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new figures from pmc; updated config and log
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actions-user committed Oct 3, 2024
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22 changes: 22 additions & 0 deletions figure_fetch.log
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2024-10-03 02:19:55 - ==========================================================

2024-10-03 03:22:49 - Starting NCBI PMC Figure Fetcher

2024-10-03 03:22:49 - Configuration loaded from query_config.yml

2024-10-03 03:22:50 - PMC search query: (((((((((((signaling pathway[Figure/Table Caption]) OR signalling pathway[Figure/Table Caption]) OR regulatory pathway[Figure/Table Caption]) OR disease pathway[Figure/Table Caption]) OR drug pathway[Figure/Table Caption]) OR metabolic pathway[Figure/Table Caption]) OR biosynthetic pathway[Figure/Table Caption]) OR synthesis pathway[Figure/Table Caption]) OR cancer pathway[Figure/Table Caption]) OR response pathway[Figure/Table Caption]) OR cycle pathway[Figure/Table Caption])) AND (2024/08/01[PUBDATE] : 2024/09/01[PUBDATE])

2024-10-03 03:23:13 - PMC search completed. Fetched 1006 results (max set to 3000).

2024-10-03 03:23:22 - Extracted 1599 figures from XML content.

2024-10-03 03:23:22 - Identified 486 pathway figures.

2024-10-03 03:23:22 - Skipped 313 figures previously processed.

2024-10-03 03:23:22 - Processed 173 pathway figures for download.

