search

waldronlab / BugSigDBcuration

For documenting issues related to BugSigDB curation.
10 stars 7 forks source link

Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants #477

Open Scholarpat opened 2 months ago

Scholarpat commented 2 months ago

Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants - Lianna F Wood – Clinical Infectious Diseases

https://academic.oup.com/cid/article/67/8/1237/4961341

Zzee2 commented 1 month ago

Zara Adwan

TheTosin commented 3 weeks ago

Hello @Zzee2

How is your day going? Do you need help with curating this issue? I am happy to assist.

Feel free to reach me as Adeshile Oluwatosin on slack.

KateRasheed commented 2 weeks ago

Hello @Zzee2 . I see that you've created a study and added a study design; however, you are yet to add experiment(s) and signature(s). Just as @TheTosin mentioned, we are happy to collaborate with you in the completion of this curation. Kindly drop your slack name so we can reach out.

Zzee2 commented 2 weeks ago

Hello @Zzee2

How is your day going? Do you need help with curating this issue? I am happy to assist.

Feel free to reach me as Adeshile Oluwatosin on slack.

Hi, thanks @TheTosin. i am Okay. appreciate the offer

Zzee2 commented 2 weeks ago

Hello @Zzee2 . I see that you've created a study and added a study design; however, you are yet to add experiment(s) and signature(s). Just as @TheTosin mentioned, we are happy to collaborate with you in the completion of this curation. Kindly drop your slack name so we can reach out.

Hi @KateRasheed thanks. I am Okay, had some technical challenges earlier which delayed me, but am fine now. appreciate the offer.

TheTosin commented 2 weeks ago

@Zzee2 Noted! Feel free to reach out if you experience any blockers still.

Have fun curating.

Zzee2 commented 2 weeks ago

@SvetlanaUP So I was done with the paper, took me a bit long cause I had some technical challenge from my end, however, now that am done with the paper, I discovered that the paper is probably curated in BugSigDB cause I got this error image

I still went ahead and filled it without the PMID just incase, you can check it out as well. https://bugsigdb.org/Study_1174

am editing this comment @SvetlanaUP the mistake is from me, I made a mistake during the time I had my technical issues by creatin the study twice, so I will correct it and update. thanks

KateRasheed commented 2 weeks ago

https://bugsigdb.org/Study_1107

Hi @Zzee2 I see that your article has been curated in this study. You can request that study 1174 be deleted while you continue working on this study 1107. Let me know if this is clear for you?

TheTosin commented 2 weeks ago

Hello @Zzee2 Please take this into consideration before submitting for review. In my opinion. From the study, these are my observations; Firstly, see a link to the curation policy: https://bugsigdb.org/w/index.php?title=Curation_Policy&veaction=edit&section=9

  1. I believe the correct condition is HIV mother to child transmission(only one condition should be curated). Statement “ We performed a prospective, longitudinal study of infants from a high-HIV-prevalence, low-income setting in South Africa.”

Here, you can see they performed the study on infants already with HIV not those susceptible.

  1. I see they mentioned feces, serum, and mouth mucosa … as body sites. I believe it’s best to curate different body sites as different experiments. But in this case, I can only see significant results using feces(stool) and blood, so the rest should be deleted.

    • Stool; V3-V4 “ The V4 region of the 16S rRNA gene was amplified using universal 515F/806R primers [16]. Pooled triplicate samples were purified (Agencourt AMPure XP beads, Beckman Coulter). Equimolar amplicon pools of 96 samples were quantified (KAPA Library Quantification kit, Kapa Biosystems) and sequenced from both ends (Illumina MiSeq platform, v3 chemistry).”

  2. Antibiotics exclusion should be left empty. There’s no need to write the statement.

  3. Group 0 is non-exclusively fed infants. Group 1 is exclusively fed infants(this is the exposed group in the study).

  4. MHT is yes.(figure out if it is no for the other experiments). “ Adjustment for multiple comparisons was performed using the Holm step-down approach [24] for immunological data and Benjamini-Hochberg [25] for microbiota data.”

  5. There should be no details in LDA score: it’s for LeFSe results only.

  6. I can’t see any confounders or matched on in the study as well. Also alpha-diversity faith was mentioned ( Figure 1B).

  7. There should be signatures in each experiments In your study, Figure 4B is curatable. Deseq (0.05) Here, only Akkermansia muciniphila is in the increased abundance. Group 0 and 1 is different here. “ Linear combinations of all immunological factors measured did not significantly improve the model compared to HLA-DR alone (permutational ANOVA P = .035). Using DeSeq2 [27], we found that counts of Akkermansia muciniphila in stool.”

  8. Here, I will state the Figures and Tables I see curatable. Also number of experiments I believe your study should have.

I apologize that it’s lengthy

SvetlanaUP commented 2 weeks ago

@Zzee2 is your curation ready for review? https://bugsigdb.org/Study_1174? https://bugsigdb.org/Study_1107?

SvetlanaUP commented 2 weeks ago

@KateRasheed @TheTosin could you please clarify the status of this curation(s)? @TheTosin since you already did a thorough review, could you please finalize one study and let me know which one to delete? Thank you.

KateRasheed commented 2 weeks ago

Good morning @SvetlanaUP . I don't think it is ready for review. @Zzee2 hasn't effected the corrections @TheTosin made.

TheTosin commented 2 weeks ago

@SvetlanaUP The last time I reviewed the study link, I saw that @Zzee2 had a lot to correct. He insisted he does not need help, that’s why I dropped my view here.

Okay, I will finalize the curation. Thank you

TheTosin commented 1 week ago

@SvetlanaUP This study is ready for review.

https://bugsigdb.org/Study_1107