Includes Pulmonary Arterial Hypertension and Chronic thromboembolic pulmonary hypertension patients.\n\nTable 7 shows NHP section scores by age group (above versus below median age) and gender in the adult GHD and PH sample combined. A Mann Whitney U-test found no significant difference in scores between older and younger patients on any of the NHP sections. Significant differences in scores were found between females and males. Females reported significantly higher scores than males on all sections except energy level and social isolation.\n\n* Includes pulmonary arterial hypertension and chronic thromboembolic pulmonary hypertension patients.\n\n** Sample divided by median age of 46.3.\n\nFigure 1 shows the Spearman’s rank correlations between scores on the NHP sections and disease-specific measures of QoL in patients with GHD (QoL-AGHDA) and PH (CAMPHOR QoL scale). Total scores on the QoL-AGHDA correlated most highly with the emotional reactions and energy level sections. The CAMPHOR QoL scale correlated relatively highly with the emotional reactions and social isolation sections but was also influenced by problems with physical mobility. A weak association was observed between total scores on the QoL-AGHDA and the sleep section of the NHP. Scores on the pain section of the NHP did not correlate highly with QoL scores on either the QoL-AGHDA or the CAMPHOR.\n\nNote: All correlations were significant at p<.01.\n\n\nDiscussion\n\nThe use of patient-reported outcomes to evaluate different interventions is becoming commonplace in clinical studies and trials. For many years, generic outcome measures such as the SF-36 and NHP were used for this purpose. However, these generic measures have been shown to lack sensitivity to change over time. In addition, all generic measures lack the responsiveness to be fully effective in clinical trials because their items are intended to be suitable for all possible illnesses. This means that they miss important aspects of the disease and include irrelevant items23–25. Consequently, there has been a move towards the use of disease-specific outcome measures which are able to ask more relevant questions and to measure outcome more accurately. Many researchers also continue to use the generic outcome measures together with disease-specific measures. While disease-specific measures are becoming more widely available, they have yet to be widely adapted for use in medium- and low-income countries. At the same time, clinical trials are being more frequently undertaken in such countries. Such studies require patient-reported outcome measures.\n\nThe current study looked at the performance of the generic NHP in two patient groups in Brazil, adult GHD and PH. NHP data were available from these patients as the measure had been used to help validate new disease-specific outcome measures. Analyses were undertaken to see whether the NHP would be a useful outcome measure for trials in other diseases.\n\nThe two populations had comparable ages. However, a greater proportion of PH patients were retired. This difference could be explained by the PH sample experiencing poorer general health, compared to the GHD sample. NHP section scores in both groups were strongly related to perceived general health.\n\nScores on the NHP sections were not influenced by age but women scored higher (had worse health status) than men. These findings are consistent with previous research reporting gender differences in QoL impairments for both patient populations studied26,27.\n\nOverall, the psychometric properties of the NHP sections were good for both disease populations. Estimates of internal consistency suggest that the items in the six sections of the NHP are sufficiently inter-related to form scales. Test-retest reliability (reproducibility) was better than that achieved by other generic measures though slightly lower than ideal. While only pain and emotional reactions demonstrated test-retest reliability coefficients of 0.85 and above in the GHD sample, all NHP sections in both patient groups were above the usually quoted acceptable value of 0.728,29.\n\nA large proportion of GHD and PH patients obtained the lowest possible score on most of the NHP sections. This indicates that the measure is not well targeted to these samples, which could be explained by the relatively mild perceived general health of the GHD and PH patients. Scores on the NHP confirmed the presence of common problems experienced by patients. Both samples reported high scores on energy level, the PH sample scored high on physical functioning and the GHD sample on emotional reactions. The correlations between scores obtained on the disease-specific measures of QoL and the NHP sections suggests that pain and sleep did not seem to be important predictors of QoL in either of the samples.\n\nA limitation of the current study is the lack of clinical information about the patient groups. It must be noted that the data collected for disease duration in the adult GHD sample should be interpreted with caution. The time between initial onset of GHD and diagnosis is likely to affect disease severity. In addition, the lack of inclusion of patients with GHD of childhood onset or GH-treated patients is a weakness, although relatively few GHD patients in Brazil are currently prescribed replacement growth hormone. It would have been valuable to collect WHO functional class information for the PH patients to explore whether the NHP could detect differences in health status relating to objective disease severity.