Discussion, revision and decision

Discussion and Revision

Author

Reviewer 1 (Takehiko Ogawa, Yokohama City University, ogawa@yokohama-cu.ac.jp ):

We had already suggested in the "Limitations" section on page 10 of the manuscript-PDF testis transplantation experiments to test biological functionality for future studies: https://www.biorxiv.org/content/10.1101/2021.10.12.464060v1.full.pdf

However, these experiments will require new cell lines, new funding, more resources, more logistics, and new ethics approval which we are considering for future studies. We believe that the observations described in our manuscript are valuable to the scientific community and are a basis to conduct further studies.

Reviewer 2 (Dr. Pradeep G Kumar, Rajiv Gandhi Centre for Biotechnology, and kumarp@rgcb.res.in )

There are no line numbers in the manuscript-PDF but the pages are numbered: https://www.biorxiv.org/content/10.1101/2021.10.12.464060v1.full.pdf Since the pages of the manuscript-PDF are numbered, we think that citation of the manuscript is unproblematic. The text of the manuscript has been checked by multiple experienced authors and found not to require the suggested changes.

Reviewer (Takehiko Ogawa)

I think that authors admit the limit of the study, which I think is serious. I think the paper has its own value with limitation as almost always in most cases. I would like to take “verified with reservation” as my final decision.

Decision

Takehiko Ogawa: Verified with reservations

Pradeep G Kumar: Verified manuscript

Verified with reservations

Discussion, revision and decision

Revision

Author

The objective of the paper was not to address a research question but to report on a more recent set of PubMed retractions due to insufficient/old information available in the papers published on this subject(PubMed, not WoS retracted articles). One of the initial objectives was to analyze the dynamic of image related retractions(a relatively new subject), a subject for which the information is at least scarce if non existing. We have also studied the impact of retracted research via two citations databases (Google Scholar and Dimensions) and tried to represent the variability of this impact when the author country is being considered. At this time, the paper is the second biggest serie of PubMed retracted articles.

There was an error from our part, thank you very much for pointing this.

We have revised the article and added the informations related to previous research on this subject. Thank you so much for this suggestion.

Discussion, revision and decision

Discussion and Revision

Author response

We would like to thank the reviewers for their valuable comments. Below we provide pointwise response and the changes made in the revised manuscript.

To Dr. Jyotsnamayee Sabat

Pt-13: I want to know how the representative sequences were selected for different states. Is it based on no. of sequences submitted or positivity rate of a particular region?

All the Indian isolates available in GISAID for the period 27th Jan – 27th May 2020 were download and considered for analysis. NO state-wise selection was done.

To Dr Parvin Abraham

Pt-12: The dataset is only from 27th Jan – 27th May 2020. Maybe they can include more Numbers.

The period of data collection was restricted to 27th Jan – 27th May 2020 to basically understand the variations observed across different states of the country during the early phase of pandemic. Also, we are interested in assessing the impact of lockdown in containing the spread of COVID19 and state-specific subclusters, if any.

To Hurng-Yi Wang:

Pt-13: Agarwal and Parekh analyzed 685 SARS-CoV-2 isolates collected during 27th Jan - 27th May 2020 from India and described the distribution of virus strains and mutations across the country. While the information might be valuable to some local readers, the results are mainly descriptive and the data are a bit out of date. In addition, I have the following comments.

The period of data collection is restricted to 27th Jan – 27th May 2020 to basically understand the variations observed across different states of the country during the early phase of pandemic. Also, we are interested in assessing the impact of lockdown in containing the spread of COVID19 and state-specific subclusters, if any.

1. Some details of the methods are lacking. For example, the MUpro provides two methods, it is necessary to specify which method was used in the analysis. The confidence score of each prediction should also be provided. Besides, some results from I-Mutant and MUpro were conflicting, the authors may want to discuss the discrepancy.

   In the revised manuscript we give the sign of DDG predicted using the tools I-Mutant2.0 and the MUpro along with the respective confidence scores. In I-Mutant2.0, the sign of protein stability change predicted and reliability index (which provides confidence to the prediction) are now incorporated in Table-1. Similarly, the sign change and confidence scores given by MUpro on using SVM and NN based models have been incorporated. We expect all the models to give same results, except in cases where the predictions may be hard to make. This has now been explicitly mentioned in the Materials and Methods section: “In I-Mutant2.0, the sign of DDG is based on SVM classifier, and the associated confidence score is given by the reliability index. On the other hand, MUpro provides sign change prediction using two models, one SVM-based and the other using Neural Networks. InTable-1, the predicted sign of DDG by I-Mutant2.0 and MuPRO along with the respective confidence scores is reported.”

