new content from pmc

figures/PMC10000909__cancers-15-01554-g001.yml

@@ -0,0 +1,30 @@
+---
+pmcid: PMC10000909
+image_filename: cancers-15-01554-g001.jpg
+figure_link: /pmc/articles/PMC10000909/figure/cancers-15-01554-f001/
+number: Figure 1
+figure_title: ''
+caption: Bioinformatics analysis of circRNAs in CLL samples. (A) Heatmap demonstration
+  of 52 differentially expressed circRNAs between CLL lymphocytes (red bar, right)
+  and normal B-cells (blue bar, left). (B) Volcano plotting of deregulated circRNAs
+  in CLL samples. (C) Interaction analysis between candidate circRNAs and other signaling
+  mediators. (D) Gene ontology (GO) biological process and (E) WikiPathways enrichment
+  analysis of gene networks. (F) Drug sensitivity prediction of gene networks in CLL.
+article_title: Circular RNA Expression Signatures Provide Promising Diagnostic and
+  Therapeutic Biomarkers for Chronic Lymphocytic Leukemia.
+citation: Ehsan Gharib, et al. Cancers (Basel). 2023 Mar;15(5):1554.
+
+doi: 10.3390/cancers15051554
+journal_title: Cancers
+journal_nlm_ta: Cancers (Basel)
+publisher_name: MDPI
+
+keywords:
+- cancer
+- chronic lymphocytic leukemia
+- circular RNA
+- diagnosis
+- prognosis
+- drug sensitivity prediction
+
+---

figures/PMC10006576__11010_2023_4686_Fig5_HTML.yml

@@ -0,0 +1,31 @@
+---
+pmcid: PMC10006576
+image_filename: 11010_2023_4686_Fig5_HTML.jpg
+figure_link: /pmc/articles/PMC10006576/figure/Fig5/
+number: Fig. 5
+figure_title: ''
+caption: Pathway and network analysis a Top ten significant pathways enriched for
+  pathway analysis through WikiPathways in upregulated genes, b host–Microbiome protein–domain
+  interaction on upregulated genes, c mutation frequency of upregulated genes, d mutated
+  genes which are upregulated in metastatic CC, e top ten significant pathways enriched
+  for pathway analysis through WikiPathways in downregulated genes, f host–microbiome
+  protein–domain interaction on downregulated genes, g Mutation frequency of downregulated
+  genes, h mutated genes which are downregulated in metastatic CC i-n Needle plot
+  for the mutations in IDS, MAP4K4, SPTBN1, COL4A2, KHDRBS1 and DST
+article_title: Multidimensional outlook on the pathophysiology of cervical cancer
+  invasion and metastasis.
+citation: Neena George, et al. Mol Cell Biochem. 2023;478(11):2581-2606.
+
+doi: 10.1007/s11010-023-04686-3
+journal_title: Molecular and Cellular Biochemistry
+journal_nlm_ta: Mol Cell Biochem
+publisher_name: Springer US
+
+keywords:
+- Cervical squamous cell carcinoma
+- Lymph angiogenesis
+- Metastasis
+- Genetic and epigenetic profile
+- Human papillomavirus
+
+---

figures/PMC10018165__fneur-14-1130378-g0002.yml

@@ -0,0 +1,29 @@
+---
+pmcid: PMC10018165
+image_filename: fneur-14-1130378-g0002.jpg
+figure_link: /pmc/articles/PMC10018165/figure/F2/
+number: Figure 2
+figure_title: ''
+caption: Identification of the DEGs in the GSE135917 dataset, GSEA analysis, and GSVA
+  heatmap analysis. (A) Heatmap plot of the DEGs for OSAS vs. controls. (B, C) GSEA
+  and GSVA analysis in wikipathways for OSAS vs. controls. (|NES| > 1, FDR < 0.1,
+  P-value < 0.05). (D) Ferroptosis genes ring heatmap.
+article_title: Identification and validation of ferroptosis-related hub genes in obstructive
+  sleep apnea syndrome.
+citation: Peijun Liu, et al. Front Neurol. 2023;14:1130378.
+
+doi: 10.3389/fneur.2023.1130378
+journal_title: Frontiers in Neurology
+journal_nlm_ta: Front Neurol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- OSAS
+- THCA
+- ferroptosis
+- CIH
+- HIF1A
+- ATM
+- immune infiltration
+
+---