\n\nThe use of the NHP in adult GHD and PH populations in Brazil is not recommended as there are high-quality disease-specific measures available for each disease. However, where no disease-specific measures are available, the NHP can provide good descriptive information of the impact of disease on different patient populations.\n\n\nData availability\n\nFigshare: Copy of Raw data.xlsx. https://doi.org/10.6084/m9.figshare.13299701.v122.\n\nThis file contains de-identified patient-reported-outcome raw data from NHP questionnaires.\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 for the efforts of the Study Investigators: Cesar Luiz Boguszewski - Universidade Federal do Paraná em Curitiba; Katia C Nogueira - Hospital do Brigadeiro (SP); Luciana A. Naves- Universidade de Brasilia (Distrito Federal); Lucio Vilar- Universidade Federal de Pernambuco em Recife; Paulo Augusto Carvalho Miranda - Santa Casa de Belo Horizonte (MG).\n\n\nReferences\n\nHunt SM, McEwen J: The development of a subjective health indicator. Sociol Health Illn. 1980; 2(3): 231–46. PubMed Abstract | Publisher Full Text\n\nGram-Hanssen A, Tolstrup A, Zetner D, et al.: Patient-Reported Outcome Measures for Patients Undergoing Inguinal Hernia Repair. Front Surg. 2020; 7: 17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArueira Chaves L, de Souza Serio Dos Santos DM, Rodrigues Campos M, et al.: Use of health outcome and health service utilization indicators as an outcome of access to medicines in Brazil: perspectives from a literature review. Public Health Rev. 2019; 40: 5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRibeiro-Oliveira A Jr, Mol SS, Twiss J, et al.: The brazilian version of the Quality of Life Assessment of Growth Hormone Deficiency in Adults (QoL-AGHDA): Four-stage translation and validation. Arq Bras Endocrinol Metabol. 2010; 54(9): 833–41. PubMed Abstract | Publisher Full Text\n\nCorrêa RA, Pereira MC, Bizzi MF, et al.: Adaptation and validation of the quality of life assessment of the Cambridge pulmonary hypertension outcome review (CAMPHOR) for Brazil. J Patient Rep Outcomes. 2020; 4(1): 43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Boer H, Blok GJ, Van der Veen EA: Clinical aspects of growth hormone deficiency in adults. Endocr Rev. 1995; 16(1): 63–86. PubMed Abstract | Publisher Full Text\n\nMolitch ME, Clemmons DR, Malozowski S, et al.: Evaluation and treatment of adult growth hormone deficiency: an Endocrine Society Clinical Practice Guideline. J Clin Endocrinol Metab. 2011; 96(6): 1587–609. PubMed Abstract | Publisher Full Text\n\nBurman P, Deijen JB: Quality of life and cognitive function in patients with pituitary insufficiency. Psychother Psychosom. 1998; 67(3): 154–67. PubMed Abstract | Publisher Full Text\n\nSimonneau G, Montani D, Celermajer DS, et al.: Haemodynamic definitions and updated clinical classification of pulmonary hypertension. Eur Respir J. 2019; 53(1): 1801913. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFrost A, Badesch D, Gibbs JSR, et al.: Diagnosis of pulmonary hypertension. Eur Respir J. 2019; 53(1): 1801904. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoward L, Lombardi S, Ryftenius H, et al.: The impact of pulmonary arterial hypertension ( PAH ) on the lives of patients and carers: results from an international survey. 2012.\n\nHunt SM, McKenna SP, Williams J: Reliability of a population survey tool for measuring perceived health problems: a study of patients with osteoarthrosis. J Epidemiol Community Health. 1981; 35(4): 297–300. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHunt SM, McKenna SP, McEwen J, et al.: A quantitative approach to perceived health status: a validation study. J Epidemiol Community Health. 1980; 34(4): 281–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHunt SM, McEwen J, McKenna SP, et al.: Subjective health assessments and the perceived outcome of minor surgery. J Psychosom Res. 1984; 28(2): 105–14. PubMed Abstract | Publisher Full Text\n\nMcKenna SP, Doward LC, Alonso J, et al.: The QoL-AGHDA: an instrument for the assessment of quality of life in adults with growth hormone deficiency. Qual Life Res. 1999; 8(4): 373–83. PubMed Abstract | Publisher Full Text\n\nMcKenna SP, Doughty N, Meads DM, et al.: The Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR): a measure of health-related quality of life and quality of life for patients with pulmonary hypertension. Qual Life Res. 2006; 15(1): 103–15. PubMed Abstract | Publisher Full Text\n\nBiller BM: Concepts in the diagnosis of adult growth hormone deficiency. Horm Res. 2007; 68 Suppl 5: 59–65. PubMed Abstract | Publisher Full Text\n\nDodson MW, Brown LM, Elliott CG: Pulmonary Arterial Hypertension. Heart Fail Clin. 2018; 14(3): 255–69. PubMed Abstract | Publisher Full Text\n\nTerwee CB, Bot SD, de Boer MR, et al.: Quality criteria were proposed for measurement properties of health status questionnaires. J Clin Epidemiol. 2007; 60(1): 34–42. PubMed Abstract | Publisher Full Text\n\nStreiner DL, Norman GR: Health Measurement Scales: A Practical Guide to Their Development and use. 2nd ed. New York: Oxford University Press; 1995. Reference Source\n\nWeiner EAS, Barbara J: Assessing individuals: psychological and educational tests and measurements. Boston: Little, Brown; 1984.\n\nRibeiro-Oliveira Jr A, Heaney A, de Oliveira WRR, et al.: Copy of Raw data.xlsx. figshare. Journal contribution. 