2. The “Analysis of the Mutational Profile of Indian Isolates” should be moved to Materials and Methods.

   There indeed was some redundancy in the information available in the Materials and Methods section and in the section “Analysis of the Mutational Profile of Indian Isolates”. We have now edited the Materials and Methods section appropriately and deleted the para under the above- mentioned section.

3. The authors provided lengthy discussion about the effect of each mutation in some lineages, such as 20A and I/A3i. However, as these mutations are tightly linked, the effect of each individual mutation is difficult to access. It is possible that some of the mutations are just hitchhikers. They may want to address this alternative point.

   For 20A we define the haplotype comprising four co-occurring mutations D614G, C241T, C3037T, and C14408T. Similarly, six co-occurring mutations C6312A, C13730T, C23929T, C28311T, C6310A (S2015R) and C19524T are shown to be associated with subclade I/A3i. Together as a set, these are useful in identifying clusters or group of isolates with similar mutational profile. However, those that are non-synonymous mutations are likely to have some individual impact on the overall stability of the respective protein. And so, we have presented both these results. To address this point, we have added a sentence at the end of Materials and Methods section and is reproduced below: “While we report individual effects of mutations on protein stability, some of the mutations in a haplotype may not be under natural selection and are just hitchhiking mutations.”

4. Several figures are confusing and lack detail. The diversity plots of Figure 3 and Figure 8 are hard to be precisely compared to the mutations that occurred among different plots. Phylogenetic trees, as well as their figure legends, are confusing, especially Figure 9 and Figure 10. For Figure 9, it is impossible to tell which mutation site had changed from C to T. For Figure 10, spots depicted in yellow are both position 29827 A>T and position 29830 G>T, green spot only notes as G, but A29827 is not mentioned in the figure. Furthermore, the mutation position of blue spot C cannot be found.

   We have now redrawn the diversity plots in Figure 3 and Figure 8, (labelled Figure 2 and Figure 4, respectively, in the revised manuscript) and are shown below. We have introduced horizontal lines to show the height of the divergence line at variant positions discussed in the manuscript, and these are also marked with the same colour in corresponding subplots for comparison.

In the revised manuscript, Figures 9 and 10 are now Supplementary Figures 2c and 2d respectively. The new figure legends are: Supplementary Figure 2: The sequences carrying the mutations a) C5700A b) C23929T c) C18877T d) G29830T are depicted in yellow colour. Figure 10 (now Supplementary Figure 2(d)) is now re-plotted, and we have removed the blue dot corresponding to ‘C’ since no samples from India had this variation.

1. Figure 9 and Figure 10 were not mentioned inside the text.

   It has now been added in the manuscript: Supplementary Figure 2(c) – On Pg-9, in the first line under the heading “Identification of novel subclade I/GJ-20A and unique mutations in Maharashtra”. Supplementary Figure 2(d) – On Pg-11, in the last paragraph under the heading “Identification of novel subclade I/GJ-20A and unique mutations in Maharashtra”.

2. The Top 10 mutations in PCA analysis are the mutations in 20A and I/A3i. It is reasonable to observed a clear association of the clusters with the clades. It is not clear, however, how these distribution correlate with lockdown, contact tracing and quarantine measures.

   From Supplementary Figure 1 clade 20A (shown in ‘Green’) is predominantly observed in Gujarat (178/201) and the distribution of clade 19A (shown in ‘Blue’) is high in Telangana (75/97), followed by Delhi (55/76), Maharashtra (31/80), and Tamil Nadu (19/34). Four mutations, C6312A, C13730T, C23929T, and C28311T are reported to be associated with subclade I/A3i, which is India-specific subclade of 19A. These co-occurring mutations are found in ~32% of Indian samples sequenced (till 31st May 2020). Only 5 isolates of this subclade were observed after May in India with the last one dated 13th June 2020 (according to data available in Nextstrain). This indicates that the spread of subclade I/A3i had been largely contained during lockdown with efforts of contact tracing and quarantining the infected individuals. Also, Telangana and Delhi isolates cluster together due to shared I/A3i mutations, primarily due to the Tablighi Jamaat congregation that occurred just before lockdown was announced. Similarly, clade 20A defining mutations were observed to occur in ~ 90% of Gujarat samples. Due to the countrywide lockdown from 25th March 2020, this clade and its sub-clusters were localized in the state, defined by Gujarat-specific mutations, e.g., I/GJ-20A.

