Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:38465231

Placebo-resistant gut bacteria: Akkermansia muciniphila spp. and Familial Mediterranean fever disease.

Elya Pepoyan · Francesco Marotta · Anahit Manvelyan · Artak Galstyan · Lena Stepanyan · Hasmik Grigoryan · Liana Grigoryan · Mikayel Mikayelyan · Marine Balayan · Natalya Harutyunyan · Susanna Mirzabekyan · Vardan Tsaturyan · Tamas Torok · Astghik Pepoyan

Frontiers in cellular and infection microbiology · 2024 doi:10.3389/fcimb.2024.1336752

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:38465231
kind
science-record
content_hash
sha256:6c5060c1c0f015c7d686fd9ca79e183f0907d8371a97f29fcfa6a72c212a4130
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:20:24Z
updated_at
2026-11-01T22:11:25Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Placebo-resistant gut bacteria: Akkermansia muciniphila spp. and Familial Mediterranean fever disease.
doi
10.3389/fcimb.2024.1336752
pmid
38465231
authors array · 14 items
[0]
Elya Pepoyan
[1]
Francesco Marotta
[2]
Anahit Manvelyan
[3]
Artak Galstyan
[4]
Lena Stepanyan
[5]
Hasmik Grigoryan
[6]
Liana Grigoryan
[7]
Mikayel Mikayelyan
[8]
Marine Balayan
[9]
Natalya Harutyunyan
[10]
Susanna Mirzabekyan
[11]
Vardan Tsaturyan
[12]
Tamas Torok
[13]
Astghik Pepoyan
journal
Frontiers in cellular and infection microbiology
year
2024
abstract
Introduction: Despite numerous investigations into the impact of drugs/probiotics on the gut microbiota composition in Familial Mediterranean Fever (FMF) patients, the question as to whether there exists a significant bacterial diversity(ies) independent of the placebo effect that can be reliably considered in clinical and nutritional trials remains unresolved. Methods: This study represents the in augural analysis of the placebo's influence on the gut microbiota of both healthy individuals and FMF afflicted men, utilizing previously collected data from PhyloChip™ DNA microarray experiments. A total of 15 healthy and 15 FMF male volunteers, aged 18 to 50, participated in this partially randomized placebo trial, which is accessible through the GEO Series accession number GSE111835. Results and Discussion: Key findings from current investigations include i. the anticipated divergence in gut bacteria resistance to placebo between healthy and FMF individuals, ii. the minor impact of placebo on gut bacterial diversities in healthy individuals, with Enterobacteriaceae diversities identified as placebo-resistant among "healthy" gut bacteria, and iii. the comprehensive influence of placebo on all bacterial phyla in the gut microbiome of FMF patients, extending to nearly all bacterial genera, except for the resilience of gut Akkermansia muciniphila spp. to placebo in FMF patients. This study underscores the susceptibility of Faecalibacterium, Blautia, and Clostridium genera to placebo. Consequently, this investigation holds significance for the proper design of placebo-controlled trials and establishes a foundation for further exploration of the gut-brain axis. Furthermore, it contributes valuable insights to discussions regarding proposals for probiotic therapies, particularly focusing on Faecalibacterium spp., Blautia spp., and Clostridium spp.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Student’s t-test and Mann-Whitney test were used for statistical analyses.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38465231
locator
sections[2] "Materials and methods" paragraph 7
quote
Student’s t-test and Mann-Whitney test were used for statistical analyses.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38465231
locator
sections[19] "Data availability statement" paragraph 2
quote
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
partial
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:38465231
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE111835
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the published analysis
kind
analysis
state
blocked
blocked_on
method:group_comparison_mann_whitney
description
Apply the paper's statistical method to the resolved series and compare the result with the published target.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE111835
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
[0]
step:run_analysis blocked on method:group_comparison_mann_whitney
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:38465231
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.3389/fcimb.2024.1336752
sha256
sha256:76d276272ad5823d7d7bb8563494ad5a60088802a5979a3039dbbba26bde6271
bytes
59384
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.3389/fcimb.2024.1336752
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC10920240
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE111835
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111835
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE111835
version
null
note
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.