figures/PMC10019437__41598_2023_30158_Fig2_HTML.yml

@@ -0,0 +1,27 @@
+---
+pmcid: PMC10019437
+image_filename: 41598_2023_30158_Fig2_HTML.jpg
+figure_link: /pmc/articles/PMC10019437/figure/Fig2/
+number: Figure 2
+figure_title: ''
+caption: Pathway enrichment analysis for differentially expressed genes. (a) 93 differentially
+  expressed genes at day 0 between COVID-19 survivors and non-survivors were evaluated
+  for enrichment of pathways. (b) 290 differentially expressed genes at day 7 between
+  COVID-19 survivors and non-survivors were evaluated for enrichment of pathways.
+  GeneOntology (Biological Processes), KEGG, Reactome, and Wikipathways were used
+  in this over-representation analysis for both DEG sets. Only pathways with an adjusted
+  p-value ≤ 0.05 for enrichment are shown.
+article_title: Identification of two early blood biomarkers ACHE and CLEC12A for improved
+  risk stratification of critically ill COVID-19 patients.
+citation: Simone Kattner, et al. Sci Rep. 2023;13:4388.
+
+doi: 10.1038/s41598-023-30158-1
+journal_title: Scientific Reports
+journal_nlm_ta: Sci Rep
+publisher_name: Nature Publishing Group UK
+
+keywords:
+- Predictive markers
+- Transcriptomics
+
+---

figures/PMC10031067__fcimb-13-1106591-g003.yml

@@ -0,0 +1,37 @@
+---
+pmcid: PMC10031067
+image_filename: fcimb-13-1106591-g003.jpg
+figure_link: /pmc/articles/PMC10031067/figure/f3/
+number: Figure 3
+figure_title: ''
+caption: Nef-mediated changes in ubiquitination of cellular proteins that directly
+  interact with Nef or the UPS. (A) Nef-mediated ubiquitination fold change in proteins
+  that directly interact with Nef. Twenty-three of the 325 cellular proteins identified
+  in  directly interact with Nef, according to the data collected from the NIH GENE
+  database (https://www.ncbi.nim.nih.gov/gene). The fold changes in ubiquitination
+  in the presence of Nef range from 6.8-fold decrease to a 4.68-fold increase, with
+  greater color intensity corresponding to larger fold changes. The fold changes associated
+  with cellular proteins for which Nef up-regulated ubiquitination are depicted in
+  green, while those with down-regulated ubiquitination are in red. (B) Nef-mediated
+  ubiquitination fold changes in proteins that directly interact with the UPS. Fifteen
+  of the 325 cellular proteins identified in  directly interact with UPS, according
+  to the data collected from the WikiPathways database (https://www.wikipathways.org/).
+  The fold changes in ubiquitination range from a 5.94-fold decrease to a 10.12-fold
+  increase. The same color coding was used in both panels (A, B).
+article_title: Novel role of HIV-1 Nef in regulating the ubiquitination of cellular
+  proteins.
+citation: Maria Ghaly, et al. Front Cell Infect Microbiol. 2023;13:1106591.
+
+doi: 10.3389/fcimb.2023.1106591
+journal_title: Frontiers in Cellular and Infection Microbiology
+journal_nlm_ta: Front Cell Infect Microbiol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- HIV-1 Nef
+- post-translational modification
+- ubiquitinated proteins
+- ubiquitin
+- proteasomal degradation system
+
+---

figures/PMC10058634__ijms-24-05651-g003.yml

@@ -0,0 +1,27 @@
+---
+pmcid: PMC10058634
+image_filename: ijms-24-05651-g003.jpg
+figure_link: /pmc/articles/PMC10058634/figure/ijms-24-05651-f003/
+number: Figure 3
+figure_title: ''
+caption: Functional annotation for co-DEGs. (a) Biological process, (b) cellular component,
+  (c) molecular function, and (d) WikiPathways of the co-DEGs.
+article_title: 'Shared Genes of PPARG and NOS2 in Alzheimer’s Disease and Ulcerative
+  Colitis Drive Macrophages and Microglia Polarization: Evidence from Bioinformatics
+  Analysis and Following Validation.'
+citation: Longcong Dong, et al. Int J Mol Sci. 2023 Mar;24(6):5651.
+
+doi: 10.3390/ijms24065651
+journal_title: International Journal of Molecular Sciences
+journal_nlm_ta: Int J Mol Sci
+publisher_name: MDPI
+
+keywords:
+- Alzheimer’s disease
+- ulcerative colitis
+- PPARG
+- NOS2
+- shared gene
+- bioinformatics
+
+---

