json
dict | jpg
imagewidth (px) 49
4.1k
| __key__
stringlengths 6
6
| __url__
stringclasses 29
values |
|---|---|---|---|
{
"caption": "Inhibiting exosome secretion disrupts NCC migration and morphology. (A) Workflow for Nexinhib20 (Nex20) treatment of NCCs prior to imaging and analysis. Diagram illustrates Nex20 inhibition of Rab27a, which prevents MVBs from docking to the plasma membrane and releasing exosomes into the extracellular space. (B–I) Vehicle (B–B‴,F–F‴) and 2.5 µM Nex20-treated (C–C‴,G–G‴) neural fold cultures (B,C) or NCCs (F,G) stained for HNK-1 (migratory NCCs, red), F-actin (cytoskeleton, green) and DAPI (nucleus, blue). (D,E) Box-and-whisker plots showing area occupied by migrating cells (D; P=3.8×10−3) and total number of cells migrated (E; P=7.0×10−7) in vehicle (n=5 folds) and 2.5 µM Nex20 (n=6 folds)-treated neural fold cultures. (H,I) Box and whisker plots showing aspect ratio (H; P=2.0×10−4) and circularity (I; P=3.0×10−2) in vehicle (n=252 cells) and 2.5 µM Nex20 (n=223 cells)-treated NCCs. Scale bars: 100 µm (B,C); 10 µm (F,G). For the box-and-whisker plots, the box represents the 25–75th percentiles, and the mean is indicated. The whiskers show the 10th and 90th percentile outlier range. All P-values were calculated with an unpaired one--tailed Student's t-test.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270958-1-joces-135-260272-g5.jpg"
}
|
008800
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Large extracellular vesicles released from NCCs are positive for multiple migrasome markers. (A) An NCC (A) expressing CD63–pH and stained with BODIPY ceramide with an inset panel (A′–A‴) to highlight a migrasome (white arrowheads) and retraction fiber (white arrow). Scale bar: 10 µm. (B–D) BODIPY ceramide and WGA co-stained NCCs with inset panels (B′–B‴,C′–C‴,D′–D‴) to show the colocalization of BODIPY ceramide and WGA in migrasomes (white arrowheads) and retraction fibers (white arrows). Scale bars: 10 µm. (E) NCCs stained with BODIPY ceramide and SYTO14, with inset panels to show colocalization (E′–E‴). Scale bars: 10 µm. Images are representative of three experiments.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270958-3-joces-135-260272-g3.jpg"
}
|
008801
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Cranial NCCs release and deposit CD63-positive vesicles into the extracellular environment. (A) Experimental workflow for electroporation, dissection, and culture of NCCs from neural fold explants. (B,C) Live neural fold cultures (B–B″) and migratory NCCs (C–C″) expressing pCMV-CD63-pHluorin (CD63–pH; exosomes, green) and stained with Hoechst 33342 (nucleus, blue). Scale bars: 100 µm (B); 10 µm (C). (D) Live NCC releasing a trail of CD63–pH-positive exosome deposits behind it. Scale bar: 10 µm. (E) 3 h time lapse frames (t=min) of cultured CD63–pH-expressing NCCs. Images represent maximum intensity projections. Scale bar: 10 µm. (F,G) Fixed neural fold cultures (F–F″″) and an individual NCC (G–G″″) expressing CD63–pH (green) and stained for HNK-1 (migratory NCCs, red), F-actin (cytoskeleton, white) and DAPI (nucleus, blue). Scale bars: 100 µm (F); 10 µm (G). Images are representative of three experiments.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270958-5-joces-135-260272-g1.jpg"
}
|
008802
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "The early area opaca can rescue the loss of regulative ability of primitive-streak-stage anterior half-embryos. (A,E) The anterior half of pre-primitive-streak-stage (‘early’) embryos spontaneously generates a primitive streak expressing cBRA (arrowhead, E) from either the left or right posterior edge. (B,F) In contrast, the anterior half of primitive-streak-stage (‘late’) embryos can no longer generate a primitive streak. (C,G) Replacing the anterior area opaca of a late anterior half-embryo with the equivalent region from an early donor rescues the regulative ability of the late-stage embryo fragment, generating a primitive streak (arrowhead, G). (D,H) As a control for the effects of manipulation itself, excision and replacement of the anterior area opaca of a late anterior half-embryo does not generate a primitive streak. (I,J,L-N) Conversely, grafting late anterior area opaca onto a younger host (I,M) reduces the regulative ability of the latter to a level comparable with anterior half-embryos deprived of the area opaca at the same stage (J,L,N). (K,O) The majority of late anterior half-embryos deprived of the area opaca do not form an ectopic primitive streak (L). (L) Quantification of the results. AO, area opaca; AP, area pellucida; MZ, marginal zone. Scale bar: 1 mm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270967-0-develop-149-200303-g4.jpg"
}
|
008803
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "A graft of posterior area opaca onto an isolated anterior half-embryo induces cVG1 expression and primitive streak formation. (A) Experimental design for B,C,E-G. (B) The posterior piece of area opaca (not expressing cVG1) is used as the donor for grafting (dotted line). (C) After 6 h, cVG1 is induced in the marginal zone adjacent to the graft (arrowhead). (D,H) When the area opaca of the isolated anterior half-embryo is cut in half and the left and right fragments exchanged (to swap the anterior and lateral aspects of the area opaca, D), an ectopic primitive streak with cBRA is induced (arrowhead, H). (E,F) After overnight culture, an ectopic primitive streak (cBRA expression) is generated near the graft (arrowhead, F), whereas control grafts (anterior area opaca) have no effect – the primitive streak forms from one edge of the isolated anterior half-embryo as it does in the absence of a graft (arrowhead, E). (G) Using donor tissue taken from GFP-transgenic embryos reveals no cellular contribution of the graft to the induced ectopic primitive streak (arrowhead, G). The proportion of embryos showing each illustrated morphology is indicated in each panel. AO, area opaca; AP, area pellucida; MZ, marginal zone. Scale bar: 1 mm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270967-1-develop-149-200303-g3.jpg"
}
|
008804
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Excision of area opaca from an isolated anterior half-embryo biases cVG1 expression and primitive streak formation. (A-D) Experimental design (A). Isolated anterior half-embryos are cultured after excision of either the right (RE; for C) or left (LE; for B,D) edge of the area opaca. Embryos were processed for expression of cVG1 after 6 h (B) or cBRA (primitive streak) after overnight culture (C,D). After 6 h, cVG1 is expressed more strongly at the contralateral side to the excision (arrowhead, B), but weak cVG1 expression is also observed in the marginal zone lying immediately anterior to the excision site of area opaca (arrow, B). After overnight culture, a single primitive streak forms from the contralateral edge of the area pellucida (opposite the excision site; arrowhead, C,D). (E) Summary graph showing the number of embryos with different expression (exp.) patterns. Asterisks indicate site of excision. AO, area opaca; AP, area pellucida; MZ, marginal zone. Scale bar: 1 mm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270967-3-develop-149-200303-g2.jpg"