Hurng-Yi Wang:

I agree to change to Verified manuscript.

Decision

Verified manuscript

Dr. Abraham: Verified manuscript

Dr. Sabat: Verified manuscript

Dr. Wang: Verified manuscript

ReconfigBehSci on Twitter: ‘RT @SciCommPSU: Today at 4! “COVID-19 Vaccines: Science versus Anti-Science” with @PeterHotez. Presented by @huckinstitutes https://t.co…’ / Twitter. (n.d.). Retrieved 14 January 2022, from https://twitter.com/SciBeh/status/1450591196653314051

ReconfigBehSci. (2021, October 20). RT @ProfJohnDrury: Sustaining mutual aid and community support groups: Covid-19 and beyond Free online event, 12.30pm November 3rd [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1453284900711370756

Question: What kind of biases in classifiers?

Network architecture in detail, generative model: StyleGAN2 -> question, are there possible alternatives to using StyleGAN2?

Interesting! If we were to use post-hoc explanations (think of SHAP and LIME), would you say that we intend to explain the true label, right?

Reminded me of this example again (https://openai.com/blog/multimodal-neurons/) how you could trick CLIP into believing an actual apple is an iPod

Would you argue that e.g. MLP is also a deep net? I would slightly rephrase the term "deep net" and change it into something like "neural network-based classifiers".

But, related to this, I actually found quite a relevant and interesting additional paper! It happened to be published 3 days ago, and the paper basically argued that you don't neccesarily need deep convnets to solve similar societal problems - any problem that can be solved using a transformer can be solved by a MLP/CNN, and vice versa, provided that you do exhaustive tuning and use the right inductive bias. Idem ditto for RNNs!

Link to CNN paper: https://arxiv.org/abs/2201.03545 Link to RNN paper: https://arxiv.org/abs/1611.09913

Discussion, revision and decision

Discussion and Revision

Author response

We would like to thank the reviewers for their valuable comments. Below we provide pointwise response and the changes made in the revised manuscript.

To Dr. Jyotsnamayee Sabat

Pt-13: I want to know how the representative sequences were selected for different states. Is it based on no. of sequences submitted or positivity rate of a particular region?

All the Indian isolates available in GISAID for the period 27th Jan – 27th May 2020 were download and considered for analysis. NO state-wise selection was done.

To Dr Parvin Abraham

Pt-12: The dataset is only from 27th Jan – 27th May 2020. Maybe they can include more Numbers.

The period of data collection was restricted to 27th Jan – 27th May 2020 to basically understand the variations observed across different states of the country during the early phase of pandemic. Also, we are interested in assessing the impact of lockdown in containing the spread of COVID19 and state-specific subclusters, if any.

To Hurng-Yi Wang:

Pt-13: Agarwal and Parekh analyzed 685 SARS-CoV-2 isolates collected during 27th Jan - 27th May 2020 from India and described the distribution of virus strains and mutations across the country. While the information might be valuable to some local readers, the results are mainly descriptive and the data are a bit out of date. In addition, I have the following comments.

The period of data collection is restricted to 27th Jan – 27th May 2020 to basically understand the variations observed across different states of the country during the early phase of pandemic. Also, we are interested in assessing the impact of lockdown in containing the spread of COVID19 and state-specific subclusters, if any.

1. Some details of the methods are lacking. For example, the MUpro provides two methods, it is necessary to specify which method was used in the analysis. The confidence score of each prediction should also be provided. Besides, some results from I-Mutant and MUpro were conflicting, the authors may want to discuss the discrepancy.

   In the revised manuscript we give the sign of DDG predicted using the tools I-Mutant2.0 and the MUpro along with the respective confidence scores. In I-Mutant2.0, the sign of protein stability change predicted and reliability index (which provides confidence to the prediction) are now incorporated in Table-1. Similarly, the sign change and confidence scores given by MUpro on using SVM and NN based models have been incorporated. We expect all the models to give same results, except in cases where the predictions may be hard to make. This has now been explicitly mentioned in the Materials and Methods section: “In I-Mutant2.0, the sign of DDG is based on SVM classifier, and the associated confidence score is given by the reliability index. On the other hand, MUpro provides sign change prediction using two models, one SVM-based and the other using Neural Networks. InTable-1, the predicted sign of DDG by I-Mutant2.0 and MuPRO along with the respective confidence scores is reported.”

