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

pmid:36744396

The Value of Ki-67 Labeling Index in Central Lymph Node Metastasis and Survival of Papillary Thyroid Carcinoma: Evidence From the Clinical and Molecular Analyses.

Yi Lei · Xin Zhao · Yang Feng · Danshuang He · Daixing Hu · Yu Min

Cancer control : journal of the Moffitt Cancer Center · 2023 doi:10.1177/10732748231155701

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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:36744396
kind
science-record
content_hash
sha256:689574a2e4511ac1b8ba7ee45291448f83312f8cb152245aeaccd0603e62dbbb
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T19:01:19Z
updated_at
2026-11-01T22:51:12Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
The Value of Ki-67 Labeling Index in Central Lymph Node Metastasis and Survival of Papillary Thyroid Carcinoma: Evidence From the Clinical and Molecular Analyses.
doi
10.1177/10732748231155701
pmid
36744396
authors array · 6 items
[0]
Yi Lei
[1]
Xin Zhao
[2]
Yang Feng
[3]
Danshuang He
[4]
Daixing Hu
[5]
Yu Min
journal
Cancer control : journal of the Moffitt Cancer Center
year
2023
abstract
BACKGROUND: Recent evidence suggests that the Ki-67 labeling index is associated with lymph node metastasis and the prognosis of papillary thyroid carcinoma (PTC). METHODS: We retrospectively evaluated the clinicopathological features of consecutive PTC patients between Jan 2019 and Oct 2020 in our medical center. The molecular analysis was also conducted by using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) program. The Chi-square test was performed for the comparison of variables between patients with central lymph node metastasis (CLNM) and not. Besides, univariate and stepwise multivariate logistic regression analyses were further used to determine the risk factors for CLNM in PTC. RESULTS: Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM. After excluding the patients with harvested central lymph nodes <3, increased Ki-67 labeling index was still associated with the number of CLNM and the lymph node ratio. Additionally, the expression level of Ki-67 was significantly correlated with a higher N stage and worse disease-free survival in TCGA and validated GSE60542 datasets. CONCLUSIONS: Higher Ki-67 labeling index (>5%) is significantly associated with the CLNM in PTC patients, like other indicators of the male gender, larger tumor size, and multifocality. Besides, the Ki-67 was also determined to be associated with CLNM and DFS in PTC patients, which may act as an important molecular marker in PTC.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67.
kind
methodological
target
null
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:36744396
locator
sections[6] "Statistical Analysis" paragraph 2
quote
The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test.
[1] object · 3 fields
asset
source:pmid:36744396
locator
sections[6] "Statistical Analysis" paragraph 2
quote
Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients.
[2] object · 3 fields
asset
source:pmid:36744396
locator
sections[6] "Statistical Analysis" paragraph 2
quote
Moreover, only statistically significant variables were included for stepwise multivariate analysis.
[3] object · 3 fields
asset
source:pmid:36744396
locator
sections[6] "Statistical Analysis" paragraph 2
quote
The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36744396
locator
sections[15] "fn-group" paragraph 1
quote
Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM.
kind
qualitative
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:36744396
locator
sections[0] "Abstract" paragraph 3
quote
Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM.