}
|
008805
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Salt-induced PME activation is inhibited by CaCl2 and EGCG application. (A) Root growth rate elongation in 7-day old Col-0 seedlings treated with mock, 125 mM NaCl (‘N’), 5 mM CaCl2 or a combination of NaCl/CaCl2 (‘NC’). Root growth rate elongation in 7-day-old Col-0 seedlings treated with mock, 125 mM NaCl, 5 mM CaCl2 or a combination of NaCl/CaCl2. Root growth rate is expressed as a ratio between NaCl and mock (‘N’) or NaCl/CaCl2 and mock (‘NC’). Each of the dots represent the average length of two independent experiments (n=30 seedlings per treatment). Statistical comparisons were performed by using a Levene's test, followed by two-tailed, unpaired t-test; *P<0.05. (B) PME activity analyzed in 5 μg protein extracts spotted on plates containing highly methyl-esterified pectins with water (mock), 100 mM NaCl, 50 μM EGCG, a combination of NaCl and EGCG (NaCl/EGCG), 5 mM CaCl2, a combination of NaCl and CaCl2 (NaCl/CaCl2), or 100 mM NaNO3. Error bars indicate s.d. n=3. One-way ANOVA and Tukey's HSD (α=0.05) were used to compare treatments. Different letters indicate statistical significance between groups. (C) Six-day-old Arabidopsis Col-0 were treated for 24 h with water (mock, ‘m’), 100 mM NaCl (‘N’), 5 mM CaCl2 (‘C’) or a combination of NaCl/CaCl2 (‘NC’) (n=3) or DMSO (‘D’), 100 mM NaCl (‘N’), 50 μM EGCG (‘E’) or a combination of NaCl/EGCG (‘NE’) (n=3). Five micrograms of total sugars were extracted and dot blots performed using the 2F4 antibody.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270968-2-develop-149-200363-g4.jpg"
}
|
008806
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Contact-mediated induction of mCherry in chimaeric blastocysts. (A) Chimaeric blastocysts containing STC clone B1 receiver cells and/or CmGP1GH1 sender cells. The images of the three embryos were taken from the same z-plane of a confocal stack and come from a single field of view. Nuclei were counterstained with DRAQ7. Scale bars: 30 µm. (B) Quantification of embryos containing cells expressing readily detectable levels of mCherry (‘mCherry-HI’) across all experiments. Embryos containing both sender and receiver cells were used as a reference for scoring sender-only chimaeras, receiver-only chimaeras and wild-type embryos.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270970-2-develop-149-200226-g6.jpg"
}
|
008807
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Cotyledon vein defects of cvp2 cvl1. (A,B) Cleared 7-day-old cotyledons from WT and cvp2 cvl1 mutants imaged with a stereomicroscope in bright field on a black background. White arrows indicate vein gaps. (C) Quantification of the frequency of ground meristem cells surrounding a disconnected vascular island (gap frequency) and vein complexity in WT and cvp2 cvl1 cotyledons. n=23-40 for each genotype. This quantification is part of the experiment represented in Fig. 5E,F. (D-G) Confocal microscopy analysis of the vein pattern of mature embryonic cotyledons (vein network at its complete stage) of WT and cvp2 cvl1 having undergone mPS-PI staining. E and G are magnifications of D and F, respectively. White arrows indicate vein gaps. Note that the picture shown in D is the same as the one that appears in Fig. 1E. (H-K) ATHB8::GUS expression in WT and cvp2 cvl1 mature embryonic cotyledons. I and K are magnifications of the veins displayed in H and J, respectively. White arrows indicate vein gaps. (L-P) Expression pattern of CVL1::GUS and CVP2::GUS in embryos. Magnification of an embryonic cotyledon (N) displaying CVP2 expression in the proximal branching points is shown in O and P. White arrows indicate branching points. (Q-S) mPSI-PI staining of mature embryonic cotyledons of WT and cvp2 cvl1 showing distal versus proximal branching. White arrows indicate the presence or absence of branching points. Note the two phenotypes observed in cvp2 cvl1 mutants when there is a third branching event (R) or not (S). (T) Quantification of the frequency of the reduced vein complexity observed in each genotype. n=23-40. BP, branching points, counted as the initiation (even if not completed) of a new secondary vein. Images are representative of two independent experiments. Scale bars: 500 µm (A,B); 200 µm (H,J,L,M); 100 µm (N); 50 µm (D,F,I,K,O,P,Q-S); 20 µm (E,G).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-0-develop-149-200403-g2.jpg"
}
|
008808
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Silencing of RPK2 expression rescues the branching defects of cvp2 cvl1. (A-D) Analysis of the continuity and complexity of the cotyledon vein network in 7-day-old seedlings from the indicated genetic backgrounds. White arrows indicate vein gaps, and yellow arrows indicate proximal branching. (E-G) Quantification of gap (E), vein complexity (F) and branching (G) frequencies observed in the cotyledons of the plants shown in A-D. n=23-50 for each genotype. BP, branching points. (H-K′) mPS-PI-stained embryos displaying the vein pattern of the indicated genotypes. H′,I′,J′ and K′ show magnified views of the squared regions in H,I,J and K, respectively. Yellow arrows mark proximal branching and the red arrow marks the lack of proximal branching. (L-M′) Confocal microscopy analysis of RPK2 expression in the cotyledons of torpedo embryos from the indicated genotypes stained with SR2200. L′ and M′ show only the GFP signal. White arrows indicate the localization of RPK2::NLS-3×VENUS in the cell. Images are representative of two experiments. Scale bars: 200 µm (A-D); 50 µm (J,J′); 20 µm (H-I′,K,K′,L-M′).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-1-develop-149-200403-g5.jpg"
}
|
008809
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "PIN-mediated auxin transport modulates distal branching but not vein continuity in embryonic cotyledons. (A-G) Representative images of 7-day-old cleared cotyledons of the indicated genotypes. Note that pin1 single mutants are in a Ler background. Magnification of the midvein region where distal branching occurs in pin1-5 (C) is displayed in G. (H,I) Quantification of branching (H) and gap (vascular discontinuities) (I) frequency in the indicated genotypes. n=12-28 for each genotype. BP, branching points, counted as the initiation (even if not completed) of a new secondary vein. (J-M) Auxin distribution analyzed by DR5 expression in WT (J,K) and cvp2 cvl1 (L,M) embryonic cotyledons counterstained with SR2200. K and M display only the GFP signal. White arrows indicate the absence of the marker in the vein gaps. (N-Q) Representative images of 7-day-old cleared cotyledons of the indicated genotypes. Orange arrows mark extra branching points, red arrows indicate the absence of proximal branching formed in a tip-to-base manner and white arrows mark gaps. (R-S) Quantification of branching (R) and gap (S) frequencies in the indicated genotypes. n=21-54 for each genotype. BP, branching points, counted as the initiation (even if not completed) of a new secondary vein. Images are representative of two experiments. Scale bars: 200 µm (A-F); 20 µm (J-M).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-2-develop-149-200403-g4.jpg"