2. The “Analysis of the Mutational Profile of Indian Isolates” should be moved to Materials and Methods.

   There indeed was some redundancy in the information available in the Materials and Methods section and in the section “Analysis of the Mutational Profile of Indian Isolates”. We have now edited the Materials and Methods section appropriately and deleted the para under the above- mentioned section.

3. The authors provided lengthy discussion about the effect of each mutation in some lineages, such as 20A and I/A3i. However, as these mutations are tightly linked, the effect of each individual mutation is difficult to access. It is possible that some of the mutations are just hitchhikers. They may want to address this alternative point.

   For 20A we define the haplotype comprising four co-occurring mutations D614G, C241T, C3037T, and C14408T. Similarly, six co-occurring mutations C6312A, C13730T, C23929T, C28311T, C6310A (S2015R) and C19524T are shown to be associated with subclade I/A3i. Together as a set, these are useful in identifying clusters or group of isolates with similar mutational profile. However, those that are non-synonymous mutations are likely to have some individual impact on the overall stability of the respective protein. And so, we have presented both these results. To address this point, we have added a sentence at the end of Materials and Methods section and is reproduced below: “While we report individual effects of mutations on protein stability, some of the mutations in a haplotype may not be under natural selection and are just hitchhiking mutations.”

4. Several figures are confusing and lack detail. The diversity plots of Figure 3 and Figure 8 are hard to be precisely compared to the mutations that occurred among different plots. Phylogenetic trees, as well as their figure legends, are confusing, especially Figure 9 and Figure 10. For Figure 9, it is impossible to tell which mutation site had changed from C to T. For Figure 10, spots depicted in yellow are both position 29827 A>T and position 29830 G>T, green spot only notes as G, but A29827 is not mentioned in the figure. Furthermore, the mutation position of blue spot C cannot be found.

   We have now redrawn the diversity plots in Figure 3 and Figure 8, (labelled Figure 2 and Figure 4, respectively, in the revised manuscript) and are shown below. We have introduced horizontal lines to show the height of the divergence line at variant positions discussed in the manuscript, and these are also marked with the same colour in corresponding subplots for comparison.

In the revised manuscript, Figures 9 and 10 are now Supplementary Figures 2c and 2d respectively. The new figure legends are: Supplementary Figure 2: The sequences carrying the mutations a) C5700A b) C23929T c) C18877T d) G29830T are depicted in yellow colour. Figure 10 (now Supplementary Figure 2(d)) is now re-plotted, and we have removed the blue dot corresponding to ‘C’ since no samples from India had this variation.

1. Figure 9 and Figure 10 were not mentioned inside the text.

   It has now been added in the manuscript: Supplementary Figure 2(c) – On Pg-9, in the first line under the heading “Identification of novel subclade I/GJ-20A and unique mutations in Maharashtra”. Supplementary Figure 2(d) – On Pg-11, in the last paragraph under the heading “Identification of novel subclade I/GJ-20A and unique mutations in Maharashtra”.

2. The Top 10 mutations in PCA analysis are the mutations in 20A and I/A3i. It is reasonable to observed a clear association of the clusters with the clades. It is not clear, however, how these distribution correlate with lockdown, contact tracing and quarantine measures.

   From Supplementary Figure 1 clade 20A (shown in ‘Green’) is predominantly observed in Gujarat (178/201) and the distribution of clade 19A (shown in ‘Blue’) is high in Telangana (75/97), followed by Delhi (55/76), Maharashtra (31/80), and Tamil Nadu (19/34). Four mutations, C6312A, C13730T, C23929T, and C28311T are reported to be associated with subclade I/A3i, which is India-specific subclade of 19A. These co-occurring mutations are found in ~32% of Indian samples sequenced (till 31st May 2020). Only 5 isolates of this subclade were observed after May in India with the last one dated 13th June 2020 (according to data available in Nextstrain). This indicates that the spread of subclade I/A3i had been largely contained during lockdown with efforts of contact tracing and quarantining the infected individuals. Also, Telangana and Delhi isolates cluster together due to shared I/A3i mutations, primarily due to the Tablighi Jamaat congregation that occurred just before lockdown was announced. Similarly, clade 20A defining mutations were observed to occur in ~ 90% of Gujarat samples. Due to the countrywide lockdown from 25th March 2020, this clade and its sub-clusters were localized in the state, defined by Gujarat-specific mutations, e.g., I/GJ-20A.