2020. http://www.doi.org/10.6084/m9.figshare.13299701.v1\n\nMehta T, Venkata Subramaniam A, Chetter I, et al.: Disease-specific quality of life assessment in intermittent claudication: review. Eur J Vasc Endovasc Surg. 2003; 25(3): 202–8. PubMed Abstract | Publisher Full Text\n\nMcKenna SP: Measuring patient-reported outcomes: moving beyond misplaced common sense to hard science. BMC Med. 2011; 9: 86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOh SJ, Hyeon Ku J: Is a Generic Quality of Life Instrument Helpful for Evaluating Women with Urinary Incontinence? Qual Life Res. 2006; 15(3): 493–501. PubMed Abstract | Publisher Full Text\n\nKoltowska-Häggström M, Mattsson AF, Shalet SM: Assessment of quality of life in adult patients with GH deficiency: KIMS contribution to clinical practice and pharmacoeconomic evaluations. Eur J Endocrinol. 2009; 161 Suppl 1: S51–64. PubMed Abstract | Publisher Full Text\n\nAmedro P, Basquin A, Gressin V, et al.: Health-related quality of life of patients with pulmonary arterial hypertension associated with CHD: the multicentre cross-sectional ACHILLE study. Cardiol Young. 2016; 26(7): 1250–9. PubMed Abstract | Publisher Full Text\n\nNunnally JC, Bernstein I: Psychometric Theory. 3rd ed. New York: McGraw-Hill; 1994. Publisher Full Text\n\nBland JM, Altman DG: Cronbach's alpha. BMJ. 1997; 314(7080): 572. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "77612",
"date": "04 Mar 2021",
"name": "Jaquelina Sonoe Ota-Arakaki",
"expertise": [
"Reviewer Expertise Pulmonary Circulation 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 present the secondary data analyses of the Nottingham Health Profile (NHP), a generic measure of perceived distress, that had been collected to assess the validity of the Brazilian Portuguese QoL-AGHDA and CAMPHOR in a sample of adult GHD and PH in Brazil and previously published in two articles.\nDespite the demonstration of high scores on energy level, functional and emotional reactions in GHD or PH patients in the studied sample, the authors concluded that the NHP should not be recommended in the presence the validating disease-specific patient-reported outcome measures. However, the aim of the study to assess the role of the NHP in outcomes in GHD and PH, has not been evaluated.\nMinor comments:\nAlthough the authors report in the introduction that the CTEPH is more prevalent, in this sample there is a greater prevalence of PAH.\n\nDescribe the patient’s inclusion period and whether it was consecutive.\n\nIn the sample there is missing demographic data (n=2) raising the fragility of data of these patients. I suggest excluding them from the analyses.\n\nThe follow-up for a 44 year in PH is unusual. Justify or remove it from the analysis (out-liner).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6997",
"date": "10 Aug 2021",
"name": "Antonio Ribeiro-Oliveira Jr",
"role": "Author Response",
"response": "Dear Reviewer, Thank you for your time dedicated to this manuscript. Please find below the answers to your comments. The authors present the secondary data analyses of the Nottingham Health Profile (NHP), a generic measure of perceived distress, that had been collected to assess the validity of the Brazilian Portuguese QoL-AGHDA and CAMPHOR in a sample of adult GHD and PH in Brazil and previously published in two articles. Despite the demonstration of high scores on energy level, functional and emotional reactions in GHD or PH patients in the studied sample, the authors concluded that the NHP should not be recommended in the presence the validating disease-specific patient-reported outcome measures. However, the aim of the study to assess the role of the NHP in outcomes in GHD and PH, has not been evaluated. First of all, thank you for the comment provided. The aim of the study was to assess the psychometric performance of the NHP in different patient populations. This was achieved through examining the reliability and validity of the measure. The results indicated that its psychometric properties are adequate but the NHP has some psychometric weaknesses. Consequently, it is only recommended in instances where there is no disease-specific measure available. Minor comments: 1. Although the authors report in the introduction that the CTEPH is more prevalent, in this sample there is a greater prevalence of PAH. We think this reviewer has not got it correctly. The introduction states that CTEPH is the most prevalent form of PH due to pulmonary artery obstructions (Group 4). It does not state that CTEPH is more prevalent than PAH in our sample. 2. Describe the patient’s inclusion period and whether it was consecutive. Thank you for flagging this. The present study is a re-analysis of a database of previous research from our team. The patients were consecutively admitted to the respective clinics and those who agreed to participate were then included. We have amended the manuscript accordingly in the methods section to include the items that have been pointed by this reviewer. 3. In the sample there is missing demographic data (n=2) raising the fragility of data of these patients. I suggest excluding them from the analyses. That's an interesting point which have discussed further, and we believe it would be unfair to remove the data of these individuals from the analyses considering they did not fail to provide responses to the questionnaire. They would be omitted where demographic variables were being tested. 4. The follow-up for a 44 year in PH is unusual. Justify or remove it from the analysis (out-liner). While we acknowledge that a 44 year follow-up in PH is quite unusual, this patient was 55yo and had developed PH as consequence of congenital cardiopathy diagnosed in his childhood."