}
|
008810
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Polar distribution of PIN1 is not affected in cvp2 cvl1 mutants. (A-D′) Confocal microscopy analysis of early torpedo stage embryos of the indicated genotypes stained with SR2200 showing PIN1-GFP distribution in distal secondary veins as they progressively form upwards. Magnifications of the region in red squares in A and C are shown in B,B′ and in D,D′, respectively. White arrows indicate the polar distribution of PIN1 in the cell. (E,F) Quantification of the polar distribution of PIN1-GFP in procambial and protophloem cells as a ratio of the GFP signal detected in the basal membrane (BM) versus the lateral membrane (LM). Data are shown as mean±s.d. NS, not significant (two-tailed paired Student's t-test). (G-J′) 6-day-old roots harboring PIN1::PIN1-GFP in WT and cvp2 cvl1 backgrounds showing PIN1 localization and strong basal polarization in the protophloem strand. Magnification of differentiating cells in the protophloem in WT (G) and cvp2 cvl1 (I) are shown in H,H′ and J,J′, respectively. White arrows indicate the polar distribution of PIN1 in the cell. (K,L) Representative images of 7-day-old cleared cotyledons of the indicated genotypes. White arrows indicate vein gaps. (M,N) Quantification of gap frequency (M) and branching (N) in the indicated genotypes. n=32-51 for each genotype. BP, branching points. Images are representative of two experiments. Scale bars: 50 µm (A-D′,G,I); 20 µm (H,H′,J,J′); 200 µm (K,L).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-3-develop-149-200403-g3.jpg"
}
|
008811
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "OPS promotes proximal branching in WT and cvp2 cvl1 embryonic cotyledons. (A-D) Representative images of cleared 8-day-old cotyledons from the indicated genotypes imaged with a stereomicroscope in bright field on a black background. White arrows mark vein gaps and yellow arrows indicate additional proximal branching sites. (E,F) Quantification of gap and branching frequency of the vein network phenotypes observed in the cotyledons represented in A-D. n=29-35 for each genotype. BP, branching points, counted as the initiation (even if not completed) of a new secondary vein. (G,H) mPS-PI-stained embryos visualized by confocal microscopy for the indicated genotypes. White arrows (G) indicate vein gaps, yellow arrows (H) indicate proximal branching points. (I-L′) Visualization of OPS distribution in early (I-J′) and late (K-L′) torpedo stage embryos stained with SR2200. J and L show magnified views of the branching regions shown in I and K, respectively. In I′,J′,K′ and L′, only the GFP signal is shown. White and yellow arrows show polar and non-polar distributions of OPS in the cell, respectively. (M) Quantification of OPS polarity in cells from early and late torpedo stages as the mean±s.d. of the ratio of the GFP signal between the apical membrane (AM) and lateral membrane (LM). *P<0.1 (two-tailed paired Student's t-test). Scale bars: 200 μm (A-D); 20 µm (G,H); 50 µm (I,I′,K,K′); 20 µm (J,J′,L,L′).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-4-develop-149-200403-g7.jpg"
}
|
008812
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Vein progression and branching in torpedo embryos. (A,B) Representative pictures of mPS-PI-stained cell walls of embryos in the late transition stage (A) and late heart stage (B). (C,D) Analysis by confocal microscopy of extracted embryos from ovules and stained with the cell-wall dye SR2200. (C) Embryo in transition between the heart and early torpedo stages in which the future midvein is marked by a white arrow. (D) Cotyledon of early torpedo stage in which the secondary vein formation can be detected. Note that, in D, based on the elongated morphology of procambial cells, secondary vein formation is initiated from the midvein and progresses upwards towards the top of the cotyledon (marked by white arrows). (E) Cotyledon of a mature embryo in which the cotyledon vein network is completed. (F-I) Representative images of PIN1::PIN1-GFP early and late torpedo stage embryos stained with the cell-wall dye SR2200 showing the progression of midvein or primary vein (F), distal secondary vein (G,H) and proximal secondary vein (I) formation. Dashed red arrows represent the directionality of the forming veins. (J,K) Cotyledons from early torpedo stage embryos harboring DR5::NLS-VENUS showing the progression of distal secondary veins (J) as well as the initiation of the proximal secondary veins (K). (L-N) Early torpedo stage embryos harboring MP::MP-GFP (L) or BAM3::NLS-3×VENUS (M,N) showing cotyledon proximal vein formation occurring in a tip-to-base manner, except in N, in which proximal vein formation also proceeds in a base-to-tip manner. (O) Scheme representing the proposed branching sites of distal and proximal secondary veins. Distal branching points 1 and 2 are represented by the red dots and the direction of vein formation is represented by the white arrows. Proximal secondary vein branching, branching points 3 and 4 (red dots) and the direction of vein formation (white arrows) are represented in the lower panels. Note that distal versus proximal secondary vein formation occurs normally in opposing directions. The appearance of proximal veins in a base-to-tip manner is represented by a dashed white arrow. (P-R) Representative images of proximal and distal branching in embryonic cotyledons stained with mPS-PI and visualized by confocal microscopy. ADB, after distal branching; BDB, before distal branching. White arrows indicate proximal branching points. (S-U) Quantification of the frequency of appearance of the indicated number of cell files (S), average midvein width (T) and average midvein cell-file width (U) in the regions marked ADB and BDB in P. Note that the differences represented in T are not due to differences in the widths of procambial cells in these regions, as indicated in U. Data are shown as mean±s.d. NS, not significant; ***P<0.01 (two-tailed paired Student's t-test). Images are representative of two experiments. Scale bars: 20 µm (A-D,F,G,J-M,P-R); 50 µm (E,H,I,N).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270971-6-develop-149-200403-g1.jpg"
}
|
008813