Hurng-Yi Wang:

I agree to change to Verified manuscript.

Decision

Verified manuscript

Dr. Abraham: Verified manuscript

Dr. Sabat: Verified manuscript

Dr. Wang: Verified manuscript

Discussion, revision and decision

Discussion and Revision

Author

Reviewer 1 (Takehiko Ogawa, Yokohama City University, ogawa@yokohama-cu.ac.jp ):

We had already suggested in the "Limitations" section on page 10 of the manuscript-PDF testis transplantation experiments to test biological functionality for future studies: https://www.biorxiv.org/content/10.1101/2021.10.12.464060v1.full.pdf

However, these experiments will require new cell lines, new funding, more resources, more logistics, and new ethics approval which we are considering for future studies. We believe that the observations described in our manuscript are valuable to the scientific community and are a basis to conduct further studies.

Reviewer 2 (Dr. Pradeep G Kumar, Rajiv Gandhi Centre for Biotechnology, and kumarp@rgcb.res.in )

There are no line numbers in the manuscript-PDF but the pages are numbered: https://www.biorxiv.org/content/10.1101/2021.10.12.464060v1.full.pdf Since the pages of the manuscript-PDF are numbered, we think that citation of the manuscript is unproblematic. The text of the manuscript has been checked by multiple experienced authors and found not to require the suggested changes.

Reviewer (Takehiko Ogawa)

I think that authors admit the limit of the study, which I think is serious. I think the paper has its own value with limitation as almost always in most cases. I would like to take “verified with reservation” as my final decision.

Decision

Takehiko Ogawa: Verified with reservations

Pradeep G Kumar: Verified manuscript

Verified with reservations

Johnston, M. (2021). What Lies Beneath: Tackling Vaccine Hesitancy. Emergency Medicine News, 43(10), 7. https://doi.org/10.1097/01.EEM.0000795760.41732.33

Discussion, revision and decision

Revision

Author

The objective of the paper was not to address a research question but to report on a more recent set of PubMed retractions due to insufficient/old information available in the papers published on this subject(PubMed, not WoS retracted articles). One of the initial objectives was to analyze the dynamic of image related retractions(a relatively new subject), a subject for which the information is at least scarce if non existing. We have also studied the impact of retracted research via two citations databases (Google Scholar and Dimensions) and tried to represent the variability of this impact when the author country is being considered. At this time, the paper is the second biggest serie of PubMed retracted articles.

There was an error from our part, thank you very much for pointing this.

We have revised the article and added the informations related to previous research on this subject. Thank you so much for this suggestion.

N, P, & R. (2021, November 27). Does omicron pose a risk to the vaccinated? Too early to tell, epidemiologist says. NPR. https://www.npr.org/2021/11/27/1059539509/too-early-to-tell-whether-omicron-poses-a-threat-to-vaccinated-epidemiologist-sa

Ahuja, A. (2021, November 7). UK dithering over Covid jabs for young must not happen again. Financial Times. https://www.ft.com/content/e5dd42d4-a555-4208-a218-738fc09a618c

ReconfigBehSci. (2021, October 30). Does there maybe need to be more distinction between points raised for discussion and any actual decision? Without knowing about votes etc., it’s maybe a bit strong to say ‘JCVI wanted x...’? I’ve sat on many bodies with minutes documenting positions I disagreed with [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1454488759785897987

ReconfigBehSci. (2021, October 31). Please join us at our upcoming workshop on ‘Science Communication as Collective Intelligence’ featuring talks (@SpiekermannKai, @dgurdasani1), panel discussions (@kakape,@CaulfieldTim, @joshua_a_becker, @suneman, @GeoffreySupran and more!) 1/2 https://t.co/isupbnF6yA [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1454763345748414465

indie_SAGE. (2021, October 29). Indie_SAGE 29.10.21. https://www.youtube.com/watch?v=1vGdRA_7hu8