figures/PMC10067640__fimmu-14-1123913-g003.yml

@@ -0,0 +1,27 @@
+---
+pmcid: PMC10067640
+image_filename: fimmu-14-1123913-g003.jpg
+figure_link: /pmc/articles/PMC10067640/figure/f3/
+number: Figure 3
+figure_title: ''
+caption: GO and pathway enrichment analysis of CORGs. (A) GO enrichment analysis of
+  CORGs. Pathway enrichment analysis of CORGs in the KEGG database (B), REACTOME database
+  (C), and WikiPathways database (D). CORGs, COVID-19-related differentially expressed
+  genes; GO, Gene Ontology; BP, biological process; CC, cellular component; MF, molecular
+  function.
+article_title: Exploration of the common genetic landscape of COVID-19 and male infertility.
+citation: Yinwei Chen, et al. Front Immunol. 2023;14:1123913.
+
+doi: 10.3389/fimmu.2023.1123913
+journal_title: Frontiers in Immunology
+journal_nlm_ta: Front Immunol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- COVID-19
+- SARS-CoV-2
+- male infertility
+- DNA damage
+- immune
+
+---

figures/PMC10068260__gr6.yml

@@ -0,0 +1,28 @@
+---
+pmcid: PMC10068260
+image_filename: gr6.jpg
+figure_link: /pmc/articles/PMC10068260/figure/fig6/
+number: Fig. 6
+figure_title: ''
+caption: The Wnt-signaling pathway is downregulated after SD at all ages but more
+  dramatically at P24. Wnt-signaling pathways adapted from KEGG (mmu04310) and WikiPathways.
+  Genes in blue are downregulated after SD in all ages. Genes colored in lime green
+  are downregulated after SD only in P24. (For interpretation of the references to
+  color in this figure legend, the reader is referred to the Web version of this article.)
+article_title: Ontogenesis of the molecular response to sleep loss.
+citation: Christine M. Muheim, et al. Neurobiol Sleep Circadian Rhythms. 2023 May;14:100092.
+
+doi: 10.1016/j.nbscr.2023.100092
+journal_title: Neurobiology of Sleep and Circadian Rhythms
+journal_nlm_ta: Neurobiol Sleep Circadian Rhythms
+publisher_name: Elsevier
+
+keywords:
+- RNA
+- Gene
+- Molecular
+- Sleep deprivation
+- Postnatal
+- Sleep regulation
+
+---

figures/PMC10070855__fimmu-14-961642-g004.yml

@@ -0,0 +1,32 @@
+---
+pmcid: PMC10070855
+image_filename: fimmu-14-961642-g004.jpg
+figure_link: /pmc/articles/PMC10070855/figure/f4/
+number: Figure 4
+figure_title: ''
+caption: 'Bar graphs showing pathway enrichment analysis of DEGs shared by SARS-CoV-2,
+  AKI, and CKD as performed by Enricher: (A) KEGG 2019 human pathway, (B) WikiPathways,
+  and (C) BioCarta. Each bar represents a pathway in KEGG/WikiPathways/BioCarta. DEGs,
+  differentially expressed genes; SARS-CoV-2, severe acute respiratory syndrome coronavirus
+  2; AKI, acute kidney injury; CKD, chronic kidney disease; KEGG, Kyoto Encyclopedia
+  of Genes and Genomes.'
+article_title: Identification of common molecular signatures of SARS-CoV-2 infection
+  and its influence on acute kidney injury and chronic kidney disease.
+citation: Weiwei Zhang, et al. Front Immunol. 2023;14:961642.
+
+doi: 10.3389/fimmu.2023.961642
+journal_title: Frontiers in Immunology
+journal_nlm_ta: Front Immunol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- SARS-CoV-2
+- acute kidney injury
+- chronic kidney disease
+- differentially expressed genes
+- gene ontology
+- protein-protein interaction
+- hub gene
+- drug molecule
+
+---