2024-10-03 03:25:44 - New pathway figures downloaded: 173

2024-10-03 03:25:44 - NCBI PMC Figure Fetcher completed

2024-10-03 03:25:44 - ==========================================================

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27 changes: 27 additions & 0 deletions figures/PMC11353926__foods-13-02573-g003.yml
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---
figid: PMC11353926__foods-13-02573-g003
pmcid: PMC11353926
image_filename: foods-13-02573-g003.jpg
figure_link: /pmc/articles/PMC11353926/figure/F3/
number: Figure 3
figure_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
caption: Enrichment analysis bubble diagrams of KEGG metabolic pathway in samples
from inhibition group and reduction group
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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27 changes: 27 additions & 0 deletions figures/PMC11353926__foods-13-02573-g004.yml
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---
figid: PMC11353926__foods-13-02573-g004
pmcid: PMC11353926
image_filename: foods-13-02573-g004.jpg
figure_link: /pmc/articles/PMC11353926/figure/F4/
number: Figure 4
figure_title: Venn diagram of enrichment pathway.
caption: Venn diagram of enrichment pathway. The yellow circle represents the Inhibition_TR
vs. Inhibition_Control group, and the blue circle represents the Reduction_TR vs.
Reduction_Control
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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31 changes: 31 additions & 0 deletions figures/PMC11353926__foods-13-02573-g005.yml
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---
figid: PMC11353926__foods-13-02573-g005
pmcid: PMC11353926
image_filename: foods-13-02573-g005.jpg
figure_link: /pmc/articles/PMC11353926/figure/F5/
number: Figure 5
figure_title: Purine metabolic pathway and major metabolites.
caption: Purine metabolic pathway and major metabolites. (A) Purine metabolic pathway;
(B) metabolites in purine metabolic pathway. Blue words indicate the metabolites
with significant differences between the inhibition group and the reduction group,
green words indicate the metabolites with significant differences only in the inhibition
group, and red words indicate the metabolites with significant differences only
in the reduction group. ↑ indicates up-regulation and ↓ indicates down-regulation.
* p < 0.05, ** p < 0.01, *** p < 0.001, ns, not significant
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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30 changes: 30 additions & 0 deletions figures/PMC11353926__foods-13-02573-g007.yml
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---
figid: PMC11353926__foods-13-02573-g007
pmcid: PMC11353926
image_filename: foods-13-02573-g007.jpg
figure_link: /pmc/articles/PMC11353926/figure/F7/
number: Figure 7
figure_title: Glycerol phospholipid metabolic pathway and major metabolites.
caption: Glycerol phospholipid metabolic pathway and major metabolites. (A) Glycerol
phospholipid metabolic pathway; (B) effect of plantaricin Q7 on metabolites of glycerol
phospholipid metabolic pathway in the inhibition group. The black words in Figure
7A represent metabolites with no significant changes, while the green words represent
metabolites with significant changes. Green ↑ indicates up-regulation and green
↓ indicates down-regulation. * p < 0.05, *** p < 0.001
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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29 changes: 29 additions & 0 deletions figures/PMC11353926__foods-13-02573-g008.yml
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---
figid: PMC11353926__foods-13-02573-g008
pmcid: PMC11353926
image_filename: foods-13-02573-g008.jpg
figure_link: /pmc/articles/PMC11353926/figure/F8/
number: Figure 8
figure_title: Arginine biosynthesis pathway and major metabolites.
caption: Arginine biosynthesis pathway and major metabolites. (A) Arginine biosynthesis
pathway; (B) effect of plantaricin Q7 on metabolites of arginine biosynthesis pathway
in the reduction group. Red indicates metabolites with significant differences.
Red ↑ indicates up-regulation and red ↓ indicates down-regulation. * p < 0.05, **
p < 0.01, *** p < 0.001
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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34 changes: 34 additions & 0 deletions figures/PMC11353926__foods-13-02573-g009.yml
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---
figid: PMC11353926__foods-13-02573-g009
pmcid: PMC11353926
image_filename: foods-13-02573-g009.jpg
figure_link: /pmc/articles/PMC11353926/figure/F9/