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:36744396
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:GSE60542
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
complete
blocked_on
null
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:GSE60542
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 · 0 items
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:36744396
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1177/10732748231155701
sha256
sha256:13acb9d4490853537c56644ddb0915bc8a3ff756670af99b6fa5d625bef6cfaa
bytes
30602
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1177/10732748231155701
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
PMC9905023
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE60542
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=GSE60542
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE60542
version
null
note
Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 92 items
[0]
GSM1481838
[1]
GSM1481839
[2]
GSM1481840
[3]
GSM1481841
[4]
GSM1481842
[5]
GSM1481843
[6]
GSM1481844
[7]
GSM1481845
[8]
GSM1481846
[9]
GSM1481847
[10]
GSM1481848
[11]
GSM1481849
[12]
GSM1481850
[13]
GSM1481851
[14]
GSM1481852
[15]
GSM1481853
[16]
GSM1481854
[17]
GSM1481855
[18]
GSM1481856
[19]
GSM1481857
[20]
GSM1481858
[21]
GSM1481859
[22]
GSM1481860
[23]
GSM1481861
[24]
GSM1481862
[25]
GSM1481863
[26]
GSM1481864
[27]
GSM1481865
[28]
GSM1481866
[29]
GSM1481867
[30]
GSM1481868
[31]
GSM1481869
[32]
GSM1481870
[33]
GSM1481871
[34]
GSM1481872
[35]
GSM1481873
[36]
GSM1481874
[37]
GSM1481875
[38]
GSM1481876
[39]
GSM1481877
[40]
GSM1481878
[41]
GSM1481879
[42]
GSM1481880
[43]
GSM1481881
[44]
GSM1481882
[45]
GSM1481883
[46]
GSM1481884
[47]
GSM1481885
[48]
GSM1481886
[49]
GSM1481887
[50]
GSM1481888
[51]
GSM1481889
[52]
GSM1481890
[53]
GSM1481891
[54]
GSM1481892
[55]
GSM1481893
[56]
GSM1481894
[57]
GSM1481895
[58]
GSM1481896
[59]
GSM1481897
[60]
GSM1481898
[61]
GSM1481899
[62]
GSM1481900
[63]
GSM1481901
[64]
GSM1481902
[65]
GSM1481903
[66]
GSM1481904
[67]
GSM1481905
[68]
GSM1481906
[69]
GSM1481907
[70]
GSM1481908
[71]
GSM1481909
[72]
GSM1481910
[73]
GSM1481911
[74]
GSM1481912
[75]
GSM1481913
[76]
GSM1481914
[77]
GSM1481915
[78]
GSM1481916
[79]
GSM1481917
[80]
GSM1481918
[81]
GSM1481919
[82]
GSM1481920
[83]
GSM1481921
[84]
GSM1481922
[85]
GSM1481923
[86]
GSM1481924
[87]
GSM1481925
[88]
GSM1481926
[89]
GSM1481927
[90]
GSM1481928
[91]
GSM1481929
sample_count
92
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Revisiting the transcriptional analysis of primary tumors and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE60542 not downloaded
[1]
asset:data:geo:GSE60542 licence not read
analysis object · 4 fields
state
complete
methods array · 2 items
[0] object · 10 fields
id
method-1
family
regression_modelling
specific
logistic
label
Regression modelling
dsl_operations array · 1 item
[0]
glm_logit_fit
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
predictors_and_outcome
evidence object · 3 fields
score
1
band
reordered
quote
The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67.
[1] object · 10 fields
id
method-2
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
0.7
band
medium
quote
Chi-square
targets array · 0 items
gaps array · 0 items
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
true
required_operations array · 1 item
[0]
glm_logit_fit
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic.
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]
GSE60542
resolved_accessions array · 1 item
[0]
GSE60542
statements array · 1 item
[0]
Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.
basis
The paper names GSE60542 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
glm_logit_fit
assets array · 2 items
[0]
source:pmid:36744396
[1]
data:geo:GSE60542
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE60542
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
2026-11-01T18:26:11Z
independence
single_reader
evidence_check object · 2 fields
method
reordered
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
9429
completion_tokens
2221
cached_tokens
264
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:36744396
type
paper
label
pmid:36744396
[1] object · 3 fields
id
source:pmid:36744396
type
manuscript
label
PMID 36744396 full text
[2] object · 3 fields
id
data:geo:GSE60542
type
dataset
label
GEO GSE60542
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:36744396
type
paper
label
pmid:36744396
[1] object · 3 fields
id
source:pmid:36744396
type
manuscript
label
PMID 36744396 full text
[2] object · 3 fields
id
data:geo:GSE60542
type
dataset
label
GEO GSE60542
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-36744396
type
extraction
used array · 1 item
[0]
source:pmid:36744396
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE60542
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE60542
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:36744396
parent_hash
sha256:ffe79673195255968bbdc4631f7e8211cdc8c7adfd7b72bd4c45e46f471ffe56
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE60542 licence not read
[1]
asset:data:geo:GSE60542 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 2 items
[0] object · 11 fields
role
data_generation
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]
The Value of Ki-67 Labeling Index in Central Lymph Node Metasta
[1]
ACKGROUND: Recent evidence suggests that the Ki-67 labeling index is associated with lymph node
[2]
ifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95%
[3]
harvested central lymph nodes <3, increased Ki-67 labeling index was still associated with the
order_basis
paper_text_order:0
id
assay:1
[1] object · 11 fields
role
analysis
definition_id
regression_modelling
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
glm_logit_fit
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67.