figures/PMC10072901__circrep-5-114-g004.yml

@@ -0,0 +1,36 @@
+---
+pmcid: PMC10072901
+image_filename: circrep-5-114-g004.jpg
+figure_link: /pmc/articles/PMC10072901/figure/F4/
+number: Figure 4
+figure_title: ''
+caption: (A) Detection of differentially expressed genes (DEGs) in the left atrium
+  of patients with atrial fibrillation (AF-LA) compared with patients with sinus rhythm
+  (Sinus-LA) using a volcano plot showing fold changes (AF-LA/Sinus-LA gene expression)
+  relative to the P value of the comparison. In this figure, the filter criterion
+  is P<0.05. All false discovery rate-corrected P values <0.2. Red dots indicate upregulated
+  genes; green dots indicate downregulated genes; and gray dots indicate the genes
+  that did not pass the filter criterion. (B) The Transcriptome Analysis Console was
+  used to summarize those upregulated (red) and downregulated (green) genes in WikiPathways.
+  The summary image is based on the original images for “Senescence and autophagy
+  in cancer (Homo sapiens)” (B) and “Autophagy (Homo sapiens)” (C) in WikiPathways.
+  WikiPathways content is covered by the Creative Commons CC0 waiver, which states
+  that we are free to share (copy, distribute and transmit) and remix (adapt) the
+  work.
+article_title: Transcriptome Discovery of Genes in the Three Phases of Autophagy That
+  Are Upregulated During Atrial Fibrillation.
+citation: Takahiro Kamihara, et al. Circ Rep. 2023 Apr 10;5(4):114-122.
+
+doi: 10.1253/circrep.CR-22-0130
+journal_title: Circulation Reports
+journal_nlm_ta: Circ Rep
+publisher_name: The Japanese Circulation Society
+
+keywords:
+- Atrial fibrillation
+- Autophagosome
+- Autophagy
+- Computational biology
+- Lysosome
+
+---

figures/PMC10079989__fimmu-14-1104560-g004.yml

@@ -0,0 +1,29 @@
+---
+pmcid: PMC10079989
+image_filename: fimmu-14-1104560-g004.jpg
+figure_link: /pmc/articles/PMC10079989/figure/f4/
+number: Figure 4
+figure_title: ''
+caption: GSVA analysis of DEGs in the inflammatory DAMPs and nuclear DAMPs subtype.
+  (A) GSVA analysis of canonical pathways (BIOCARTA, KEGG, PID, REACTOME and WIKIPATHWAYS)
+  for patients in the inflammatory DAMPs and nuclear DAMPs subtype. (B) GSVA analysis
+  of gene ontology (GO) for patients in the inflammatory DAMPs and nuclear DAMPs subtype.
+  (C) GSVA analysis of hallmark gene sets for patients in the inflammatory DAMPs and
+  nuclear DAMPs subtype.
+article_title: Damage-associated molecular patterns and sensing receptors based molecular
+  subtypes in malignant pleural mesothelioma and implications for immunotherapy.
+citation: Zheng Liu, et al. Front Immunol. 2023;14:1104560.
+
+doi: 10.3389/fimmu.2023.1104560
+journal_title: Frontiers in Immunology
+journal_nlm_ta: Front Immunol
+publisher_name: Frontiers Media S.A.
+
+keywords:
+- malignant mesothelioma
+- damage-associated molecular patterns
+- immunogenic cell death
+- immunotherapy
+- tumor microenvironment
+
+---

figures/PMC10104258__nihpp-rs2688729v1-f0003.yml

@@ -0,0 +1,30 @@
+---
+pmcid: PMC10104258
+image_filename: nihpp-rs2688729v1-f0003.jpg
+figure_link: /pmc/articles/PMC10104258/figure/F3/
+number: Figure 3
+figure_title: ''
+caption: Network diagram of the main intracellular processes affected. Genes involved
+  in different intracellular processes are shown as rectangles in red (upregulated)
+  or blue (downregulated) according to their expression from RNA-Seq profiles under
+  different conditions, insulin 100 nM for 2 h or aggregated LDL 100 μg/ml for 8 h.
+  Conditions are displayed at the top of each rectangle as black (insulin) or white
+  (aggLDL) squares. The network was manually adjusted to show the main genes obtained
+  in the unsupervised GO enrichment and WikiPathways analysis.
+article_title: Transcriptional analysis reveals that the intracellular lipid accumulation
+  impairs gene expression profiles involved in insulin response-associated cardiac
+  functionality.
+citation: Virginia Actis Dato, et al. Res Sq. 2023 Apr 4:rs.3.rs-2688729.
+
+doi: 10.21203/rs.3.rs-2688729/v1
+journal_title: Research Square
+journal_nlm_ta: Res Sq
+publisher_name: American Journal Experts
+
+keywords:
+- LRP1
+- aggregated low-density lipoprotein
+- transcriptome analysis
+- cardiovascular disease
+
+---