access_statement_kind
data_availability_statement
sample_accessions array · 166 items
[0]
GSM3040616
[1]
GSM3040617
[2]
GSM3040618
[3]
GSM3040619
[4]
GSM3040620
[5]
GSM3040621
[6]
GSM3040622
[7]
GSM3040623
[8]
GSM3040624
[9]
GSM3040625
[10]
GSM3040626
[11]
GSM3040627
[12]
GSM3040628
[13]
GSM3040629
[14]
GSM3040630
[15]
GSM3040631
[16]
GSM3040632
[17]
GSM3040633
[18]
GSM3040634
[19]
GSM3040635
[20]
GSM3040636
[21]
GSM3040637
[22]
GSM3040638
[23]
GSM3040639
[24]
GSM3040640
[25]
GSM3040641
[26]
GSM3040642
[27]
GSM3040643
[28]
GSM3040644
[29]
GSM3040645
[30]
GSM3040646
[31]
GSM3040647
[32]
GSM3040648
[33]
GSM3040649
[34]
GSM3040650
[35]
GSM3040651
[36]
GSM3040652
[37]
GSM3040653
[38]
GSM3040654
[39]
GSM3040655
[40]
GSM3040656
[41]
GSM3040657
[42]
GSM3040658
[43]
GSM3040659
[44]
GSM3040660
[45]
GSM3040661
[46]
GSM3040662
[47]
GSM3040663
[48]
GSM3040664
[49]
GSM3040665
[50]
GSM3040666
[51]
GSM3040667
[52]
GSM3040668
[53]
GSM3040669
[54]
GSM3040670
[55]
GSM3040671
[56]
GSM3040672
[57]
GSM3040673
[58]
GSM3040674
[59]
GSM3040675
[60]
GSM3040676
[61]
GSM3040677
[62]
GSM3040678
[63]
GSM3040679
[64]
GSM3040680
[65]
GSM3040681
[66]
GSM3040682
[67]
GSM3040683
[68]
GSM3040684
[69]
GSM3040685
[70]
GSM3040686
[71]
GSM3040687
[72]
GSM3040688
[73]
GSM3040689
[74]
GSM3040690
[75]
GSM3040691
[76]
GSM3040692
[77]
GSM3040693
[78]
GSM3040694
[79]
GSM3040695
[80]
GSM3040696
[81]
GSM3040697
[82]
GSM3040698
[83]
GSM3040699
[84]
GSM3040700
[85]
GSM3040701
[86]
GSM3040702
[87]
GSM3040703
[88]
GSM3040704
[89]
GSM3040705
[90]
GSM3040706
[91]
GSM3040707
[92]
GSM3040708
[93]
GSM3040709
[94]
GSM3040710
[95]
GSM3040711
[96]
GSM3040712
[97]
GSM3040713
[98]
GSM3040714
[99]
GSM3040715
[100]
GSM3040716
[101]
GSM3040717
[102]
GSM3040718
[103]
GSM3040719
[104]
GSM3040720
[105]
GSM3040721
[106]
GSM3040722
[107]
GSM3040723
[108]
GSM3040724
[109]
GSM3040725
[110]
GSM3040726
[111]
GSM3040727
[112]
GSM3040728
[113]
GSM3040729
[114]
GSM3040730
[115]
GSM3040731
[116]
GSM3040732
[117]
GSM3040733
[118]
GSM3040734
[119]
GSM3040735
[120]
GSM3040736
[121]
GSM3040737
[122]
GSM3040738
[123]
GSM3040739
[124]
GSM3040740
[125]
GSM3040741
[126]
GSM3040742
[127]
GSM3040743
[128]
GSM3040744
[129]
GSM3040745
[130]
GSM3040746
[131]
GSM3040747
[132]
GSM3040748
[133]
GSM3040749
[134]
GSM3040750
[135]
GSM3040751
[136]
GSM3040752
[137]
GSM3040753
[138]
GSM3040754
[139]
GSM3040755
[140]
GSM3040756
[141]
GSM3040757
[142]
GSM3040758
[143]
GSM3040759
[144]
GSM3040760
[145]
GSM3040761
[146]
GSM3040762
[147]
GSM3040763
[148]
GSM3040764
[149]
GSM3040765
[150]
GSM3040766
[151]
GSM3040767
[152]
GSM3040768
[153]
GSM3040769
[154]
GSM3040770
[155]
GSM3040771
[156]
GSM3040772
[157]
GSM3040773
[158]
GSM3040774
[159]
GSM3040775
[160]
GSM3040776
[161]
GSM3040777
[162]
GSM3040778
[163]
GSM3040779
[164]
GSM3040780
[165]
GSM3040781
sample_count
166
group_sizes
null
group_sizes_basis
null
platform
24736
taxon
human gut metagenome; Archaea; Bacteria
title
PhyloChip-based characterization of stool samples from Familial Mediterranean Fever patients and the effects of probiotic Lactobacillus acidophilus INMIA 9602 Er 317/402
resolution_checked_at
2026-11-01T20:16:08Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE111835 not downloaded
[1]
asset:data:geo:GSE111835 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
mann_whitney
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
Student’s t-test and Mann-Whitney test were used for statistical analyses.
