Re: [AUDITORY] preprints, community journals, and the carbon footprint of hearing healthcare (Alejandro Osses )

Subject: Re: [AUDITORY] preprints, community journals, and the carbon footprint of hearing healthcare From: Alejandro Osses <ale.a.osses@xxxxxxxx> Date: Sat, 5 Nov 2022 07:01:33 +0100 --000000000000dcb07d05ecb2ec7e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hoi Jan-Willem, These are very interesting questions. I just read Ra=C3=BAl's answers with = his clarifications about these new ""publishing schemes", so my answer here is based on my own experience about some of the platforms you mentioned (this means that I am not answering directly to your questions). You mentioned BioRxiv, ArXiv, OSF, and Zenodo. I happened to have used all these platforms and I actually use them for different purposes. - BioRxiv and ArXiv I use them to host preprints. I use BioRxiv if my paper contains collected behavioural data (human data from perceptual studies in my case), whereas I use ArXiv when I only use computational simulations as main component of my study. For both cases, I use them as= a quick way to generate the permanent identifier while I sumit the papers = to a peer-reviewed journal. (Some of my examples: One of my papers from BioRxiv <https://www.biorxiv.org/content/10.1101/2020.03.13.984542v1>; one of my ArXiv papers that has many versions <https://arxiv.org/abs/2107.01753>) - OSF: I am using it now for my first pre-registered project. The idea is to pre design your study and clearly state your hypothesis before you run the actual study, in a way that if you get non-significant results o= r if you reject some of your hypotheses you still pulish your study. This = is a way to avoid p-hacking. Of course OSF provides a permanent identifier = for your project (I didn't realise it was a doi number), but my goal here is= to cite the pre-registered document from OSF once my paper is finished and published (My current OSF project, I think is still embargoed: https://osf.io/4ju3f/) - Zenodo: I use it to host all binary data, meaning WAV files or any other data that I cannot store using TXT files and codes from Python or MATLAB and that are related to my study. Complementary to that, I linked Zenodo to my Github, so that my "main codes" get tracked and obtain a do= i number every time I make a new release of my software codes. This way "Zenodo Git" and "Zenodo data" contain all the data I need to reproduce = my paper data (Zenodo linked to one of my Github MATLAB toolboxes <https://zenodo.org/record/6530154#.Y2X6zr7MJpg>; Zenodo containing just binary data for one of my studies <https://zenodo.org/record/5483835#.Y2X7XL7MJpg>-the study where those data were used/cited is here <https://hal.archives-ouvertes.fr/hal-03345050v1>) I have used these platforms without peer review, but the idea is for me, to always publish in a peer review journal soon after. My own papers have suffered big transformations during a couple of reviews. Therefore, I found it somehow a "risk" that my first preprint versions are circulating. My workaround is that, once a paper is published, I make a new final version of the preprint, so that people who will download my preprint in the future will not only see the link to the published paper (an automatic option from BioRxiv and ArXiv), but if the press "download" they will get the most recent preprint version of the paper. Of course not every person sticks to these rules very strictly, so it can well be that you run into papers that never got through a peer review (and are not planning to). To this extent BioRxiv and ArXiv may not be the best for relying 100% on what is hosted there. I hope the insights here are useful :) Success... Groetjes, Alejandro Op vr 4 nov. 2022 om 05:04 schreef Wasmann, Jan-Willem < Jan-Willem.Wasmann@xxxxxxxx>: > Dear list, > > Via this thread, I=E2=80=99d like to touch upon preprints, community jour= nals, and > the carbon footprint of hearing healthcare. If you are in a hurry, please > skip this message TLDR. Otherwise, it would be great to tap into your > collective wisdom. > > > > In recent years, preprints have become increasingly popular to increase > open access. Some preprints get cited a lot (e.g., > https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2.abstract > > 300 times). And especially in AI, some preprints will probably never get > peer-reviewed. A well-known example is: > > Saon G, Kurata G, Sercu T, Audhkhasi K, Thomas S, Dimitriadis D, et al. > English Conversational Telephone Speech Recognition by Humans and Machine= s. > ArXiv170302136 Cs (2017). Available online at: http://arxiv.org/ > abs/1703.02136 > > > > There are multiple platforms to use. The most well-known is Biorxiv > <https://www.biorxiv.org/> or Arxiv <https://arxiv.org/>. But also OSF > <https://osf.io/preprints/?utm_term=3Dopen%20science%20framework&utm_camp= aign=3DOSF+General&utm_source=3Dadwords&utm_medium=3Dppc&hsa_acc=3D52223453= 73&hsa_cam=3D217339509&hsa_grp=3D36452477753&hsa_ad=3D150809658182&hsa_src= =3Dg&hsa_tgt=3Dkwd-300201585279&hsa_kw=3Dopen%20science%20framework&hsa_mt= =3Db&hsa_net=3Dadwords&hsa_ver=3D3&gclid=3DEAIaIQobChMIp-_k7sGR-wIVFweLCh2S= bw5YEAAYASAAEgIj7vD_BwE> > or Zenodo <https://zenodo.org/record/5600535#.Y2NxnaSZOUk>. I have used > OSF since it has a broad scope and allows you to upload projects. It > provides a preprint DOI, which remains the same if you update the preprin= t > at a later stage. Also, you can link the DOI of the final peer-reviewed > version of your paper. Zenodo can also be used for projects (data+paper), > but every update will create a new DOI. > > > > *Q1a How do you regard the status of preprints? * > > *Q1b Is it a missed opportunity if one decides not to go for a peer-revie= w > process of a preprint? * > > > > Another new development is open community-driven peer review procedures. = I > found examples in other fields; see below. > > > > *Q2a Do you know of examples of community-driven peer review in hearing > sciences? * > > *Q2b Can you recommend a community-driven journal? * > > > > Many scientists have responded to the new transparent consultative > peer-review procedure by eLife ( > https://elifesciences.org/about/peer-review). This might be an exciting > venue for those looking for new ways of peer review. However, the charges > amount to $2000. The charges for open access can be enormous (Nature > $7000?) and a barrier for early career researchers. > > > > So far, I have found the following examples of community journal/peer > review processes: > > > > Pubpeer (The *PubPeer* Foundation *is a California-registered > public-benefit corporation with 501(c)(3) nonprofit status in the United > States. The overarching goal of the Foundation is to improve the quality = of > scientific research by enabling innovative approaches for community > interaction. The bylaws of the Foundation establish pubpeer.com > <http://pubpeer.com> as a service run for the benefit of its readers and > commenters, who create its content. Our current focus is maintaining and > developing the PubPeer online platform for post-publication peer review*. > https://pubpeer.com/static/about_) > > > > Here you can find our preprint on that platform > > https://pubpeer.com/publications/AE2235B5F9F35577B977F87F9834B8 > > It looks like an easy platform to use. It can be used for creating specia= l > issues/collections (see https://pubpeer.com/publications/peeriodicals). > At the start, I had trouble registering using my name/institution. An > anonymous account was created quickly. Currently, PubPeer is used for > post-publication review. I heard that in other disciplines, Pubpeer is us= ed > to flag suspicious publications (read fraud). > > > > Another exciting example is ReviewCommons (*Review Commons* *provides > authors with a Refereed Preprint, which includes the authors=E2=80=99 man= uscript, > reports from a single round of peer review and the authors=E2=80=99 respo= nse. These > Refereed Preprints are transferred on the author=E2=80=99s behalf to bioR= xiv. The > most recently-completed Review Commons peer-reviews are listed below, wit= h > the most recently posted reviews at the top*. > https://www.reviewcommons.org/authors/) > > Unfortunately, auditory sciences and audiology are not within the scope o= f > the peer-review initiative. > > > > The last example I know of is NBDT (NBDT *is a community journal. If your > handling editor sees it as in-scope it is appropriate. Editors are > instructed to only handle papers that they consider running as a journal > club paper for their own lab* https://nbdt.scholasticahq.com/for-authors)= . > It=E2=80=99s interesting to see their procedures, including =E2=80=9C*Can= you propose > reviewers?