}
]
},
{
"id": "78848",
"date": "18 Mar 2021",
"name": "Günter K. Stalla",
"expertise": [
"Reviewer Expertise Endocrine disorders"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nHeany and colleagues have studied in two cohorts of patients with adult growth hormone deficiency (GHD) or pulmonary hypertension (PH) whether the Nottingham Health Profile (NHP), a generic measure of perceived distress, gives similar information as specific tests for quality of life (QoL) such as the QoL-AGHDA (for patients with GHD) or CAMPHOR (for patients with PH). They found that the NHP provides good information about the disease for the two groups of patients and may therefore an option in countries with less well developed health care system.\nHowever, when possible the disease-specific tests should be used as they predict more reliably state and outcome of the corresponding disease. In general, the study is well done and the results are important and interesting.\nMinor comment I'm wondering why the authors have not excluded patients, for which demographic data are missing (table 2), from the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/9-1399
|
https://f1000research.com/articles/10-784/v1
|
10 Aug 21
|
{
"type": "Research Article",
"title": "Anthropometric and physical fitness characteristics of male university cricket club players in accordance to player position and height categories",
"authors": [
"Habib Noorbhai",
"Andrew Khumalo",
"Andrew Khumalo"
],
"abstract": "Background: The scientific research into the varied factors that influence cricket performance has become a focal area for overall improved performance. Although there has been documented evidence for both anthropometry and physical fitness among elite cricketers, there is a paucity of evidence among the club cricket cohort. This pilot study aims to evaluate the anthropometric and fitness measurements among a pilot sample of university club cricketers (n = 17; 9 batsmen and 8 bowlers) in South Africa. Methods: Retrospective data were collected from the university’s male first cricket team of the 2019/2020 season. The data included both anthropometric (height, body mass, and body mass index) and physical fitness (explosive power, strength, Yo-Yo, speed and agility) parameters. The results exhibited for every parameter were presented according to height categories and player positions (batsman and bowler). Student t-tests were performed to determine the differences between fitness and anthropometric variables among both height categories and player positions. All data were analysed using SPSS (Version 26, IBM). The level of significance was set at p<0.05. Results: The results indicated significant differences for height categories with regards to stature (p = 0.000) and agility (p = 0.03). Significant differences were also evident for different player positions with regards to body fat percentage (p = 0.02) and vertical jump distance (p = 0.03). Conclusions: The findings of this pilot study indicated that cricketers who are shorter in stature are less superior with regards to anthropometric and fitness capabilities than their taller counterparts. In addition to being aware of the variances that exist for anthropometry, stature and fitness among cricketers at any level; this study provides implications for both coaches and sports scientists at the club level (under-researched level) in terms of how this can translate to player performances in accordance to height categories and player positions.",
"keywords": [
"Anthropometry",
"physical fitness",
"height categories",
"player positions",
"cricket"
],
"content": "Introduction\n\nCricket performance is influenced by many underlying factors which can further determine the success of cricketers in various distinct levels of experience and game formats (Noorbhai, 2015). The role played by batsmen and bowlers is evident in all game formats which can place various demands on athletes (Scanlan et al., 2016). Stretch et al. (2000) discusses some of the crucial demands in cricket, which include physiological, perception and action (motor skills), biomechanics and psychological factors. For the purpose of this research, focus will be placed on the physiological aspect, which includes anthropometric and fitness profiles, and its impact on performance. In a study by Nazeer et al. (2018), it was concluded that stronger anthropometric and physical fitness characteristics elicit optimal performance at various competition levels.\n\nKoley (2011) defines anthropometry as the study of measurement of physical properties of the human body in terms of dimensions such as size and shape. Anthropometric profiles of athletes enable the establishment of whether an athlete will perform better in a certain sport and how they can meet the demands of the tasks involved (Stuelcken, Pyne and Sinclair, 2007; Koley, 2011).\n\nIn studies conducted by Stretch et al. (2000) and Koley (2011), they used the same methods to acquire anthropometric profiles of elite and university batsmen and found that batsmen tend to be shorter, with lesser body mass and with a greater body fat percentage than other cricketers. In addition, having a smaller size might be a selective advantage, especially for batting (Noakes, 2000). Having excess body mass could have a negative impact on the performance of cricketers, as it reduces the ground reaction forces for batsmen when making runs and for bowlers, at the point of delivery (Tanner and Gore, 2012).\n\nEven though there are limited research findings on anthropometry for batsmen (Noorbhai, 2017), Johnstone and Ford (2010) looked at the overall physiological profiles of professional cricketers. Various anthropometric tools were used for physical assessment tests and some of these assessments used were commonly performed resulting in valid and reliable data. Stuelcken et al. (2007) adds that the gathering of information on anthropometric profiles helps in determining the potential for athletes to be successful.\n\nAnother crucial aspect of cricket performance is physical fitness, which includes components such as physical strength, speed, aerobic capacity, and agility. Physical fitness is considered a measure of the body’s ability to function efficiently and effectively in work and leisure activities (Javali and Koppad, 2017). According to Nazeer et al. (2018), running and the swinging of the bat are the movements that make up the batting skill. Hence, the development of physical fitness characteristics is paramount to meet the physical demands of cricket batting performance.