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Chondrogenesis and osteogenesis defects in ncl−/− embryos. (A) qPCR revealed a significant downregulation of sox9a and col2a1 chondrogenesis markers in 36 hpf ncl−/− embryos compared with ncl+/+ embryos (n=10 per replicate). actb was used as a housekeeping control. (B,B′) Sox9a protein expression was significantly reduced in branchial arches 2-5 (white arrows) in ncl−/− embryos at 36 hpf (n=15). (C) qPCR of osteogenesis markers in 36 hpf ncl+/+ and ncl−/− embryos indicates significant upregulation in runx2a transcripts and downregulation in both col1a2 and col10a1 transcripts in ncl−/− embryos (n=10 per replicate). (D,D′) runx2a mRNA expression was significantly increased ncl−/− embryos at 3 dpf (n=15). Black arrows indicate expression of runx2a in the ceratohyal and otic vesicles. (E,E′) At 3 dpf, Runx2 protein expression was significantly increased in the palatoquadrate and the parasphenoid in ncl−/− embryos. (F) qPCR indicates a significant upregulation of the early osteoblast markers bglap and spp1 and downregulation of the late osteoblast marker sp7 in 36 hpf ncl−/− embryos compared with controls (n=10 per replicate). (G-H′) Alkaline phosphatase staining of ncl+/+ and ncl−/− embryos reveals reduced staining in the lower jaw (ventral view, black arrows) at 3 dpf (G,G′) and 5 dpf (H,H′) (n=15). All experiments were performed three times. cb, ceratobranchial. Scale bars: 200 µm (B,B′); 100 µm (D-E′,G,G′); 140 µm (H,H′). Data are represented as mean±s.d. ns, not significant; *P<0.05 (two-tailed, paired Student's t-test).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-0-develop-149-200349-g4.jpg"
}
|
008814
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Nucleolin is required for rRNA transcription and p53 regulation. (A) qPCR for 5′ETS, ITS1, ITS2 and 18S segment of the pre-rRNA in ncl+/+ and ncl−/− zebrafish (n=10 per sample) indicates that rRNA transcripts were significantly lower in ncl−/− embryos compared with their ncl+/+ siblings. canx was used as an internal control. (B) RNA immunoprecipitation (RIP) using a Nucleolin-specific antibody indicates that Nucleolin binds to the 5′ETS and ITS1 region of the 47S rRNA but not to the ITS2 or 18S in wild-type zebrafish (n=100 per replicate and condition). The y-axis indicates fold change of RNA pulldown compared with its absolute expression in the embryos. (C) p53 transcript expression was not significantly altered in ncl−/− mutant zebrafish between 18 and 36 hpf; however, expression of its downstream target p21 was significantly higher between 24 and 30 hpf in the ncl−/− mutants compared with wild-type zebrafish (n=5 per sample). (D) Nucleolin and IgG binding to p53 mRNA was similar in wild-type zebrafish, as observed by RNA immunoprecipitation (n=100 per replicate and condition). The y-axis indicates fold change of RNA pulldown compared with its absolute expression in the embryos. (E) p53 protein levels were higher in ncl−/− mutants at 24 hpf compared with their ncl+/+ siblings and comparable between ncl+/+ and ncl−/− embryos at 36 hpf as observed by western blotting (n=5 per sample). γ-tubulin was used as a loading control. (F) Immunoprecipitation (IP) with a Nucleolin-specific antibody followed by western blotting for p53 and Nucleolin indicates that p53 and Nucleolin bind to each other in wild-type zebrafish (n=25 per replicate and condition). (G) In ncl−/− mutants, Nucleolin expression was significantly reduced compared with controls (n=25 per replicate). α-tubulin was used as a loading control. (H) At 28 hpf, control zebrafish displayed higher binding of Mdm2 and p53 compared with that seen in mutant zebrafish (n=25 per replicate and condition). (I) Quantification of p53 protein levels in 24 hpf and 36 hpf ncl+/+ and ncl−/− embryos (n=3). (J) Quantification of p53-Mdm2 binding in ncl+/+ and ncl−/− embryos (n=3). (K-L′) ncl−/− mutants have more TUNEL+ cells (red in K,L; white in K′,L′) at 24 hpf compared with their ncl+/+ siblings (n=15 per genotype). (M-N′) By 36 hpf, apoptosis (red in M,N; white in M′,N′) is confined to the midbrain-hindbrain boundary in both ncl+/+ and ncl−/− embryos (n=15 per genotype). (O-P′) On a p53−/− mutant background, the number of TUNEL+ cells (red in O,P; white in O′,P′) in both ncl+/+ and ncl−/− embryos (n=15 per genotype) at 24 hpf is reduced. All experiments were performed three times. Scale bars: 70 µm. Data are represented as mean±s.d. in A-D; circles and squares represent individual data points and horizontal lines represent the mean in I,J. ns, not significant; *P<0.05 (two-tailed, paired Student's t-test).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-1-develop-149-200349-g3.jpg"
}
|
008815
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "ncl−/− mutants exhibit craniofacial defects. (A,B) Compared with 24 hpf ncl+/+ clutch mates, ncl−/− mutants had necrotic tissue (indicated by black arrows) in the craniofacial region (n=25). (C,D) By 36 hpf, the frontonasal prominence and midbrain-hindbrain boundary were misshapen in ncl−/− mutants compared with their ncl+/+ siblings (indicated by black arrows) (n=50). The craniofacial region is magnified in C′,D′. (E,F) At 3 dpf, the ncl−/− mutants had smaller jaws and a misshapen head (indicated by black arrows) (n=15). The craniofacial region is magnified in E′,F′. (G,H) Skeletal preparations of 5 dpf wild-type and ncl−/− mutant zebrafish reveal defects in the cartilages of the jaw (n=50). (I,J) In the neurocranium, the chondrocytes in the ethmoid plate were delayed in development, and the trabeculae were smaller and wider compared with the wild-type zebrafish at the same stage. (K,L) Magnified images of the ethmoid plate showing differential Alcian Blue staining, as well as the loss of medial cells in ncl−/− larvae. (M) Quantification of the length of trabecula in ncl+/+ and ncl−/− embryos as a ratio of the length of the head measured from the anterior-most point of the ethmoid plate to the posterior-most point of the parachordal (pc) (n=10). Horizontal lines represent the mean. *P<0.05 (two-tailed, paired Student's t-test). (N,O) In the viscerocranium, Meckel's cartilage was bent, the basihyal was missing, the polarity of the ceratohyal was inverted and the ceratobranchials were hypoplastic. In addition, the mutants had hypoplastic teeth and the 4V1 teeth were missing. The experiment was performed three times. ep, ethmoid plate; t, trabecula; pc, parachordal; m, Meckel's cartilage; bh, basihyal; ch, ceratohyal; cb, ceratobranchial. Scale bars: 200 µm (A-F); 50 µm (C′-F′); 70 µm (G-J,N,O); 25 µm (K,L).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-2-develop-149-200349-g2.jpg"
}
|
008816
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Nucleolin regulates Fgf8a expression. (A) Immunostaining of 36 hpf ncl+/+ and ncl−/− embryos with an Fgf8a-specific antibody reveals reduced expression of Fgf8a in ncl−/− embryos (n=15). (B) qPCR using craniofacial tissues from ncl+/+ and ncl−/− embryos at 18, 24, 30 and 36 hpf indicates that ncl and fgf8a expression gradually reduce over time (n=10 per replicate). (C) RNA immunoprecipitation followed by qPCR indicates higher binding of fgf8a mRNA to Nucleolin compared with the IgG control. actb was used as a negative control (n=100 per replicate per condition). The y-axis indicates fold change of RNA pulldown compared with its absolute expression in the embryos. (D-F) Skeletal preparations of 5 dpf ncl+/+ and ncl−/− larvae as controls (D) for 0.25 µg/µl (E) and 1 µg/µl (F) FGF8 exogenous treatment. Exogenous FGF8 rescued the cranioskeletal phenotype of ncl−/− larvae (n=45). Black arrows indicate the improvement of the basihyal phenotype in FGF8-treated larvae. All experiments were performed three times. Scale bars: 100 µm (A); 70 µm (D-F). Data are represented as mean±s.d. ns, not significant; *P<0.05 (two-tailed, paired Student's t-test).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-3-develop-149-200349-g5.jpg"