* Short answer: no. Long answer: we did our own statistical > analysis on a private dataset and have concluded that it produces huge > undesirable biases without leading to better reviews.=E2=80=9D > > > > > > The Carbon Footprint of Hearing Healthcare > > > > With Jan de Laat, I have just written a perspective paper/blog about the > Carbon Footprint of Hearing Healthcare (see version 2, Preprint DOI > 10.31219/osf.io/3sj5u <https://doi.org/10.31219/osf.io/3sj5u>). The > hearing tracker will publish the content today/tomorrow as a blog. So far= , > we have extracted information from ESG reports > <https://www.pwc.com/sk/en/environmental-social-and-corporate-governance-= esg/esg-reporting.html> > and our contacts within the hearing healthcare industry. Ideally, we woul= d > like to organize a community-driven review process to collect comments fr= om > engineers, industry, sustainability officers, authors from ESG reports, a= nd > scientists. > > > > *Q3a What would be a suitable platform to organize and publish a > community-driven review process of a perspective paper about carbon > footprint in hearing healthcare? * > > > > Another ambition could be to create a carbon footprint tracker of hearing > healthcare by annually updating table 1 from the preprint, including an > assessment of whether climate ambitions by industry were updated and > achieved. > > > > *Q3b What would be a suitable approach to annually monitor the carbon > footprint of the hearing healthcare industry? *(Maybe not peer-reviewed?) > > > > Please let me know what you think is the best community journal for > auditory sciences. Don't hesitate to let us know if you believe opinion > pieces shouldn=E2=80=99t get into the review process. For me publishing t= his > perspective paper is a low-risk experiment. If it goes well, I will > consider submitting an original research manuscript. > > > > Thank you for your time. I am looking forward to your responses and advic= e. > > > > > Best regards, > > Jan-Willem Wasmann > > De informatie in dit bericht is uitsluitend bestemd voor de geadresseerde= . > Aan dit bericht en de bijlagen kunnen geen rechten worden ontleend. Heeft= u > deze e-mail onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen e= n > de afzender te informeren. Openbaar maken, kopi=C3=ABren en verspreiden v= an deze > e-mail of informatie uit deze e-mail is alleen toegestaan met voorafgaand= e > schriftelijke toestemming van de afzender. Het Radboudumc staat > geregistreerd bij de Kamer van Koophandel in het handelsregister onder > nummer 80262783. > > The content of this message is intended solely for the addressee. No > rights can be derived from this message or its attachments. If you are no= t > the intended recipient, we kindly request you to delete the message and > inform the sender. It is strictly prohibited to disclose, copy or > distribute this email or the information inside it, without a written > consent from the sender. Radboud university medical center is registered > with the Dutch Chamber of Commerce trade register with number 80262783. > --000000000000dcb07d05ecb2ec7e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Hoi Jan-Willem,</div><div> </div><div>These are ve= ry interesting questions. I just read Ra=C3=BAl's answers with his clar= ifications about these new ""publishing schemes", so my answ= er here is based on my own experience about some of the platforms you menti= oned (this means that I am not answering directly to your questions).</div>= <div> </div><div>You mentioned BioRxiv, ArXiv, OSF, and Zenodo. I happen= ed to have used all these platforms and I actually use them for different p= urposes.