order_basis
consumes_earlier_output
id
assay:2
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36744396", "kind": "science-record", "revision": 3, "content_hash": "sha256:689574a2e4511ac1b8ba7ee45291448f83312f8cb152245aeaccd0603e62dbbb", "created_at": "2026-11-01T19:01:19Z", "updated_at": "2026-11-01T22:51:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Value of Ki-67 Labeling Index in Central Lymph Node Metastasis and Survival of Papillary Thyroid Carcinoma: Evidence From the Clinical and Molecular Analyses.", "doi": "10.1177/10732748231155701", "pmid": "36744396", "authors": ["Yi Lei", "Xin Zhao", "Yang Feng", "Danshuang He", "Daixing Hu", "Yu Min"], "journal": "Cancer control : journal of the Moffitt Cancer Center", "year": 2023, "abstract": "BACKGROUND: Recent evidence suggests that the Ki-67 labeling index is associated with lymph node metastasis and the prognosis of papillary thyroid carcinoma (PTC).\nMETHODS: We retrospectively evaluated the clinicopathological features of consecutive PTC patients between Jan 2019 and Oct 2020 in our medical center. The molecular analysis was also conducted by using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) program. The Chi-square test was performed for the comparison of variables between patients with central lymph node metastasis (CLNM) and not. Besides, univariate and stepwise multivariate logistic regression analyses were further used to determine the risk factors for CLNM in PTC.\nRESULTS: Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM. After excluding the patients with harvested central lymph nodes <3, increased Ki-67 labeling index was still associated with the number of CLNM and the lymph node ratio. Additionally, the expression level of Ki-67 was significantly correlated with a higher N stage and worse disease-free survival in TCGA and validated GSE60542 datasets.\nCONCLUSIONS: Higher Ki-67 labeling index (>5%) is significantly associated with the CLNM in PTC patients, like other indicators of the male gender, larger tumor size, and multifocality. Besides, the Ki-67 was also determined to be associated with CLNM and DFS in PTC patients, which may act as an important molecular marker in PTC.", "claims": [{"id": "claim-method", "statement": "The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36744396", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test."}, {"asset": "source:pmid:36744396", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients."}, {"asset": "source:pmid:36744396", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "Moreover, only statistically significant variables were included for stepwise multivariate analysis."}, {"asset": "source:pmid:36744396", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36744396", "locator": "sections[15] \"fn-group\" paragraph 1", "quote": "Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36744396", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our results showed that male gender (odd ratio (OR) = 3.02; 95% CI: 1.81-5.04), tumor size >1 cm (OR = 2.81; 95% CI: 1.84-4.29), multifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95% CI: .73-1.97; >5%: OR = 3.85; 95% CI: 1.62-9.14) were independent risk factors for CLNM.", "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:36744396"], "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:GSE60542"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE60542"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36744396", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/10732748231155701", "sha256": "sha256:13acb9d4490853537c56644ddb0915bc8a3ff756670af99b6fa5d625bef6cfaa", "bytes": 