\n\nThe vertical jump test, which is an indicator of lower body strength and explosive power, is a key physiological component of cricket skills for various cricket positions (Tanner and Gore, 2012). Furthermore, it is important to note that there are field based methods to measure lower body strength and power, which is the static vertical jump and the counter movement vertical jump. Another component is upper body strength, which was found to be positively correlated with superior batting performance, using the one-repetition maximum of a bench press (Taliep et al., 2010). Furthermore, it was acknowledged that upper strength alone cannot be used as a predictor of overall batting performance.\n\nThe fitness component of speed in relation to cricket performance has not been well documented. In an article by Dana et al. (2014), speed was explored in terms of comparison between batsmen and bowlers, to determine who is the fastest using the 40m sprint test. It was discovered that batsmen are faster than bowlers and speed is directly proportional to power. As a result, muscular power is the force resulting from the sum of movements involving both strength and velocity factors (Wang et al., 2017). Both muscular strength and power are crucial physical fitness components for explosive, short duration movements in sports.\n\nLastly, agility is a physical component commonly used by cricket batsmen for optimal performance. It is defined as the ability to efficiently change the body’s direction, decelerate, and explosively accelerate again while maintaining body control and using a combination of coordinating skills (Srivastava et al., 2017). According to Dana et al. (2014), batsmen were found to have faster running times as well as turning times than bowlers, which translates into agility.\n\nThe majority of anthropometric characteristics and physical fitness components have shown a strong relationship with body composition and performance test variables as experimented by Koley et al. (2011). However, further research is required that needs to be conducted in terms of measuring the anthropometric profiles of cricketers. Scientific research into the varied factors that influence cricket performance has become a focal area for overall improved performance. Although there has been documented evidence for both anthropometry and physical fitness among elite cricketers, there is a paucity of evidence among the club cricket cohort and in particular, the university cricket club cohort. This is imperative for investigation, as most cricketers in such a cohort have finished their growth spurt after being involved in adolescent cricket (Noorbhai and Noakes, 2016). This research study aims to address this gap and provide insight into the physiological attributes of university club cricketers and how this influences their success in accordance to their player position and height categories.\n\n\nMethods\n\nThis pilot study employed a cross-sectional research design in which analytical methods were employed. Anthropometric and physical fitness characteristics of male university cricket players were assessed at a specific point in time. The participants were male cricket players (n = 17) and were classified as bowlers and batsmen for comparative purposes.\n\nRetrospective data was collected and recorded from University of Johannesburg’s first cricket team (n = 17) for the 2019/2020 season in which consent was obtained with the understanding that their data will be kept confidential and anonymised. The data included both fitness (explosive power, strength, aerobic capacity, speed, and agility) and anthropometric (body mass index (BMI) and skinfolds) parameters (Noorbhai, 2021). All anthropometric and fitness measurements were conducted in accordance to the guidelines and procedures by Miller (2012), and Howley and Faigenbaum (2016), respectively.\n\nDue to the limited studies conducted on the role of anthropometric and physical fitness capabilities in performance among the club cricket cohort, this study will focus on parameters specific to cricket such as height, body mass, body fat percentage, explosive body power in the lower and upper body extremities, speed, aerobic capacity and agility. These will also be in relation to player height categories (short or tall) and player positions (batsman or bowler).\n\nParametric statistical tests were used to analyse data, whereby the population from which the sample was drawn was normally distributed on the variables of interest. Samples drawn from the population had the same variance (i.e. batsmen) and the observations were independent. Student t-tests were performed to determine the differences between fitness and anthropometric variables among both height categories and player positions. All data was analysed using SPSS (Version 26, IBM). The level of significance was set at p < 0.05.\n\nEthical approval for the study was granted by the Faculty of Health Sciences Research Ethics Committee at the University of Johannesburg (REC: 503-2020). Secondary data permission was also sought from the Research Ethics Committee. This research study also conforms to the World Medical Association Declaration of Helsinki on Ethical Principles for Research Involving Human Subjects.\n\n\nResults\n\nDescriptive results including stature, body mass and body fat percentage for the total group sample are shown below for both the two height categories (Table 1) and player position (Table 2). The two height categories were short (below 1.7m in height) and tall (above 1.7 m in height).\n\nThere were no significant differences for body mass and body fat percentage between the two height categories (short and tall) (Table 1). There was no significant difference for stature and body mass between batsmen and bowlers. However, there was a significant difference for body fat percentage between batsmen and bowlers (p = 0.02) (Table 2).\n\nTable 3 outlines the fitness parameters which includes explosive leg power, explosive upper body power, speed, aerobic capacity and agility for the total group sample by the two height categories.\n\nThere are no significant differences for explosive power (lower and upper body), speed and aerobic capacity between the height categories (short and tall). However, there is a significant difference for agility (both right and left) between the height categories (short and tall) (p = 0.03) (Table 3).