</div><div><ul><li>BioRxiv and ArXiv I use them to host preprints. = I use BioRxiv if my paper contains collected behavioural data (human data f= rom perceptual studies in my case), whereas I use ArXiv when I only use com= putational simulations as main component of my study. For both cases, I use= them as a quick way to generate the permanent identifier while I sumit the= papers to a peer-reviewed journal. (Some of my examples: One of my papers = from <a href=3D"https://www.biorxiv.org/content/10.1101/2020.03.13.984542v1= ">BioRxiv</a>; one of my <a href=3D"https://arxiv.org/abs/2107.01753">ArXiv= papers that has many versions</a>) </li><li>OSF: I am using it now for = my first pre-registered project. The idea is to pre design your study and c= learly state your hypothesis before you run the actual study, in a way that= if you get non-significant results or if you reject some of your hypothese= s you still pulish your study. This is a way to avoid p-hacking. Of course = OSF provides a permanent identifier for your project (I didn't realise = it was a doi number), but my goal here is to cite the pre-registered docume= nt from OSF once my paper is finished and published (My current OSF project= , I think is still embargoed: <a href=3D"https://osf.io/4ju3f/">https://osf= .io/4ju3f/</a>) </li><li>Zenodo: I use it to host all binary data, meani= ng WAV files or any other data that I cannot store using TXT files and code= s from Python or MATLAB and that are related to my study. Complementary to = that, I linked Zenodo to my Github, so that my "main codes" get t= racked and obtain a doi number every time I make a=C2=A0 new release of my = software codes. This way "Zenodo Git" and "Zenodo data"= contain all the data I need to reproduce my paper data (Zenodo linked to o= ne of my <a href=3D"https://zenodo.org/record/6530154#.Y2X6zr7MJpg">Github = MATLAB toolboxes</a>; Zenodo containing just <a href=3D"https://zenodo.org/= record/5483835#.Y2X7XL7MJpg">binary data for one of my studies</a>-the stud= y where those data were used/cited is <a href=3D"https://hal.archives-ouver= tes.fr/hal-03345050v1">here</a>) </li></ul><div>I have used these platfo= rms without peer review, but the idea is for me, to always publish in a pee= r review journal soon after. My own papers have suffered big transformation= s during a couple of reviews. Therefore, I found it somehow a "risk&qu= ot; that my first preprint versions are circulating. My workaround is that,= once a paper is published, I make a new final version of the preprint, so = that people who will download my preprint in the future will not only see t= he link to the published paper (an automatic option from BioRxiv and ArXiv)= , but if the press "download" they will get the most recent prepr= int version of the paper.</div><div> </div><div>Of course not every pers= on sticks to these rules very strictly, so it can well be that you run into= papers that never got through a peer review (and are not planning to). To = this extent BioRxiv and ArXiv may not be the best for relying 100% on what = is hosted there.=C2=A0</div><div> </div><div>I hope the insights here ar= e useful :)</div><div> </div><div>Success...</div><div>Groetjes,</div><d= iv>Alejandro </div></div></div> <div class=3D"gmail_quote"><div dir= =3D"ltr" class=3D"gmail_attr">Op vr 4 nov. 2022 om 05:04 schreef Wasmann, J= an-Willem <<a href=3D"mailto:Jan-Willem.Wasmann@xxxxxxxx">Jan-Wille= m.Wasmann@xxxxxxxx</a>>: </div><blockquote class=3D"gmail_quote"= style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);p= adding-left:1ex"><div class=3D"msg3774073632584404549"> <div dir=3D"ltr"> <div style=3D"font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt= ;color:rgb(0,0,0);background-color:rgb(255,255,255)"> Dear list,=C2=A0 Via this thread, I=E2=80=99d like to touch upon prepri= nts, community journals, and the carbon footprint of hearing healthcare. If= you are in a hurry, please skip this message TLDR. Otherwise, it would be great to tap into your collective wisdom.