}
|
008817
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "FGF8 rescues rRNA transcription in ncl−/− embryos. (A) qPCR for 5′ETS, ITS1, ITS2 and 18S in untreated and FGF8-treated ncl+/+ and ncl−/− zebrafish (n=10 per sample) indicates rescue of pre-RNA transcription in FGF8-treated ncl−/− zebrafish at 36 hpf. (B) TUNEL staining of untreated and FGF8-treated ncl+/+ and ncl−/− zebrafish at 28 hpf indicates reduced TUNEL+ cells in FGF8-treated ncl−/− embryos compared with untreated ncl−/− embryos (n=15). (C) qPCR for bmp2 in 36 hpf ncl+/+ and ncl−/− embryos (n=10 per sample) that were untreated or treated with 1 µg/µl FGF8 indicates significant downregulation in bmp2 in untreated ncl−/− embryos and significant upregulation in FGF8-treated ncl+/+ embryos. In FGF8-treated ncl−/− embryos, the bmp2 transcript levels were rescued and comparable with untreated ncl+/+ embryos. actb was used as a housekeeping control. (D) Skeletal preparations of 5 dpf ncl+/+ and ncl−/− larvae that were untreated or treated with FGF8, BMH21, FGF8+BMH21 or BMP2. Exogenous FGF8 and BMP2 treatment rescued the cranioskeletal phenotype of ncl−/− larvae (n=45). All experiments were performed three times. Scale bars: 100 µm (B); 70 µm (D). Data are represented as mean±s.d. *P<0.05 (two-tailed, paired Student's t-test).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-4-develop-149-200349-g6.jpg"
}
|
008818
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Ncl expression during zebrafish development. (A) During embryogenesis, Nucleolin (Ncl, red) was ubiquitously expressed in the cytoplasm of four-cell stage wild-type embryo at 1.5 hpf as observed by immunostaining. (B) Similarly, 3 hpf embryos also had ubiquitous cytoplasmic expression of Nucleolin. (C,C′) At 12 hpf, ncl+/+ and ncl−/− embryos exhibited similar Nucleolin expression in the nucleus and cytoplasm in most cells of the embryos. (D-D″) At 18 hpf, the expression of Nucleolin in ncl+/+ embryos was ubiquitous and was confined to the nucleus (D″). In the ncl−/− embryos, the expression pattern of Nucleolin was similar to that of wild-type embryos; however, the expression levels were significantly lower than that of the wild type. (E,E′) By 24 hpf, the expression of Nucleolin was still ubiquitous, with higher levels in the eye and the midbrain-hindbrain boundary in ncl+/+ embryos, whereas it was absent in ncl−/− embryos. (F) At 36 hpf, the expression of Nucleolin became specific to the craniofacial region in the pharyngeal arches as well as the eye. (G) In 72 hpf (3 dpf) wild-type zebrafish, Nucleolin was highly expressed in the jaw of the embryo. (F′,G′) In the ncl−/− mutants, there was no expression of Nucleolin. n=15 for each panel. The experiment was performed three times. NT, neural tube. Scale bars: 35 µm (A,B); 70 µm (C,C′); 140 µm (D,D′); 50 µm (D″); 250 µm (E,E′); 300 µm (F,F′,G,G′).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270975-5-develop-149-200349-g1.jpg"
}
|
008819
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Differentially expressed genes in the testis and altered protein abundances in sperm in protamine-deficient males. (A) Number of differentially expressed genes subdivided into higher and lower expressed genes in testis of Prm1+/− and Prm1−/− males compared with WT males. (B) Venn diagram illustrating changes in abundances of proteins from sperm basic protein extractions of Prm1−/−, Prm1+/− and Prm2−/− males compared with WT. Proteins that were more abundant are in bold. Non-bold proteins showed lower abundance compared with WT. (C) IHC stainings against histone H3 (red) and PRM2 (green) of Prm1+/+, Prm1+/− and Prm1−/− caput epididymal tissue sections. DAPI (in gray) was used as the counterstain. The H3 stainings are additionally shown as single gray channel pictures. Scale bars: 50 µm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270976-0-develop-149-200330-g5.jpg"
}
|
008820
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Spermatogenesis of Prm1-deficient mice. (A) Mean testis weight of Prm1+/+, Prm1+/− and Prm1−/− males (n=8-10). (B) Mean diameter of seminiferous tubules of Prm1+/+, Prm1+/− and Prm1−/− mice (n=4); 25 tubules per mouse were evaluated. (C) Quantification of elongating spermatids per seminiferous tubule cross-section in Prm1+/+, Prm1+/− and Prm1−/− males (n=3). Five tubules per mouse were evaluated. (D) Hematoxylin and Eosin staining of testis of Prm1+/+, Prm1+/− and Prm1−/− males. Tubules at stages VII to VIII of the epithelial cycle with spermatozoa lining up at the edge of tubule lumen are marked by asterisks. (E) PAS staining of testis of Prm1+/+, Prm1+/− and Prm1−/− males. Acrosomal structures are indicated by vermillion arrowheads. Data are mean±s.d. and were analyzed using a two-tailed, unpaired Student's t-test. Scale bars: 50 µm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270976-1-develop-149-200330-g2.jpg"
}
|
008821
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Analysis of chromatin condensation and ROS-induced DNA damage in epididymal Prm1-deficient sperm. (A) Representative transmission electron micrographs of Prm1+/+, Prm1+/− and Prm1−/− epididymal sperm. (B) Quantification of DNA condensation of epididymal sperm from Prm1+/+, Prm1+/− and Prm1−/− males (n=3); 100 sperm per male were analyzed. (C) Transmission electron micrograph of Prm1−/− epididymal sperm. (D) Agarose gel loaded with genomic DNA isolated from epididymal sperm of Prm1+/−, Prm1−/−, Prm2+/−, Prm2−/− and WT males separated by electrophoresis. Additional lanes loaded with ladders (L) were cut from the image. (E) Percentage of 8-OHdG-positive sperm on tissue sections of caput and cauda epididymis of Prm1+/+, Prm1+/− and Prm1−/− mice (n=3). (F) Representative IF staining against 8-OHdG in testis, caput epididymis and cauda epididymis tissue sections from Prm1+/+, Prm1+/− and Prm1−/− males. Data are mean±s.d. and were analyzed using a two-tailed, unpaired Student's t-test (*P<0.05; **P<0.005). Scale bars: 2 µm in A,C; 50 µm in F.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270976-2-develop-149-200330-g3.jpg"
}
|
008822