number: Figure 9
figure_title: Metabolic pathways related to the inhibition and reduction in L.
caption: Metabolic pathways related to the inhibition and reduction in L. monocytogenes
biofilm by plantaricin Q7. The red text boxes indicate up-regulation and the blue
text boxes indicate down-regulation. The orange dashed circles represent the two
metabolites with the largest difference in fold in the inhibition groups, and the
green dashed circles represent the two metabolites with the largest difference in
fold in the reduction groups. The remaining dashed lines indicate direct or indirect
connections between metabolic pathways. The green background indicates purine metabolism,
the gray background indicates arginine biosynthesis, the pink background indicates
glycerol phospholipid metabolism, and the light orange background indicates plantaricin
Q7 acting on the L. monocytogenes biofilm
article_title: Metabolomic Approaches to Study the Potential Inhibitory Effects of
Plantaricin Q7 against Listeria monocytogenes Biofilm
citation: Yinxue Liu, et al. Foods. 2024 Aug;13(16).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-17
doi: 10.3390/foods13162573
journal_title: Foods
journal_nlm_ta: Foods
publisher_name: MDPI
keywords:
- plantaricin Q7
- Listeria monocytogenes biofilm
- metabolomics
- inhibition
- reduction
---
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41 changes: 41 additions & 0 deletions figures/PMC11357534__pharmaceuticals-17-01094-g004.yml
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---
figid: PMC11357534__pharmaceuticals-17-01094-g004
pmcid: PMC11357534
image_filename: pharmaceuticals-17-01094-g004.jpg
figure_link: /pmc/articles/PMC11357534/figure/F4/
number: Figure 4
figure_title: Effects of 5-fluorouracil with or without thymol on the p-AKT/p-GSK3α,3β
signaling pathway in liver tissue of rats.
caption: 'Effects of 5-fluorouracil with or without thymol on the p-AKT/p-GSK3α,3β
signaling pathway in liver tissue of rats. (I) Representative immunoblot of protein
levels of AKT, p-AKT, GSK3α,3β, and p-GSK3α,3β (the upper band for α and the lower
band for β) in liver tissues. Proteins were immunoblotted with Akt antibody in “the
first upper panel,” p-Akt antibody in “the second panel,” GSK3α,3β antibody in “the
third panel,” p-GSK3α,3β antibody in “the fourth panel,” and after stripping with
GAPDH antibody as a loading control in the “lower panel.” (II) Quantitative results
for the immunoblot, showing (a) the ratio of p-Akt/Akt and (b) the ratio of p-GSK3α,3β/GSK3α,3β
protein levels expressed, and the relative quantities were normalized to the control
and expressed as a fold of induction. The densities of immunoblots were quantified
using analysis software. Values are mean ± SEM (n = 3). x, y, or z: The 5-fluorouracil
and Fu+ thymol (60 mg/kg) groups are significantly different at p < 0.05. p ≤ 0.05
was evaluated using ANOVA followed by Tukey–Kramer as a post-hoc test. 5-FU: 5-fluorouracil;
Akt: protein Kinase B; p-Akt: phosphorylated Akt, GSK3α,3β: glycogen synthase kinase
3 α and 3β; p-GSK3α,3β: phosphorylated glycogen synthase kinase 3 α and 3β'
article_title: Thymol Protects against 5-Fluorouracil-Induced Hepatotoxicity via the
Regulation of the Akt/GSK-3β Pathway in In Vivo and In Silico Experimental Models
citation: Yasmen F. Mahran, et al. Pharmaceuticals (Basel). 2024 Aug;17(8).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-21
doi: 10.3390/ph17081094
journal_title: Pharmaceuticals
journal_nlm_ta: Pharmaceuticals (Basel)
publisher_name: MDPI
keywords:
- thymol
- 5-flourouracil
- hepatotoxicity
- apoptosis
- GSK-3β signaling
- p44/42 MAPK(ERK1/2) signaling
---
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31 changes: 31 additions & 0 deletions figures/PMC11359896__toxics-12-00609-g005.yml
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---
figid: PMC11359896__toxics-12-00609-g005
pmcid: PMC11359896
image_filename: toxics-12-00609-g005.jpg
figure_link: /pmc/articles/PMC11359896/figure/F5/
number: Figure 5
figure_title: KEGG analysis of DEGs.
caption: KEGG analysis of DEGs. (A) Bar chart of KEGG classification statistics. The
horizontal coordinate indicates the names of the KEGG metabolic pathway; the vertical
coordinate is the number of genes or transcripts annotated to the pathway. (B) Top
20 enriched KEGG signaling pathways. The size of the dots indicates the number of
genes in this KEGG term, and the color of the dots corresponds to different Padjust
ranges
article_title: Toxicity Evaluation and Transcriptome Analysis of Yellowstripe Goby