=C2=A0<= /span> =C2=A0 In recent years, preprints have become increasingly po= pular to increase open access. Some preprints get cited a lot (e.g., <a href=3D"https://www.biorxiv.org/content/10.1101/2021.10.04.463034= v2.abstract" target=3D"_blank">https://www.biorxiv.org= /content/10.1101/2021.10.04.463034v2.abstract</a> > 300 times). And especially in AI, some preprints will probably never = get peer-reviewed. A well-known example is: =C2=A0 Saon G, Kurata G, Sercu T, Audhkhasi K, Thomas S, Dimi= triadis D, et al. English Conversational Telephone Speech Recognition by Hu= mans and Machines. ArXiv170302136 Cs (2017). Available online at: <a href=3D"http://arxiv.org/" target=3D"_blank">http://arxiv.or= g/</a> abs/1703.02136=C2=A0 =C2=A0 There are multiple platforms to use. The most well-kno= wn is <a href=3D"https://www.biorxiv.org/" target=3D"_blank">Biorxiv</a> or <a href=3D"https://arxiv.org/" target=3D"_blank">Arxiv</a>. But also <a href=3D"https://osf.io/preprints/?utm_term=3Dopen%20science%20fra= mework&utm_campaign=3DOSF+General&utm_source=3Dadwords&utm_medi= um=3Dppc&hsa_acc=3D5222345373&hsa_cam=3D217339509&hsa_grp=3D364= 52477753&hsa_ad=3D150809658182&hsa_src=3Dg&hsa_tgt=3Dkwd-300201= 585279&hsa_kw=3Dopen%20science%20framework&hsa_mt=3Db&hsa_net= =3Dadwords&hsa_ver=3D3&gclid=3DEAIaIQobChMIp-_k7sGR-wIVFweLCh2Sbw5Y= EAAYASAAEgIj7vD_BwE" target=3D"_blank">OSF</a><= span lang=3D"EN-US"> or <a href=3D"https://zenodo.org/record/5600535#.Y2NxnaSZOUk" targe= t=3D"_blank">Zenodo</a>. I= have used OSF since it has a broad scope and allows you to upload projects. It provides a prep= rint DOI, which remains the same if you update the preprint at a later stag= e. Also, you can link the DOI of the final peer-reviewed version of your pa= per. Zenodo can also be used for projects (data+paper), but every update will create a new DOI.=C2= =A0 =C2=A0 Q1a How do you regard the status of preprints?</= u>=C2=A0 Q1b Is it a missed opportunity if one decides not t= o go for a peer-review process of a preprint?=C2=A0</b= > =C2=A0 Another new development is open community-driven peer = review procedures. I found examples in other fields; see below. =C2=A0 =C2=A0 Q2a Do you know of examples of community-driven pee= r review in hearing sciences? =C2=A0 Q2b Can you recommend a community-driven journal?<u= >=C2=A0 =C2=A0 Many scientists have responded to the new transparent = consultative peer-review procedure by eLife (<a href=3D"https://elifescienc= es.org/about/peer-review" target=3D"_blank">https://elifesciences.org/about= /peer-review</a>). This might be an exciting venue for those looking for new ways of peer review. However, the charges amount to $2000.= The charges for open access can be enormous (Nature $7000?) and a barrier = for early career researchers.=C2=A0 =C2=A0 So far, I have found the following examples of communi= ty journal/peer review processes:=C2=A0 =C2=A0 Pubpeer (The=C2=A0PubPeer=C2= =A0Foundation is a California-registered public-benefit co= rporation with 501(c)(3) nonprofit status in the United States. The overarc= hing goal of the Foundation is to improve the quality of scientific research by enabling innovative approaches for community int= eraction. The bylaws of the Foundation establish <a href=3D"http://pubpeer.= com" target=3D"_blank">pubpeer.com</a> as a service run for the benefit of = its readers and commenters, who create its content. Our current focus is ma= intaining and developing the=C2=A0PubPeer=C2=A0online platform for post-publi= cation peer review. <a href=3D"https://pubpeer.com/static/about_" target=3D"_blank">https://pu= bpeer.com/static/about_</a>)=C2=A0</u= > =C2=A0 Here you can find our preprint on that platform= =C2=A0 <a href=3D"https://pubpeer.com/publications/AE2235B5F9= F35577B977F87F9834B8" target=3D"_blank">https://pubpeer.com/publications/AE= 2235B5F9F35577B977F87F9834B8</a> =C2=A0 It looks like an easy platform to use. It can be used = for creating special issues/collections (see <a href=3D"https://pubpeer.com= /publications/peeriodicals" target=3D"_blank">https://pubpeer.com/publicati= ons/peeriodicals</a>). At the start, I had trouble registering using my name/institution. An anonymous account was created quickly. Curre= ntly, PubPeer is used for post-publication review. I heard that in other di= sciplines, Pubpeer is used to flag suspicious publications (read fraud). =C2=A0 =C2=A0 Another exciting example is ReviewCommons (= Review Commons=C2=A0provides= authors with a Refereed Preprint, which includes the authors=E2=80=99 manuscript, reports from a s= ingle round of peer review and the authors=E2=80=99 response. These Referee= d Preprints are transferred on the author=E2=80=99s behalf to bioRxiv. The = most recently-completed Review Commons peer-reviews are listed below, with the most recently posted reviews at the top<= span style=3D"font-family:Lora;color:rgb(45,45,45);background:white" lang= =3D"EN-US">. <a href=3D"https://www.reviewcommons.org/authors/" target=3D"_blank"= >https://www.reviewcommons.org/authors/</a><spa= n lang=3D"EN-US">)=C2=A0 Unfortunately, auditory sciences and audiology are not= within the scope of the peer-review initiative.