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Establishment of Prm1-deficient mice and fertility analysis. (A) Graphical representation of CRISPR-Cas9-mediated gene editing of the Prm1 locus. Two sgRNAs were used (black arrowheads), targeting the Prm1 coding sequence in exon 1 and exon 2, respectively. A 167 bp in-frame deletion was generated, leading to loss of crucial arginine-rich DNA-binding sites (marked in blue). The epitope of the anti-PRM1 antibodies used in (C) is marked in red. (B) Agarose gel of genotyping PCR of Prm1+/+, Prm1+/− and Prm1−/− mice. Amplification of WT Prm1 or the Prm1− allele generated products of 437 bp or 270 bp, respectively. (C) IHC staining against PRM1 and PRM2 on Bouin-fixed, paraffin-embedded testis sections of Prm1+/+, Prm1+/− and Prm1−/− mice counterstained with Hematoxylin. (D) Mendelian distribution of genotypes (n=10 litters) from crossings of Prm1+/− males and females. (E) Scatter plot of mean litter sizes monitored per male after mating with female WT C57BL/6J mice. The mean litter size per genotype is indicated by vermillion lines. (F) Pregnancy frequency (%) per male after mating with female WT C57BL/6J mice. n=number of males used; data are means and were analyzed using a two-tailed, unpaired Student's t-test (***P<0.001). Scale bars: 50 µm. L=ladder.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270976-4-develop-149-200330-g1.jpg"
}
|
008823
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Dynamics and mechanism of CD34+ HSPC homing. (a) Schematic illustration of the homing dynamics of HSPCs (red) into BMOs (magenta/beige/gray). (b) Representative confocal images of CFSE-labeled HSPCs (CFSE, green) and the network (CD31, magenta) within BMOs (DAPI, blue) at 4, 8, 12, 16, 20, 24, 48, 72, and 96 h after seeding of HSPCs. The maximum intensity projections of z-stack acquisitions are shown. Scale bar, 100 μm. (c) Quantitative analysis of the number of CFSE+ cells per BMO over time. Results of two independent experiments. Symbols indicate mean values, and the error bars show the standard deviations. (d) Representative confocal images of the inhibition of homing of HSPCs into BMOs 24 h after seeding (left panel). The purified HSPCs (CFSE, green) are treated with either AMD3100 or SB290157 before seeding on BMOs. In the third condition, BMOs are treated with anti-PTN before seeding of the HSPCs to negatively influence the migration behavior of the HSPCs. The network is marked with CD31 (magenta) and the nuclei with DAPI (blue). The maximum intensity projections of z-stack acquisitions are shown. Scale bar, 100 μm. The number of homed CFSE+ cells is quantified per BMO per treatment (right panel). Violin plots represent the distributions, red horizontal lines indicate the medians, and black dotted lines the quartiles. Results of two independent experiments. Statistical analysis by ordinary one-way ANOVA and multiple comparisons.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-0-ABPID9-000006-036101_1-g005.jpg"
}
|
008824
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Self-renewing and differentiated MSCs in bone marrow organoids. (a)–(c) Representative immunofluorescence images of the expression of mesenchymal markers (a) nestin (NES, orange), (b) transgelin (TAGLN, orange), and (c) endoglin (ENG, orange) in BMOs cultured for seven days. Maximum intensity projection of z-stack confocal images. Scale bars, 100 μm. (d) Representative flow diagrams show the percentage of ENG+ and CD146+ cells of the CD71−/CD31−/CD45− population in the three different conditions (100/0, 75/25, 50/50). (e) Representative single-plane images of histological stainings of the 75/25 BMO condition cultured for seven days. The morphology is represented by hematoxylin and eosin (HE) staining and Oil Red O (ORO) stained lipid droplets. The Alcian blue (AB) staining marks acidic polysaccharides, such as glycosaminoglycans, and alizarin red (AR) detects calcium deposits. Periodic Acid Schiff (PAS) stains for polysaccharides, Sirius red (SR) stains for collagen, Marius Scarlett Blue (MSB) stains for fibrin, and Miller (M) stains for elastin. Scale bar, 100 μm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-1-ABPID9-000006-036101_1-g002.jpg"
}
|
008825
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Establishment of a self-organized, network-like structure. (a) Representative single-plane confocal images of the endothelial marker CD31 (magenta) and DAPI (blue) in different BMOs (100/0, 75/25, 50/50). Scale bar, 100 μm. (b) Representative flow diagrams show the percentage of CD31+ cells among all live cells of BMOs from the different conditions (100/0, 75/25, 50/50). (c) 3D visualization (maximum intensity projection) of a z-stack image of CD31 (top panel) and the resulting rendered data (bottom panel) of the self-organized endothelial network-like structure in the BMO condition 75/25. Scale bar, 100 μm. (d)–(f) Quantification of the network architecture by estimating (d) the volume, (e) the number of branches, and (f) junctions. Results from four independent experiments. (g) Representative images of the endothelial marker CD31 in BMOs at day 4–7. Maximum intensity projection of z-stack confocal images. Scale bar, 100 μm. (h)–(j) Quantification of the endothelial network (h) volume, (i) branches, and (j) junctions at different time points (day 4–7). Results of three independent experiments. (d)–(f) and (h)–(j) Violin plots show medians (red dashed line) and quartiles (black dotted lines). Statistical analysis by ordinary one-way ANOVA and multiple comparisons. **p <0.01; ****p <0.0001.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-2-ABPID9-000006-036101_1-g003.jpg"
}
|
008826
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Bone marrow organoids as a 3D migration assay. (a) Schematic representation of the seeding of HSPCs (red) onto BMOs on day 3 and the subsequent analysis of efficiently homed HSPCs on day 7. (b) Representative confocal images of the HSPCs (CD45, green) and the network (CD31, magenta) in BMOs (DAPI, blue) from the three conditions (100/0, 75/25, 50/50). The maximum intensity projections of z-stack acquisitions are shown. Scale bar, 100 μm. (c) Quantitative analysis of the percentage of homed CD45+ cells per BMO normalized to the initial number of seeded HSPCs. Violin plots represent the distributions, red horizontal lines indicate the medians, and black dotted lines the quartiles. Results of four independent experiments. Statistical analysis by ordinary one-way ANOVA and multiple comparisons. *p <0.05; ***p <0.001. (d) Quantitative analysis of the number of homed CD45+ cells per BMO (condition: 75/25), derived from different initial seeding numbers of lineage-depleted HSPCs. Violin plots represent the smoothened distributions, red horizontal lines indicate the medians, and black dotted lines the quartiles. Results of three independent experiments. Statistical analysis by ordinary one-way ANOVA and multiple comparisons. **p <0.01; ***p <0.001; ****p <0.0001. (e) Schematic illustration of the definition of the distance to the organoid (Do) and network surface (Dn) in BMOs. (f) Relative frequency distributions of the distance of the HSPCs from the organoid surface (Do) in the different BMO conditions (100/0, 75/25, 50/50). The dashed lines indicate the expected average distance by modeling per condition [100/0: 36.7 ± 4.2 μm, 75/25: 33.2 ± 5.6 μm, 50/50: 25.4 ± 4.7 μm; mean ± SD (shaded regions)]. Around 79% of HSPCs in the 100/0, 68% in the 75/25, and 73% in the 50/50 condition migrate deeper in BMOs than the expected distance. Results of three independent experiments. (g) Example confocal images (single plane) illustrating proximity of homed HSPCs to the endothelial network. Scale bar, 10 μm. (h) Absolute frequency distributions of the distance of the HSPCs from the endothelial network surface in the multicellular BMOs (75/25 and 50/50). The dashed lines indicate the average expected distance by modeling per condition [75/25: 9.8 ± 4.1 μm, 50/50: 10.0 ± 6.8 μm; mean ± SD (shaded region)]. Around 94% of HSPCs in the 75/25 and 92% in the 50/50 condition reside closer to the endothelial structure in the BMO than the expected distance that would result from a uniform distribution. Results of three independent experiments.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-3-ABPID9-000006-036101_1-g004.jpg"