Godlee, F. (2021). Why healthcare needs rebels. BMJ, 375, n2559. https://doi.org/10.1136/bmj.n2559

Puryear, C., & Gray, K. (2021). Using “Balanced Pragmatism” in Political Discussions Increases Cross-Partisan Respect. PsyArXiv. https://doi.org/10.31234/osf.io/yhpdt

The Evidence - Coronavirus: The Evidence - To boost or not to boost? - BBC Sounds. (n.d.). Retrieved 8 October 2021, from https://www.bbc.co.uk/sounds/play/w3ct2yqg

Diotime, n°71 (01/2017)

Mazumdar, S., & Thakker, D. (2020). Citizen Science on Twitter: Using Data Analytics to Understand Conversations and Networks. Future Internet, 12(12), 210. https://doi.org/10.3390/fi12120210

https://www.mdpi.com/1999-5903/12/12/210

It's really sad how the continuation of discrimination of African Americans is so rooted in the history of America and how it still persists today and it really just takes different forms, such as police brutality, language discrimination, etc

This is another example of how people often misjudge AAVE as unintelligent, when it does have many set grammatical rules that justify it

Similar to my last annotation, the more I learn about the grammar in AAVE the more I am impressed by the original people who started speaking it

It's sad to see people discriminate against AAVE and arguing that their lack of "proper" grammar is a sign of lesser intelligence when there are actual rules and reasonings behind the grammar.

It's also interesting to read about the history and the original reasonings behind AAVE

manual action time to think

Exactly like what I was thinking in one of my earlier annotations. It's very unfair that many people are all but forced to do this.

This also makes me think about the idea of code switching and how people that speak AAVE must switch their language simply to be able to make it in some professional areas.

This again leads me to think about the court case regarding the usage of AAVE and I believe that there should be laws enacted to further protect African American children in schools, as well as to mark it more clear that it is its own language.

I recall being very surprised about this when I first began learning about AAVE. It's very interesting and impressive how a unique language has been created through the African American culture. It also makes it worse when people discriminate against and refuse to accept AAVE as its own legitimate language.

Whenever I usually think of the broad discrimination that African Americans face, I often don't even think about all the different ways that they are. It really goes to show how deeply rooted racism is in America to discriminate someone based off of their speech which is a result of their culture.

This phrase makes me think of how a lot of the time southern people are regarded as less intelligent due to their accents and thats often how they are portrayed in movies and T.V shows.

I've always found the idea of ones language to be an extension of their personality to be a very interesting idea. For instance, my dads whole family has a completely different way of speaking than I have ever heard other people speak. I'm always able to tell if my dad is talking to one of his family on the phone cause his changes as well if he's speaking to one of them.

I saw this in high school: Black, Asian, and low-income students were all corrected more on their English and punished more severely for things like talking in class than the majority of the upper-class white students. I graduated in 2011.

When reading this, I feel a little bit of guilty. This is due to not recognizing this until a class last year and also having the same attitude that the "non linguists" were referenced to have

This line, as well as the examples, stood out because children were actively denied a form of communication that they knew - or is important to their families. I feel like this would hurt the children's motivation to learn as well as their comfort level socially.

I have often wondered both questions, I know I always felt shame if I made a grammatical mistake and a teacher would point it out to the class. Also, am I problematic if I use SAE? Or is it more problematic to force my students to use SAE?

What is their definition of lesser educated? Is it people who do not hold a college degree? Anyone without a doctorate? Not finishing high school? What is their definition of education and lesser educated?

I think we have already hit a form of linguistic anarchy through text abbreviations, instant messaging (especially my own use of MSN in 2005-2008, and social media.

Children who are from lower-income homes are not going to get the same opportunities for developing their linguistic skills. Is that because of their parents? Or do more socio-economic factors come into play here?

This challenged an internal belief (or at least already defined word) of literacy being reading and writing skills - much like the problematic definition given to us at the start of the paper.

This one challenges me, I think it's because of my bias of if we learn a language naturally, we would understand it's societal use better and that would help push linguistics studies to understand how language is actually used in the world.

This exactly describes my experience with Spanish in college. During class periods when I was required to speak or write, I would get lost in my head trying to remember how to do every little thing correctly. One of the assignments was to have a half hour conversation with someone who speaks Spanish as a first language, and during those I felt more confident because even though I wasn't getting things 100% grammatically right, I was still being understood.