=C2=A0= =C2=A0 The last example I know of is NBDT (NBDT is a community journal. If your handling editor sees it as in-scope it i= s appropriate. Editors are instructed to only handle papers that they consi= der running as a journal club paper for their own lab <a href=3D"https://nbdt.scholasticahq.com/for-authors" target=3D"_bl= ank">https://nbdt.scholasticahq.com/for-authors= </a>). It=E2=80=99s interesting to see their procedures, including =E2=80=9CCa= n you propose reviewers?=C2=A0Short answer: no. Long answer: we did our= own statistical analysis on a private dataset and have concluded that it p= roduces huge undesirable biases without leading to better reviews.=E2=80=9D=C2=A0 <div style=3D"border-color:currentcolor currentcolor windowtext;border-styl= e:none none solid;border-width:medium medium 1pt;padding:0cm 0cm 1pt"> =C2=A0 </div> =C2=A0 The Carbon Footprint of Hearing Healthcare=C2= =A0 =C2=A0 With Jan de Laat,=C2=A0I have just written a= perspective paper/blog about the Carbon Footprint of Hearing Healthcare (see version 2= , Preprint DOI <a href=3D"https://doi.org/10.31219/osf.io/3sj5u" target=3D"_blank">= 10.31219/osf.io/3sj5u</a>)= . The hearing tracker will publish the content today/tomorrow as a blog. So far, we have extract= ed information from <a href=3D"https://www.pwc.com/sk/en/environmental-social-and-corpor= ate-governance-esg/esg-reporting.html" target=3D"_blank">ESG reports</a> and our contacts within the hearing healthcare industry. Ideally, we would= like to organize a community-driven review process to collect comments fro= m engineers, industry, sustainability officers, authors from ESG reports, a= nd scientists.=C2=A0 =C2=A0 Q3a What would be a suitable platform to organize a= nd publish a community-driven review process of a perspective paper about c= arbon footprint in hearing healthcare? =C2=A0 =C2=A0 Another ambition could be to create a carbon footprint= tracker of hearing healthcare by annually updating table 1 from the prepri= nt, including an assessment of whether climate ambitions by industry were updated and achieved.=C2=A0 =C2=A0 Q3b What would be a suitable approach to annually m= onitor the carbon footprint of the hearing healthcare industry? (Maybe not peer-reviewed?)=C2=A0<= u> =C2=A0 Please let me know what you think is the best communit= y journal for auditory sciences. Don't hesitate to let us know if you b= elieve opinion pieces shouldn=E2=80=99t get into the review process. For me publishing this perspective paper is a low-risk experiment. If it g= oes well, I will consider submitting an original research manuscript.</u= >=C2=A0 =C2=A0 Thank you for your time. I am looking forward to your = responses and advice.=C2=A0 =C2=A0 Best regards,=C2=A0 Jan-Willem Wasmann =C2=A0 </div> De informat= ie in dit bericht is uitsluitend bestemd voor de geadresseerde. Aan dit ber= icht en de bijlagen kunnen geen rechten worden ontleend. Heeft u deze e-mai= l onbedoeld ontvangen? Dan verzoeken wij u het te vernietigen en de afzender te informeren. Openbaar maken, kop= i=C3=ABren en verspreiden van deze e-mail of informatie uit deze e-mail is = alleen toegestaan met voorafgaande schriftelijke toestemming van de afzende= r. Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 80262783.<= br> The content of this message is intended solely for the addressee. No rights= can be derived from this message or its attachments. If you are not the in= tended recipient, we kindly request you to delete the message and inform th= e sender. It is strictly prohibited to disclose, copy or distribute this email or the information inside it, w= ithout a written consent from the sender. Radboud university medical center= is registered with the Dutch Chamber of Commerce trade register with numbe= r 80262783. </div> </div></blockquote></div> --000000000000dcb07d05ecb2ec7e--

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