}
|
008827
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Formation of bone marrow organoids in a scalable manner. (a) Schematic illustration of the concept of BMOs. Self-aggregation of MSCs (beige) and ECs (magenta) in the microwell platform for the formation of BMOs. After the initial aggregation, HUVECs self-organize to form an endothelial network within the mesenchymal tissue. HSPCs and leukemic blasts (red) are attracted by the presence of multiple BM cell types in a homing-like behavior and take up residence in this BM-mimicking environment. Together with the easily accessible and scalable characteristics of BMOs, they offer a promising in vitro 3D model system for BM research and drug candidate screening. (b) Schematic illustration of the aggregation of different ratios of MSCs (beige) and ECs (magenta). The control condition consists of only mesenchymal cells (100/0, left), and the two multi-cell type conditions contain either 25% (75/25, center) or 50% (50/50, right) endothelial cells. (c) Representative brightfield images of BMOs with different cell ratios in the Gri3D platform at different time points (day 1, 4, 7). Scale bar, 200 μm. (d) Representative confocal images of the mesenchymal marker expression endoglin (ENG, orange), the endothelial marker CD31 (magenta), and DAPI (4′,6-diamidino-2-phenylindole, blue) marking the cell nuclei in BMOs. The maximum intensity projections of z-stack acquisitions are shown. Scale bar, 100 μm. (e) Growth of BMOs via the analysis of brightfield images by an automated script in Fiji. Analysis of 300–1600 BMOs per condition. Symbols indicate the mean values, and the error bars show the standard deviation. Results of four independent experiments. (f) Spheroids were cultured for seven days, and after fixation, the estimated BMO volume was calculated based on a mask made from the data of ENG expression on the surface of BMOs. Violin plots represent the smoothened distributions, red horizontal lines indicate the medians, and black dotted lines the quartiles. Results of four independent experiments. Statistical analysis by ordinary one-way analysis of variance (ANOVA) with multiple comparisons. ****p <0.0001.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-4-ABPID9-000006-036101_1-g001.jpg"
}
|
008828
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Bone marrow organoids as a niche for leukemic cells. (a) Representative confocal images of leukemic blast cells (CFSE, green) and the network (CD31, magenta) within BMOs (DAPI, blue) at 4, 8, 12, 16, 20, 24, 48, 72, and 96 h after their addition. The maximum intensity projections of z-stack acquisitions are shown. Scale bar, 100 μm. (b) Quantitative analysis of the number of CFSE+ cells per BMO over time. Results of two independent experiments. Symbols indicate mean values, and the error bars show the standard deviations. (c) Quantification of the CFSE intensity of individual homed leukemic stem cells (LSCs) over 96 h. Representative data from one out of three independent experiments. Violin plots represent the smoothened distributions with individually analyzed CFSE+ cells represented as gray dots. Dotted horizontal lines indicate the medians.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_45-PMC9270995-5-ABPID9-000006-036101_1-g006.jpg"
}
|
008829
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Videostroboscopy. A comparison of images taken 7 months before the SARS-CoV-2 infection (a, c, e) with images taken 2 months after the SARS-CoV-2 infection (b, d, f). Images (a, b) show abduction, images (c, d) show adduction, and images (e, f ) show relaxed phonation. Previous videostroboscopy was available for comparison due to prior evaluation of the patient's muscle tension dysphonia and vocal cord nodules.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271004-0-CRIOT2022-6059487p001.jpg"
}
|
008830
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "miR-127-5p targeted JAM3 expression. (a) Venn diagram showing the JAM3-targeted miRNAs. (b) JAM3 expression. (c) Dual luciferase assay. (d) CCK8. (e) Flow cytometry. (f and g) Transwell assay (100×). (h) The expression of GPX4 was detected by western blot. ∗P < 0.05 vs. mimic-NC. #P < 0.05 vs. miR-127-5p mimic.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271006-3-DM2022-6423237p004.jpg"
}
|
008831
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Peritoneal incision procedure in circular incision transabdominal preperitoneal inguinal hernia repair (C‐TAPP) (right side case). The incision is made by following the blue arrow from the yellow circle on the dorsal side",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271018-3-AGS3-6-577-g004.jpg"
}
|
008832
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Scanning electron microscopic image of Lead Sulfide thin films from Avocado (Glycosmis cochinchinensis) Leaf extract at different PH values varied as (a) 2, (b) 4, (c) 6 and (d) 8.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271032-3-41598_2022_15785_Fig7_HTML.jpg"
}
|
008833
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Loss of TCTN1 causes ultrastructural defects of the ciliary membrane and the TZ.a EM images showing ciliary bulges with electron-dense material (white arrowheads) in a portion of tctn1 cells. Scale bar, 200 nm. b, c Longitudinal sections (b) and cross sections (c) through the TZ (b, brackets) of WT, tctn1 and rescued cells. The wedge-shaped structures (b, black arrowheads) and Y-links (c, black arrowheads) were indicated. Quantification of the presence of wedge-shaped structures in the longitudinal section (n = 20, number of wedge-shaped structures) and Y-links in the cross section (n = 17 for WT, n = 23 for tctn1, number represents the thin sections counted.). The presence of at least one Y-link in the thin section is considered as normal. Scale bar, 200 nm. d Scatter plot depicting the distances between the “H” structure and the ciliary membrane in WT, tctn1, and rescued cells. Data are the mean ± SD (n = 20). Statistical significance was determined with an unpaired t test. n.s., not significant; **P < 0.01 by two tailed. e, f TEM images of longitudinal (e) and cross (f) sections of the cilia from WT and tctn1 cells. Glycocalyx on the surface of ciliary membrane was indicated with black arrowheads. The high magnification regions were indicated by dotted boxes. OD outer doublet microtubule, mb ciliary membrane, g glycocalyx. Scale bar, 200 nm. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271036-0-41467_2022_31751_Fig2_HTML.jpg"