(Mugilogobius chulae) in Response to 2,7-Dibromocarbazole Exposure during Early
Development
citation: Caixia Gao, et al. Toxics. 2024 Aug;12(8).
year: '2024'
pub_date: 2024-8-
epub_date: 2024-8-20
doi: 10.3390/toxics12080609
journal_title: Toxics
journal_nlm_ta: Toxics
publisher_name: MDPI
keywords:
- Mugilogobius chulae
- 2,7-DBCZ
- fish embryo acute toxicity (FET)
- concentration–effect curves
- differentially expressed genes (DEGs)
---
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29 changes: 29 additions & 0 deletions figures/PMC11364484__nihms-2018135-f0001.yml
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---
figid: PMC11364484__nihms-2018135-f0001
pmcid: PMC11364484
image_filename: nihms-2018135-f0001.jpg
figure_link: /pmc/articles/PMC11364484/figure/F1/
number: Fig. 1.
figure_title: Pathogenesis of pulmonary fibrosis
caption: Alveolar inflammation and injury induce fibroblast activation and differentiation
to myofibroblast and ECM accumulation. Activation of TGF-β pathway and reduced BMP
pathway contribute to the pathogenesis of PF
article_title: Emerging role of BMPs/BMPR2 signaling pathway in treatment for pulmonary
fibrosis
citation: Qinmao Ye, et al. Biomed Pharmacother. 2024 Aug 23;178(NA).
year: '2024'
pub_date: 2024-8-23
epub_date: 2024-8-13
doi: 10.1016/j.biopha.2024.117178
journal_title: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
journal_nlm_ta: Biomed Pharmacother
publisher_name: .na.character
keywords:
- Pulmonary fibrosis
- TGF-β pathway
- BMP ligands
- BMP receptors
- Myofibroblast differentiation
- Pro-fibrotic responses
- Anti-fibrosis
---
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31 changes: 31 additions & 0 deletions figures/PMC11364484__nihms-2018135-f0002.yml
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---
figid: PMC11364484__nihms-2018135-f0002
pmcid: PMC11364484
image_filename: nihms-2018135-f0002.jpg
figure_link: /pmc/articles/PMC11364484/figure/F2/
number: Fig. 2.
figure_title: TGF-β and BMP receptors and their signaling pathways
caption: BMP type I receptors have 4 subtypes including ALK1 (ACVRL1), ALK2 (ACVR1),
ALK3 (BMPR1A) and ALK6 (BMPR1B); type II receptors consist of ACVR2A (ActRIIA),
ACVR2B (ActRIIB) and BMPR2B (BMPR2). TGF-β signaling pathway plays a pro-fibrotic
role to promote the α-smooth muscle actin (SMA), fibronectin (FN), and collagen
expression; while BMP signaling pathway indicates the anti-fibrotic function
article_title: Emerging role of BMPs/BMPR2 signaling pathway in treatment for pulmonary
fibrosis
citation: Qinmao Ye, et al. Biomed Pharmacother. 2024 Aug 23;178(NA).
year: '2024'
pub_date: 2024-8-23
epub_date: 2024-8-13
doi: 10.1016/j.biopha.2024.117178
journal_title: Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
journal_nlm_ta: Biomed Pharmacother
publisher_name: .na.character
keywords:
- Pulmonary fibrosis
- TGF-β pathway
- BMP ligands
- BMP receptors
- Myofibroblast differentiation
- Pro-fibrotic responses
- Anti-fibrosis
---
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28 changes: 28 additions & 0 deletions figures/PMC11370353__nihpp-2024.08.15.608164v2-f0004.yml
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---
figid: PMC11370353__nihpp-2024.08.15.608164v2-f0004
pmcid: PMC11370353
image_filename: nihpp-2024.08.15.608164v2-f0004.jpg
figure_link: /pmc/articles/PMC11370353/figure/F4/
number: Figure 4.
figure_title: Gene expression in the core dauer pathway is robust
caption: 'A. Density plot of the Coefficient of Variation (CV) of genes in the core
dauer pathway. Labels of the pathway on top. X-axis: CVs of all genes in the pathway
computed by dividing the standard deviation (SD) of its expression across all dauers
by its mean expression across all dauers. Dotted lines demarcating CVs: low, (CV
< 30), moderate (30 < CV < 50), high (CV > 50). Y-axis (left) density.B. Dumbbell
Plot showing Spearman’s correlation coefficient (rho) between pairs of dauers in
‘core’ dauer pathways. TOP labels: the pair of dauers compared. Y-axis: pathway.
X-axis: rho value and confidence interval (CI): blue dot represents lower CI, yellow
dot represents rho value, and red dot represents high CI. p-values, Bonferroni corrected.
*p-value <0.05; ns, not-significant'
article_title: Robustness and variability in Caenorhabditis elegans dauer gene expression
citation: Johnny Cruz Corchado, et al. bioRxiv. 2024 Aug 26;NA(NA).
year: '2024'
pub_date: 2024-8-26
epub_date: 2024-8-26
doi: 10.1101/2024.08.15.608164
journal_title: bioRxiv
journal_nlm_ta: bioRxiv
publisher_name: Cold Spring Harbor Laboratory
keywords: []
---
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