Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status

[cmirzayi]

Presti, Rachel M.a; Handley, Scott A.a; Droit, Lindsaya; Ghannoum, Mahmoudb; Jacobson, Markc; Shiboski, Caroline H.c; Webster-Cyriaque, Jenniferd; Brown, Todde; Yin, Michael T.f; Overton, Edgar T.g. Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status. AIDS 32(10):p 1279-1287, June 19, 2018. | DOI: 10.1097/QAD.0000000000001811

https://journals.lww.com/aidsonline/Fulltext/2018/06190/Alterations_in_the_oral_microbiome_in_HIV_infected.8.aspx

[MyleeeA]

Name: Mildred Andokie Anashie

I will like to claim this article please

[MyleeeA]

Please I need help deleting signature 1 and 2 for experiment 1 Here's the link https://bugsigdb.org/Study_819

[lwaldron]

Why do you want these deleted @MyleeeA? I only delete a page if it was added in error and doesn't belong there at all.

[lwaldron]

Deleted now @MyleeeA .

[MyleeeA]

Thank you 🙏

[MyleeeA]

Hi @lwaldron @cmirzayi @SvetlanaUP I finished my curation: https://bugsigdb.org/Study_819. Waiting for your reviews.

[cmirzayi]

Marked as ready for review.

[cmirzayi]

Great curation! There is an experiment missing and I have some small changes that need to be made. I count 4 experiments worth of findings presented:

24W vs BL all samples (present) BL low CD4 vs. BL high CD4 (present) BL low CD4 vs 24W low CD4 (missing) 24W low CD4 vs. 24W high CD4 (present)

Condition should be antiviral agent.

Statistical test was DESeq2.

Item	Description	max	points
1	All elements marked "Needs review" (none "Incomplete")	1	1
2	Correct study design	1	1
3	Entered all relevant experiments and no irrelevant experiments	1	0
4	Body site correctly identified (i.e. does not include multiple sites)	1	1
5	Condition entered according to contrast (correct EFO ontology)	1	0
6	Contrast groups correctly identified	1	1
7	Groups correctly labeled as 1 and 0 (1=cases, 0=controls)	1	1
8	Antibiotic exclusion correctly identified	1	1
9	Correctly identified sequencing details	2	2
10	Identified correct statistical test	1	0
11	Identified MHT correction	1	1
12	Correctly recorded matched on factors	1	1
13	Entered correct number of statistical tests per experiment	1	1
14	All diversity measures identified	1	1
15	Diversity results correctly entered as increased/decreased/unchanged	1	1
16	All signature sources correctly identified (-1 for each error)	2	2
17	Abundance direction correctly selected	1	1
18	Members of Signatures identified correctly	2	2
19	Correct use of NCBI taxonomy	2	2
	TOTAL	23	20

[MyleeeA]

Thank you for your review… This is way better than I imagined I’ll do, I’m more confident now 😊 I’ll effect the changes accordingly

I’ve looked at the paper again and I noticed the experiment you pointed out I missed

[MyleeeA]

Hi

I’ve made some changes with regards the statistical test for the differential abundant taxas recorded and the condition (Changed it from HIV-1 infection to Response to antiviral drug) since antiviral drug wasn’t available Also can experiments take any order?, I’ll like to edit the experiment 1 to the experiment missing, I just noticed the experiment 1 and 2 are similar, curated the same thing for both without realizing Please review this, I’m hoping this works

[Peacesandy]

https://bugsigdb.org/Study_819

Reviewed