targets array · 0 items
gaps array · 1 item
[0]
method.group_comparison_mann_whitney
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_mann_whitney
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE111835
resolved_accessions array · 1 item
[0]
GSE111835
statements array · 1 item
[0]
The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.
basis
The paper names GSE111835 in GEO Series and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:38465231
[1]
data:geo:GSE111835
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
group_comparison_mann_whitney
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE111835
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T19:11:35Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
17752
completion_tokens
1013
cached_tokens
256
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:38465231
type
paper
label
pmid:38465231
[1] object · 3 fields
id
source:pmid:38465231
type
manuscript
label
PMID 38465231 full text
[2] object · 3 fields
id
data:geo:GSE111835
type
dataset
label
GEO GSE111835
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:38465231
type
paper
label
pmid:38465231
[1] object · 3 fields
id
source:pmid:38465231
type
manuscript
label
PMID 38465231 full text
[2] object · 3 fields
id
data:geo:GSE111835
type
dataset
label
GEO GSE111835
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-38465231
type
extraction
used array · 1 item
[0]
source:pmid:38465231
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE111835
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE111835
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:38465231
parent_hash
sha256:45a6709dfc6ff8d398b4e799ff70273215c1aae03e421d0718d856fde508d44b
fork_of
null
gaps array · 8 items
[0]
asset:data:geo:GSE111835 licence not read
[1]
asset:data:geo:GSE111835 not downloaded
[2]
execution.not_run
[3]
method.group_comparison_mann_whitney
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
[7]
step:run_analysis blocked on method:group_comparison_mann_whitney
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
reviously collected data from PhyloChip™ DNA microarray experiments. A total of 15 healthy and 15 FM
[1]
lyzed by leveraging the prior PhyloChip™ DNA-microarray-based data (Tsaturyan et al., 2023; Pepoyan
[2]
ation, culture-independent, high-density DNA microarray analysis (PhyloChip™; Affymetrix, Santa Clar
[3]
density DNA microarray analysis (PhyloChip™; Affymetrix, Santa Clara, CA, USA), according to the inv
order_basis
paper_text_order:633
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
clinical_trial
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 3 items
[0]
ged 18 to 50, participated in this partially randomized placebo trial, which is accessible through the GEO Series
[1]
holds significance for the proper design of placebo-controlled trials and establishes a foundation for furt
[2]
5) aged 18 to 50 took part in this partially randomized placebo trial accessible through GEO Series accession numb
order_basis
paper_text_order:753
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
amplicon_seq
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
ectrophoresis. gDNA was extracted/amplified (16S rRNA gene) from fecal materials frozen at -80оC.
[1]
he primer sequences used for microarrays and 16S rRNA clone libraries were: 27f.jgi (Bacteria-spec
order_basis
paper_text_order:3962
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Student’s t-test and Mann-Whitney test were used for statistical analyses.