\n\nTable 4 outlines the fitness parameters of explosive leg power, explosive upper body power, speed, aerobic capacity and agility for the total group sample according to player positions.\n\nThere are no significant differences for explosive power (upper body), speed, aerobic capacity and agility between batsmen and bowlers. However, there is a significant difference for explosive power (lower body) between batsmen and bowlers (p = 0.03) (Table 4).\n\nThis section presented the results in terms of mean scores with their corresponding standard deviations for the anthropometric and fitness parameters of height categories and different playing positions. The results indicated significant differences for the height categories with regards to stature and agility. The tall group showed a significantly higher stature than the short group. For agility time scores, the tall group showed faster times for both sides (right and left) than the short group.\n\nTwo significant differences were also evident for the different cricket positions with regards to body fat percentage and vertical jump distance. The batsmen showed the highest body fat percentage compared to bowlers. In terms of vertical jump distance, bowlers showed the highest mean score than batsmen.\n\n\nDiscussion\n\nAnthropometric characteristics and physical fitness components have been shown to have a considerable influence on the potential success of cricketers (Koley et al., 2017; Srivastava et al. 2017; Wang et al. 2017; Talib et al., 2010). This pilot study aimed to evaluate the anthropometric and fitness variables among cricketers and to determine whether cricketers who are shorter in stature perform better than their taller counterparts. The different cricket positions were also evaluated in terms of anthropometric and fitness measurements among university club level cricketers.\n\nThis study found anthropometric and physical fitness differences between short and tall cricketers. However, significant differences were only found in stature and agility between the short and tall group. Similarly, the findings documented by Koley (2011) which evaluated anthropometric profiles of Indian inter-university male cricketers, found that the tall group had a higher mean score for stature than the total group mean, while the short group had a lower mean score for stature than the total group mean. This is also in accordance with Noakes and Durandt (2000), who found that most batsmen were shorter than the other cricket positions. However, it is crucial to note the paucity in research on fitness parameters with regards to height categories. As a result, reference was made to normative data for physically active adults by Tanner and Gore (2012).\n\nWith reference to normative data, both the short and tall groups fell below the norms for vertical jump distance, whereas the tall group performed better. In terms of speed, both short and tall cricketers performed significantly better compared to the normative data, with the tall group obtaining faster times. The short and tall groups were slightly below the norms for the Yo-Yo Intermittent Recovery Test, with the short group being slightly better than the tall group. With regards to agility, both the short and tall groups obtained excellent ratings, whilst the tall group obtained faster times than their counterparts.\n\nThe current study found interesting results across the cricket positions (batsmen and bowlers) for anthropometric and fitness tests. According to Johnstone and Ford (2010), bowlers are heavier and taller than batsmen, which contradicts the current findings in which bowlers were taller but lighter than batsmen. Body fat percentage and vertical jump distance between the batsmen and bowlers also showed a significant difference. Batsmen were found to have a higher body fat percentage than bowlers, which corresponds with the research conducted by Stretch et al. (2000) and Koley et al. (2011). This current study supports the findings by Dana et al. (2014) which found that bowlers are significantly taller than batsmen. With regards to stature and body composition (body mass), a significant difference among batsmen and bowlers regarding body fat percentage was evident. Hence, these findings partly support findings by Koley (2011), who found no significant difference for bowlers and batsmen in height and body composition. Johnstone and Ford (2010) found insignificant differences between batsmen and bowlers with regards to the vertical jump test, which contrast with the findings of this study, as the results highlighted a significant difference.\n\nAccording to Noakes and Durandt (2000), batsmen were found to have faster running times and turning times than bowlers in relation to agility which is in contrast with the current findings. In terms of speed, current finding suggests that running speeds for batsmen and bowlers are alike, however the bowlers performed better in the sprint tests. This is similar to findings by Johnstone and Ford (2010) but in contrast to Dana et al. (2014), who discovered that batsmen were faster than bowlers. Current findings suggest that batsmen have superior aerobic fitness and these results have been linked with improved recovery and maintenance of optimal performance. With regards to upper body strength, the current findings indicate that bowlers performed better than batsmen (supported by MacDonald (2013)). However, the relevance of such results to match performance is unclear.\n\nThis was a pilot study due to a smaller sample size and the inclusion of only male data. The data was also limited to only two cricket playing positions and can’t be generalisable. Another limitation was the absence of the 505 Agility Test (which has been identified as a more specific test for change of direction specific to running between the wickets) and somatotype of the players. In this study, only the Illinois test was available. However, the depth of tests conducted has provided adequate insights into the anthropometric and physical fitness characteristics of male university cricket club players in accordance to height categories and player position.