There is a very limited amount of things said in this reading that I wish to try to make connections to because I know I cannot even if I wish to. This, though, I see on a much broader scale. Our connections with each other, the way we form them, and the willingness we have to form them in the first place.

The process of ubuntu draws out one's qualities to support and supply the greater common good as opposed to their own personal needs, which avoids selfish decisions and pride. There is a struggle that comes with avoiding being selfish, and debating this within yourself is a difficult process.

One question I have here is how do we teach this kind of concept in the classroom? Since we will be in high schools, how do we embrace this ideology when students may not even know how to engage with this kind of thing because they were not taught to do so prior to our class?

I chose this to discuss in class because it includes some of the most bipartisan opinions in politics. These topics expect a far right/left response, but the study doesn't examine those who might be only moderately left/right and do not have a strong opinion either way.

Are these apples, or any of the other delectable goodies on Genome Island, stored in an OAR (or LOR)? Can one find apples of the same design in OSGrid or another VW?

Note: Annotations for this page, a 'category' listing of posts, are not seen if one views any one of the posts. (See this post, for example.)

This is an interesting point I've been wrestling with.

This is a really interesting insight. These conversations can really veer into "whatchgonnado" or "not my job".

When meetings are framed around reading titles, they suggest a level of certainty. Framing around questions starts with what is unknown instead of known - more open to novices? (See next paragraph - "facilitators located expertise in readings and research ... not themselves")

Prof Tolullah Oni. (2021, February 19). Last night @SliderCuts & I discussed qq his 95k+ followers have about #COVID19 vaccines. Went on > 1.5 hrs in the end!! Pple have reasonable concerns that need to be heard and understood & happy to (hopefully) help address. Watch here https://instagram.com/tv/CLcu-UFB8Xy/?igshid=irvs1mlis0o9 @IndependentSage https://t.co/ssxAX2fcfE [Tweet]. @DrTolullah. https://twitter.com/DrTolullah/status/1362702943179464706

Point solutions could evolve socially, and so, collaboratively.

Strands of content form fibers that can be tthreaded best in a local K-12 space.

Karen Costa suggests that someone "create a tool for students to plan their online work and time management. It needs to aggregate all of their courses and include due dates"

Digital literacy taught alongside science curriculum = Disciplinary Literacy?

Here, Hypothes.is annotation layer provides a collaborative space for communication. Next, I will post a comment to this old, old blog post, given readers a link to this public annotation.

Edit

Reaching out again with new project MentorsOnline.NET

Notes: 1st edit of annotation for update of info

• 2nd use of tag: LTI-test-team

Scenario: Team building exercise, group tag(s) sorting downstream readers/ viewers (audience).

Note: First use of tag: LTI-test-team

"mythological status"

Reinforcing middle school grammar and writing skills while promoting social learning around topics such as a mythology in a game such as Minecraft or Roblox.

APB: Ephemeral Flan, Booklady...wilson Huckleberry too

This annotation flags archive.org's 2009 capture (its earliest) of this Second Life Wiki article. It could also be a launchpad* for an assignment.

LTI Note archive.org's timeline panel, in the context of constructive learning, could lead to engaging inquiry about particular subjects.

"They all had music; but... No knobs and dials."

components, connectors and data...oh my

Thank you, Jön.

Cup o' joe with folks at Cool Beans was a steady blend of irregulars with some top shelf virtual world designers .

"Enjoy some good music and great coffee."

The music was good.

Howdy, Tim, others! Here's a fine resource. But, I'm biased.

Staking out the Canvas annotation space on a hunch. Will we see Hypothes.is implement Presence first? Messaging and presence mean chat/notifications, right there in the sidebar, managing presence.

"a manual for new users, and a reference tool"Genius!

Yes!

Scenario: students follow lesson links to this page, having

• easy tagging, posting and sharing of webpages
• bookmarking and annotation
• chat/IM, wiki-blog-forum, notification options, online indicators for notices and assignments, online availability of mentor(s), classmates, course outlines, resources...

...and, all bundled in one tool [or a new browser]...

...then plug content from another space (i.e., Canvas, or maybe WebQuests) and sky's the limit.

Late in '16, when this browser extension came to life, several functions and features jumped out as likely candidates for secondary education.