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38465231", "kind": "science-record", "revision": 4, "content_hash": "sha256:6c5060c1c0f015c7d686fd9ca79e183f0907d8371a97f29fcfa6a72c212a4130", "created_at": "2026-11-01T19:20:24Z", "updated_at": "2026-11-01T22:11:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Placebo-resistant gut bacteria: Akkermansia muciniphila spp. and Familial Mediterranean fever disease.", "doi": "10.3389/fcimb.2024.1336752", "pmid": "38465231", "authors": ["Elya Pepoyan", "Francesco Marotta", "Anahit Manvelyan", "Artak Galstyan", "Lena Stepanyan", "Hasmik Grigoryan", "Liana Grigoryan", "Mikayel Mikayelyan", "Marine Balayan", "Natalya Harutyunyan", "Susanna Mirzabekyan", "Vardan Tsaturyan", "Tamas Torok", "Astghik Pepoyan"], "journal": "Frontiers in cellular and infection microbiology", "year": 2024, "abstract": "Introduction: Despite numerous investigations into the impact of drugs/probiotics on the gut microbiota composition in Familial Mediterranean Fever (FMF) patients, the question as to whether there exists a significant bacterial diversity(ies) independent of the placebo effect that can be reliably considered in clinical and nutritional trials remains unresolved.\nMethods: This study represents the in augural analysis of the placebo's influence on the gut microbiota of both healthy individuals and FMF afflicted men, utilizing previously collected data from PhyloChip™ DNA microarray experiments. A total of 15 healthy and 15 FMF male volunteers, aged 18 to 50, participated in this partially randomized placebo trial, which is accessible through the GEO Series accession number GSE111835.\nResults and Discussion: Key findings from current investigations include i. the anticipated divergence in gut bacteria resistance to placebo between healthy and FMF individuals, ii. the minor impact of placebo on gut bacterial diversities in healthy individuals, with Enterobacteriaceae diversities identified as placebo-resistant among \"healthy\" gut bacteria, and iii. the comprehensive influence of placebo on all bacterial phyla in the gut microbiome of FMF patients, extending to nearly all bacterial genera, except for the resilience of gut Akkermansia muciniphila spp. to placebo in FMF patients. This study underscores the susceptibility of Faecalibacterium, Blautia, and Clostridium genera to placebo. Consequently, this investigation holds significance for the proper design of placebo-controlled trials and establishes a foundation for further exploration of the gut-brain axis. Furthermore, it contributes valuable insights to discussions regarding proposals for probiotic therapies, particularly focusing on Faecalibacterium spp., Blautia spp., and Clostridium spp.", "claims": [{"id": "claim-method", "statement": "Student’s t-test and Mann-Whitney test were used for statistical analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38465231", "locator": "sections[2] \"Materials and methods\" paragraph 7", "quote": "Student’s t-test and Mann-Whitney test were used for statistical analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38465231", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38465231"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE111835"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE111835"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38465231", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcimb.2024.1336752", "sha256": "sha256:76d276272ad5823d7d7bb8563494ad5a60088802a5979a3039dbbba26bde6271", "bytes": 59384, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcimb.2024.1336752", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10920240", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE111835", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111835", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE111835", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3040616", "GSM3040617", "GSM3040618", "GSM3040619", "GSM3040620", "GSM3040621", "GSM3040622", "GSM3040623", "GSM3040624", "GSM3040625", "GSM3040626", "GSM3040627", "GSM3040628", "GSM3040629", "GSM3040630", "GSM3040631", "GSM3040632", "GSM3040633", "GSM3040634", "GSM3040635", "GSM3040636", "GSM3040637", "GSM3040638", "GSM3040639", "GSM3040640", "GSM3040641", "GSM3040642", "GSM3040643", "GSM3040644", "GSM3040645", "GSM3040646", "GSM3040647", "GSM3040648", "GSM3040649", "GSM3040650", "GSM3040651", "GSM3040652", "GSM3040653", "GSM3040654", "GSM3040655", "GSM3040656", "GSM3040657", "GSM3040658", "GSM3040659", "GSM3040660", "GSM3040661", "GSM3040662", "GSM3040663", "GSM3040664", "GSM3040665", "GSM3040666", "GSM3040667", "GSM3040668", "GSM3040669", "GSM3040670", "GSM3040671", "GSM3040672", "GSM3040673", "GSM3040674", "GSM3040675", "GSM3040676", "GSM3040677", "GSM3040678", "GSM3040679", "GSM3040680", "GSM3040681", "GSM3040682", "GSM3040683", "GSM3040684", "GSM3040685", "GSM3040686", "GSM3040687", "GSM3040688", "GSM3040689", "GSM3040690", "GSM3040691", "GSM3040692", "GSM3040693", "GSM3040694", "GSM3040695", "GSM3040696", "GSM3040697", "GSM3040698", "GSM3040699", "GSM3040700", "GSM3040701", "GSM3040702", "GSM3040703", "GSM3040704", "GSM3040705", "GSM3040706", "GSM3040707", "GSM3040708", "GSM3040709", "GSM3040710", "GSM3040711", "GSM3040712", "GSM3040713", "GSM3040714", "GSM3040715", "GSM3040716", "GSM3040717", "GSM3040718", "GSM3040719", "GSM3040720", "GSM3040721", "GSM3040722", "GSM3040723", "GSM3040724", "GSM3040725", "GSM3040726", "GSM3040727", "GSM3040728", "GSM3040729", "GSM3040730", "GSM3040731", "GSM3040732", "GSM3040733", "GSM3040734", "GSM3040735", "GSM3040736", "GSM3040737", "GSM3040738", "GSM3040739", "GSM3040740", "GSM3040741", "GSM3040742", "GSM3040743", "GSM3040744", "GSM3040745", "GSM3040746", "GSM3040747", "GSM3040748", "GSM3040749", "GSM3040750", "GSM3040751", "GSM3040752", "GSM3040753", "GSM3040754", "GSM3040755", "GSM3040756", "GSM3040757", "GSM3040758", "GSM3040759", "GSM3040760", "GSM3040761", "GSM3040762", "GSM3040763", "GSM3040764", "GSM3040765", "GSM3040766", "GSM3040767", "GSM3040768", "GSM3040769", "GSM3040770", "GSM3040771", "GSM3040772", "GSM3040773", "GSM3040774", "GSM3040775", "GSM3040776", "GSM3040777", "GSM3040778", "GSM3040779", "GSM3040780", "GSM3040781"], "sample_count": 166, "group_sizes": null, "group_sizes_basis": null, "platform": "24736", "taxon": "human gut metagenome; Archaea; Bacteria", "title": "PhyloChip-based characterization of stool samples from Familial Mediterranean Fever patients and the effects of probiotic Lactobacillus acidophilus INMIA 9602 Er 317/402", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE111835 not downloaded", "asset:data:geo:GSE111835 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student’s t-test and Mann-Whitney test were used for statistical analyses."}}], "targets": [], "gaps": ["method.group_comparison_mann_whitney"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE111835"], "resolved_accessions": ["GSE111835"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: GEO Series accession number GSE111835."], "basis": "The paper names GSE111835 in GEO Series and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38465231", "data:geo:GSE111835"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_mann_whitney", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE111835"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:11:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17752, "completion_tokens": 1013, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38465231", "type": "paper", "label": "pmid:38465231"}, {"id": "source:pmid:38465231", "type": "manuscript", "label": "PMID 38465231 full text"}, {"id": "data:geo:GSE111835", "type": "dataset", "label": "GEO GSE111835"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38465231", "type": "paper", "label": "pmid:38465231"}, {"id": "source:pmid:38465231", "type": "manuscript", "label": "PMID 38465231 full text"}, {"id": "data:geo:GSE111835", "type": "dataset", "label": "GEO GSE111835"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38465231", "type": "extraction", "used": ["source:pmid:38465231"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE111835", "type": "accession_resolution", "used": ["data:geo:GSE111835"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38465231", "parent_hash": "sha256:45a6709dfc6ff8d398b4e799ff70273215c1aae03e421d0718d856fde508d44b", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE111835 licence not read", "asset:data:geo:GSE111835 not downloaded", "execution.not_run", "method.group_comparison_mann_whitney", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_mann_whitney"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["reviously collected data from PhyloChip™ DNA microarray experiments. A total of 15 healthy and 15 FM", "lyzed by leveraging the prior PhyloChip™ DNA-microarray-based data (Tsaturyan et al., 2023; Pepoyan", "ation, culture-independent, high-density DNA microarray analysis (PhyloChip™; Affymetrix, Santa Clar", "density DNA microarray analysis (PhyloChip™; Affymetrix, Santa Clara, CA, USA), according to the inv"], "order_basis": "paper_text_order:633", "id": "assay:1"}, {"role": "data_generation", "definition_id": "clinical_trial", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ged 18 to 50, participated in this partially randomized placebo trial, which is accessible through the GEO Series", "holds significance for the proper design of placebo-controlled trials and establishes a foundation for furt", "5) aged 18 to 50 took part in this partially randomized placebo trial accessible through GEO Series accession numb"], "order_basis": "paper_text_order:753", "id": "assay:2"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ectrophoresis. gDNA was extracted/amplified (16S rRNA gene) from fecal materials frozen at -80оC.", "he primer sequences used for microarrays and 16S rRNA clone libraries were: 27f.jgi (Bacteria-spec"], "order_basis": "paper_text_order:3962", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Student’s t-test and Mann-Whitney test were used for statistical analyses."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}