\n\n\nConclusion\n\nAnthropometry and physical fitness are key to ensuring success in cricket performance. This study demonstrates that cricketers who are shorter in stature are less superior with regards to anthropometric and fitness capabilities than their taller counterparts, which makes the latter group more likely to be successful in cricket. The batsmen showed the highest body fat percentage compared to bowlers. In terms of the vertical jump distance, bowlers showed a higher mean score than batsmen. This study will assist coaches in terms of team selection by providing information that is essential for determining the potential for athletes to enhance performance. Future studies should include a larger sample size and also consider female data, along with the inclusion of the various cricket playing positions and height categories. In addition to being aware of the variances that exist for anthropometry, stature and fitness among cricketers at any level, this study provides implications for both coaches and sports scientists at the club level in terms of how this can translate to player performances in accordance to height categories and player positions.\n\n\nData availability\n\nFigShare: Anthropometric and physical fitness variables. https://doi.org/10.6084/m9.figshare.15086652.v1 (Noorbhai, 2021).\n\nThis project contains the following underlying data:\n\n• Dataset_Cricket_Anthro and Fitness_2020.xlsx (Anthropometric and physical fitness variables).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe authors would like to thank the UJ Sport Bureau as well as Malibongwe Mabaso for their assistance in this study.\n\n\nReferences\n\nDana K, Webster Z, Travill AL: Anthropometric and physical fitness characteristics of male cricket players at the University of the Western Cape. J Community Health Sciences. 2014; 9(1).\n\nEmery CA: Is there a clinical standing balance measurement appropriate for use in sports medicine? A review of the literature. J Sci Med Sport. 2003; 6(4):492–504. PubMed Abstract | Publisher Full Text\n\nHowley ET, Thompson D: Fitness professional’s handbook. 7th ed. Champaign, Illinois: Human Kinetics; 2016.\n\nKoley S: A study of anthropometric profiles of inter-university male cricketers. J Human Sport Exercise. 2011; 6(2):427–435. Publisher Full Text\n\nJavali MSS, Koppad SS: A Study on Selected Physical Fitness Variables of Professional College Football and Cricket Players. Int J Physical Education Sports Sciences. 2017; 11(18):24–28. Publisher Full Text\n\nJohnstone J, Ford P: Physiologic Profile of Professional Cricketers. J Strength Cond Res. 2010; 24(11):2900–2907. PubMed Abstract | Publisher Full Text\n\nKoley S, Kumaar BS, Shadagopan SP: Anthropometric, physical strength, body composition and performance test profiles of inter-district level male cricketers of Punjab, India. Anthropologist. 2012; 14(5):445–451. Publisher Full Text\n\nMiller TA: National Strength and Conditioning Association (NSCA)’s Guide to Tests and Assessments. Washington: Human Kinetics; 2012.\n\nNoakes TD, Durandt JJ: Physiological requirements of cricket. J Sports Sci. 2000; 18(12):919–929. PubMed Abstract | Publisher Full Text\n\nNoorbhai MH: The batting backlift technique in cricket. PhD Thesis: University of Cape Town; 2021.\n\nNoorbhai MH: Anthropometric and physical fitness variables. figshare. Dataset. 2021. Publisher Full Text\n\nNoorbhai H, Noakes TD: An analysis of batting backlift techniques among coached and uncoached cricket batsmen. South African J Res Sport, Physical Education Recreation. 2016; 38(3):143–161.\n\nScanlan AT, Berkelmans DM, Vickery WM, et al.: A Review of the Internal and External Demands Associated With Batting in Cricket. Int J Sports Physiol Perform. 2016; 11(8):987–997. PubMed Abstract | Publisher Full Text\n\nSrivastava R, Sharma A, Prasad R: Agility and its Impact on Performance of Cricketers with Relation to Anthropometry. Int J Physical Education Sports. Sci. 2017; 2(3):8–11.\n\nStretch A, Bartlett R, Davids K: A review of batting in men’s cricket. J Sports Sci. 2000; 18(12):931–949. PubMed Abstract | Publisher Full Text\n\nStuelcken M, Pyne D, Sinclair P: Anthropometric characteristics of elite cricket fast bowlers. J Sports Sci. 2007; 25(14):1587–1597. PubMed Abstract | Publisher Full Text\n\nTahir M, Zia UI Haq M, Habib MB: Anthropometric and Physical Fitness of the Under-16 Regional-School Cricket Players, of Bahawalpur, Pakistan. Global Regional Rev. 2018; 3(1):333–342. Publisher Full Text\n\nTaliep MS, Prim SK, Gray J: Upper body muscle strength and batting performance in cricket batsmen. J Strength Cond Res. 2010; 24(12):3484–3487. PubMed Abstract | Publisher Full Text\n\nTanner R, Gore C: Physiological Tests for Elite Athletes. Champaign, Illinois: Human kinetics; 2012.\n\nWang R, Hoffman JR, Sadres E, et al.: Evaluating upper-body strength and power from a single test: The ballistic push-up. J Strength Cond Res. 2017; 31(5):1338–1345. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "91648",
"date": "02 Sep 2021",
"name": "Takalani Clearance Muluvhu",
"expertise": [
"Reviewer Expertise Physical activity",
"health",
"wellness and cardiometabolic risk factors."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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:\nIn the background, maybe shorten the opening statement and only include: “The scientific research into the varied factors that influence cricket performance has become a focal area for overall improved performance”. Remove the entire second statement which you can insert at the end of the introduction to address your problem and why you choose to research in this area, which will be able to clarify the rationale of the study. (Although there has been documented evidence for both anthropometry and physical fitness among elite cricketers, there is a paucity of evidence among the club cricket cohort.)\n\nInclude study design on the methods within the abstract. And then indicate that 'Retrospective data were collected from the university’s male first cricket team of the 2019/2020 season.'\nIntroduction:\nThe introduction needs to be revised: avoid headings in the introduction. Make sure your introduction flows while including all parameters of the article that was written in different headings.\n\nThe authors are applauded for using current literature in the introduction, however addressing the above concern will solidify the introduction.\nMethods:\nStudy design - the only concern is the number of participants, which, if expanded, will surely lead to a valid result, which will represent a large cohort and address the physical fitness characteristics measured. Surely it will lead to bias results due to small sample used?\n\nData collection - The authors are commended in terms of explaining how data was collected, the method was clearly explained. However, there is missing information in terms of how the following parameters were measured ((explosive power, strength, aerobic capacity, speed, and agility) and anthropometric (body mass index (BMI) and skinfolds) parameters). The authors should expand in this area to give readers an idea on how these parameters were measured.\n\nStatistical analysis - The statistical analysis of the study is well explained in terms of how the data will be analysed and which statistical methods was applied/done. The authors are commended in this area.\n\nResults and discussion- The results of the study were well presented in tables addressing all the parameters measured and the discussion the article was in line with the findings of the study.\n\nConclusion - the authors are commended on the way they crafted the conclusion to summarize the findings of the study, finally and well capturing of the recommendations of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "100897",