One of these was vocabulary highlighting: importing a vocabulary set to highlight each term (where it appears in any page) with tooltip definitions...on any page visited...incredible!

Evernote's UI/UX is top shelf; slick, elegant; but, is it extensible? Does it bring the X in XMPP?

For example: An empty button could be added to the pop-up. A module that can be customized to inject approved widgets...such as chat/IM, or just a Home button keyed to the school's website.

I once bought a game add-on ($2-3) that came with an extensible button by default. That was a million dollar seller, if memory serves. (See mystical cookie).

Agreed!

Adding messaging and chat to Hypothesis could go a long way toward helping with this.

David Bokan proposes WebAnnotation in the Browser

Many threads emerging in the annotations here: https://github.com/bokand/web-annotations

Do you have any information about when your ancestors arrived in America? Can you trace your people this far back?

Panel Discussions. (n.d.). Association for Psychological Science - APS. Retrieved 14 June 2021, from https://www.psychologicalscience.org/conventions/2021-virtual/panel-discussions

An easy access dashboard now provides links to scientific discussion and evaluation of bioRxiv preprints. (n.d.). Retrieved 30 May 2021, from https://connect.biorxiv.org/news/2021/05/14/dashboard .

How will covid-19 vaccine safety concerns impact vaccine confidence? (2021, April 16). The BMJ. https://blogs.bmj.com/bmj/2021/04/16/how-will-the-uks-decision-to-offer-an-alternative-to-the-oxford-astrazeneca-covid-19-vaccine-for-under-30s-following-safety-signals-impact-vaccine-confidence/

Special Track 3. (n.d.). Data for Policy CIC. Retrieved 8 March 2021, from https://dataforpolicy.org/data-fof-policy-2021/special-track-3/

Stephan Lewandowsky. (2021, March 6). 25 March deadline for submissions to our ‘special track’ https://t.co/qwLxCCSjks at Data for Policy conference, 14-16 September at UCL. Please consider submitting @SciBeh @stefanmherzog @Sander_vdLinden https://t.co/A8KSC1Tkh9 [Tweet]. @STWorg. https://twitter.com/STWorg/status/1368280722709110789

ReconfigBehSci. (2020, November 25). We didn’t have explicit discussion of Red Team process at our SciBeh workshop, but I suspect it’s an extremely useful way to manage criticism- simply because the recipient is inviting it [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1331558570668806147

r/BehSciAsk—Behavioural science one year on. (n.d.). Reddit. Retrieved May 2, 2021, from https://www.reddit.com/r/BehSciAsk/comments/mw8mdr/behavioural_science_one_year_on/

r/BehSciResearch - Behavioural Science one year on: How did we do? (n.d.). Reddit. Retrieved May 2, 2021, from https://www.reddit.com/r/BehSciResearch/comments/mw8ngy/behavioural_science_one_year_on_how_did_we_do/

https://github.com/rails/sprockets/issues/162 was already closed as duplicated (so this just creates another duplicate).

Technically this could be added there.

Oh, I see, it was from so long ago (2015), that it would probably be frowned upon to reopen such an old issue.

dawnlxh. (2020, October 30). Ideas for discussion: what is the role of open science is crisis knowledge management? [Reddit Post]. R/BehSciAsk. https://www.reddit.com/r/BehSciAsk/comments/jkzooc/ideas_for_discussion_what_is_the_role_of_open/gbtktep/

ReconfigBehSci on Twitter. (n.d.). Twitter. Retrieved 5 March 2021, from https://twitter.com/SciBeh/status/1326159560835555328

https://www.reddit.com/r/BehSciAsk/comments/jkzuig/ideas_for_discussion_how_can_research_interface/?utm_source=share&utm_medium=web2x&context=3

https://www.reddit.com/r/BehSciMeta/comments/jkzirk/ideas_for_discussion_how_to_manage_online/?utm_source=share&utm_medium=web2x&context=3

World Health Organization (WHO). (2021, January 27). #COVID19​ LIVE Q&A virus variants with Dr M. Ryan and Dr M. Van Kerkhove - #AskWHO​ of 27 January 2021. https://www.youtube.com/watch?v=4SxRq45yVFY

ReconfigBehSci. (2021, February 19). RT @DrTolullah: Last night @SliderCuts & I discussed qq his 95k+ followers have about #COVID19 vaccines. Went on > 1.5 hrs in the end!! Ppl… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1363423504935366657