30602, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/10732748231155701", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9905023", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE60542", "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=GSE60542", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60542", "version": null, "note": "Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1481838", "GSM1481839", "GSM1481840", "GSM1481841", "GSM1481842", "GSM1481843", "GSM1481844", "GSM1481845", "GSM1481846", "GSM1481847", "GSM1481848", "GSM1481849", "GSM1481850", "GSM1481851", "GSM1481852", "GSM1481853", "GSM1481854", "GSM1481855", "GSM1481856", "GSM1481857", "GSM1481858", "GSM1481859", "GSM1481860", "GSM1481861", "GSM1481862", "GSM1481863", "GSM1481864", "GSM1481865", "GSM1481866", "GSM1481867", "GSM1481868", "GSM1481869", "GSM1481870", "GSM1481871", "GSM1481872", "GSM1481873", "GSM1481874", "GSM1481875", "GSM1481876", "GSM1481877", "GSM1481878", "GSM1481879", "GSM1481880", "GSM1481881", "GSM1481882", "GSM1481883", "GSM1481884", "GSM1481885", "GSM1481886", "GSM1481887", "GSM1481888", "GSM1481889", "GSM1481890", "GSM1481891", "GSM1481892", "GSM1481893", "GSM1481894", "GSM1481895", "GSM1481896", "GSM1481897", "GSM1481898", "GSM1481899", "GSM1481900", "GSM1481901", "GSM1481902", "GSM1481903", "GSM1481904", "GSM1481905", "GSM1481906", "GSM1481907", "GSM1481908", "GSM1481909", "GSM1481910", "GSM1481911", "GSM1481912", "GSM1481913", "GSM1481914", "GSM1481915", "GSM1481916", "GSM1481917", "GSM1481918", "GSM1481919", "GSM1481920", "GSM1481921", "GSM1481922", "GSM1481923", "GSM1481924", "GSM1481925", "GSM1481926", "GSM1481927", "GSM1481928", "GSM1481929"], "sample_count": 92, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Revisiting the transcriptional analysis of primary tumors and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE60542 not downloaded", "asset:data:geo:GSE60542 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67."}}, {"id": "method-2", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.7, "band": "medium", "quote": "Chi-square"}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["GSE60542"], "resolved_accessions": ["GSE60542"], "statements": ["Data Availability: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE60542 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:36744396", "data:geo:GSE60542"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE60542"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:26:11Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9429, "completion_tokens": 2221, "cached_tokens": 264}}, "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:36744396", "type": "paper", "label": "pmid:36744396"}, {"id": "source:pmid:36744396", "type": "manuscript", "label": "PMID 36744396 full text"}, {"id": "data:geo:GSE60542", "type": "dataset", "label": "GEO GSE60542"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36744396", "type": "paper", "label": "pmid:36744396"}, {"id": "source:pmid:36744396", "type": "manuscript", "label": "PMID 36744396 full text"}, {"id": "data:geo:GSE60542", "type": "dataset", "label": "GEO GSE60542"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36744396", "type": "extraction", "used": ["source:pmid:36744396"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE60542", "type": "accession_resolution", "used": ["data:geo:GSE60542"], "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:36744396", "parent_hash": "sha256:ffe79673195255968bbdc4631f7e8211cdc8c7adfd7b72bd4c45e46f471ffe56", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE60542 licence not read", "asset:data:geo:GSE60542 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["The Value of Ki-67 Labeling Index in Central Lymph Node Metasta", "ACKGROUND: Recent evidence suggests that the Ki-67 labeling index is associated with lymph node", "ifocality (OR = 2.08; 95% CI: 1.31-3.30, and Ki-67 labeling index (>3% and ≤5%: OR = 1.20; 95%", "harvested central lymph nodes <3, increased Ki-67 labeling index was still associated with the"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The categorical variables in PTC patients were compared using the Pearson-chi square test or Fisher’s exact chi-square test (based on the expected value), The continuous variables were compared using Student’s two-tailed t-test. Univariate logistic regression analysis was initially used to identify the potential risk factors involved in CLNM of PTC patients. Moreover, only statistically significant variables were included for stepwise multivariate analysis. The recurrence-free survival analysis was assessed by Kaplan–Meier curves to compare the high and low expression of Ki-67."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}