"date": "15 Dec 2021",
"name": "Leonidas Petridis",
"expertise": [
"Reviewer Expertise Sport science",
"fitness testing",
"neuromuscular performance"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors conducted a study with cricket players, which may be interesting to readers, primarily regarding performance determinants and the physical demands of cricket. While acknowledging the value of the descriptive data provided in the manuscript, an important aspect to consider is how the results in the fitness tests reflect the physical demands of the game. Does better performance in the fitness tests indicate better performance in cricket? The initial question is very promising: what are the factors that influence cricket performance? This aspect should be better discussed and analysed in the manuscript. Also, the authors should explain in the introduction the need to compare performance indicators between elite and sub-elite players, discussing the potential of the fitness tests to discriminate between players from various competition levels. Most probably elite players have better results when compared to sub-elite players, but is there any evidence to support this? Such an analysis could strengthen the rationale of the study also providing to coaches and practitioners some benchmark values in the applied fitness tests based on competition level.\nAbstract:\nThe abstract should contain the most important results rather than p values. The conclusion that cricketers with lower body height are less superior than their taller counterparts is not adequately supported by the results. Please reconsider or explain.\n\nIntroduction:\nThe introduction contains several paragraphs with a general description of anthropometric and physical test measurements. These paragraphs seem redundant and should be removed. The authors should rather include reports from the literature with reference to cricket performance, to the physical demands of this sport, and to characteristics of elite cricket players.\n\nPlease remove subheadings from the introduction.\n\nThe authors mention that excess body mass reduces ground reaction forces for batsmen. Is this correct? Increase in body mass increases ground reaction forces, this is a general rule. Please reconsider this statement and correct accordingly.\n\nThe rationale of the study should be better explained. Why to conduct such a data collection? Although the authors aim to examine how performance in fitness test influence success in cricket, there is no reference to this aspect in the rest of the manuscript. Please clarify the purpose of the study according to the collected data and to the analysis you have conducted.\n\nMethods:\nPlease add background information for the participants: age, training background, weekly training load.\n\nPlease add a detailed description of the protocols and the devices you used for measuring power, strength, aerobic capacity, and agility.\n\nPlease add effect size measurements to support student t-test statistics.\n\nResults:\nWhat was the reason to use 1.7m as a cut off value for body height categories? Please, explain. Moreover, the authors mention that short category included players with body height below 1.7m. The mean value for stature of short players however was 1.71±0.05m (table 1). How is this possible?\n\nAlso, you need to explain why you used body height as a discriminator factor to divide participants. Is there a reference to support this?\n\nHaving similar body fat, taller individuals are usually heavier than shorter individuals. This is not the case in this study; however, this result is not mentioned, nor discussed at all throughout the manuscript.\n\nMeasurement unit for medicine ball throw is cm. This seems not to be correct, please check.\n\nDiscussion:\nThe discussion needs revision. The results should be analysed in more depth, referring to their practical application in cricket game performance. Analysis should be sport-specific. The discussion should also include the relevance of body height in cricket performance.\n\nPlease avoid repeating the results in the discussion.\n\nThe authors highlight the significant difference in body height between short and tall groups. This is more than obvious, since body height was used to separate the two groups. This is not a result of the measurements, but a result of the methodology used.\n\nShort and tall groups differed only in agility test. This indicates that body height has limited effects on performance in fitness tests. What does this mean regarding cricket performance? These results deserve more discussion.\n\nReference to normative data should be supported by data from the literature. Also, some numeric values from normative data could help to better understand these differences.\n\nBased on table 4, batsmen and bowlers differ only in the vertical jump test. Does this refer to similar fitness profiles between these two playing positions? The authors mention that batsmen have superior aerobic fitness compared to bowlers, but this was not confirmed by the results. Please, reconsider. Also, is there a reference to support the connection of aerobic fitness with improved recovery in cricket? How specific is the yo-yo fitness test to measure aerobic capacity in cricket?\n\nConclusions:\nThe authors mention that cricketers with lower body height are less superior than those with higher body height. How is this supported from the results? This should be better explained.\n\nPlease provide a more extensive explanation on how can coaches use this data for selection or training purposes.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-784
|
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