}
|
008834
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Fluoxetine induces hepatic injury via triggering the activation of the NLRP3 inflammasome in vivo.A–D WT C57BL/6 mice were injected with LPS (2 mg/kg) and then stimulated with fluoxetine (10 mg/kg, 20 mg/kg, n = 6/group). The levels of mouse serum ALT (A) and AST (B) were measured by GTP and GOT kits, and IL-1β (C) and TNF-α (D) were detected by ELISA kits. E H&E staining (scale bar: 200 μm) and TUNEL staining (scale bar: 100 μm) were used to assess inflammatory infiltration and TUNEL positive. Data are shown as the mean ± SEM. *P < 0.05, **P < 0.01, ***P < 0.001vs LPS group, ns, not significant. One-Way ANOVA analysis followed by Dunnett’s post-hoc test.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271040-2-41420_2022_1109_Fig5_HTML.jpg"
}
|
008835
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "MCC950 pretreatment rescues LPS/fluoxetine-induced hepatotoxicity.A–D WT C57BL/6 mice were pretreatment with MCC950 (50 mg/kg, n = 5 LPS and LPS/FLU groups, n = 6 other groups) and then treated with LPS (2 mg/kg) and finally fluoxetine (20 mg/kg) was administrated. The levels of mouse serum ALT (A), AST (B), IL-1β (C), and TNF-α (D) were assessed by corresponding kits. E H&E staining (scale bar: 200 μm), TUNEL staining (scale bar: 100 μm) and F4/80 staining (scale bar: 100 μm) were used to analyze the liver inflammatory infiltration and TUNEL positive. Data are shown as the mean ± SEM. ***P < 0.001 vs the LPS/FLU group, ns, not significant, Statistics differences were analyzed using Student’s t test.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271040-5-41420_2022_1109_Fig6_HTML.jpg"
}
|
008836
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Ferroportin 1, Ferritin L and H chain protein cellular allocation in Ctx and Hip. (A) Immunofluorescence anti-Fpn1 antibody (red) in cerebral cortex (Ctx) and hippocampus (Hip). (B) Immunofluorescence of neuronal and astrocytic cells using anti-GLUT1 (green), anti-GLAST (red) and anti-Fpn1 antibodies in cerebral cortex (Ctx) and hippocampus (Hip). (C, D) Immunofluorescence of astrocytic and neuronal cells using anti-GFAP (green), anti-MAP2 (red), anti-Ft-L and anti-Ft-H antibodies in cerebral cortex (Ctx) and hippocampus (Hip). 4,6-diamidino-2-phenylindole (DAPI) (blue) was used to counterstain cell nuclei. Scale bars: 63X. Number of analyzed mice: WT Y n = 5, WT A n = 5, WT M-A n = 5 and WT O n = 5. Specifically, neuronal (MAP2) and Ferritins (Ft-L and Ft-H) localization are shown in Supplementary Figure 6S.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271044-2-41598_2022_15812_Fig4_HTML.jpg"
}
|
008837
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Iron-dependent inflammatory response and oxidative stress during aging. (A) Real-time PCR of SAA1 in total brain from all genotypes. (B) Nrf2 mRNA expression levels in total brain. The expression levels of the two genes were normalized to levels of β-glucuronidase (Gus-β) housekeeping gene (material and methods section). (C) Immunofluorescence anti-GFAP (green) and anti-IBA1 (pink) antibodies in cerebral cortex (Ctx) and hippocampus (Hip); 4,6-diamidino-2-phenylindole (DAPI) (blue) was used to counterstain cell nuclei. Scale bars:40X. *Statistically significant vs WT A control group *P < 0.05; **P < 0.01 ***P < 0.001 using OneWay ANOVA followed by Bonferroni’s post hoc analysis. Number of analyzed mice: (A–B): WT Y n = 5, WT A n = 7, WT M-A n = 5 and WT O n = 5; (C–D): WT A n = 5 and WT O n = 5.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271044-3-41598_2022_15812_Fig2_HTML.jpg"
}
|
008838
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "The change in Stat92E pairing states is required for subsequent silencing of transcription.a A schematic of BacTg/Df(3 R)BSC516 (BacTg/Df) genotype. b Representative images of Stat92E DNA FISH puncta (red, white arrowheads) at the indicated stages of germ cells (Vasa, cyan) in BacTg/Df genotype. c Violin plots show distances between DNA FISH puncta. d Representative images of Stat92E mRNA (exon probe smFISH, green) at the indicated stages of germ cells in indicated genotypes. e Quantification of Stat92E mRNA levels. Y axis values are the number of mRNA dots present in a middle plane of the cell (dot#/plane). SIs (see text) are shown in boxes above bars. f Representative images of Stat92E nascent transcript (intron probe, red) at the indicated stages of germ cells in BacTg/Df testes. DAPI (cyan). g, h, i Representative images of Stat92E DNA FISH (red, white arrowheads) at the indicated stages of germ cells (Vasa, cyan) in indicated genotypes. j Violin plots show distances between DNA FISH puncta. k Quantification of Stat92E mRNA levels. Y axis values are the number of mRNA dots scored in a middle plane of the cell (dot#/plane). SIs (see text) are shown in boxes above bars. Adjusted p values are provided for comparison between control (wild type, yw) and BacTg/Df data in (c) and (e) and comparison between temperature-shifted experiment (temp shift) and no temperature-shift control (no temp shift) in (j) and (k). The adjusted p values were calculated using Šidák’s multiple comparisons. Violin plots show KDE and quantile lines and the width of each curve corresponds with the frequency of data points. Box plots show 25–75% (box), median (band inside) and minimum to maximum (whiskers) with all data points. All plotted data points are provided in Source Data. Number of scored cells, which are randomly chosen from at least 10 testes for each experiments, is shown for each data point. For RNAi experiments, temperature sensitive nosGal4 driver, nosGal4ts, was used. All scale bars represent 2 μm. Representative pairing states are shown in lower left corner of each image.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271046-0-41467_2022_31737_Fig4_HTML.jpg"
}
|
008839
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "The change in Stat92E pairing states does not reflect the difference in cell-cycle stages.a A representative image of Stat92E nascent transcript (red) in Fly-Fucci testis. GFP-E2F1-230 (blue) is positive in G2-phase and negative in S-phase cells. White dotted lines encircle germ cells in indicated cell cycle stages. DAPI is shown in green. Right panel shows GFP channel. Stat92E nascent transcript was typically weak or undetectable in S-phase cells. b Representative images of G2 phase germ cells in indicated stages. Stat92E intron FISH signal (white arrowheads) indicate pairing states at the indicated stage of germ cells. Representative pairing states are shown in the upper right corner of each image. Lower panels show GFP channel. c Violin plots show distances between Stat92E nascent transcript puncta at the indicated stages of germ cell development measured in all cell-cycle stages or only in G2-phase cells. Violin plots show KDE and quantile lines and the width of each curve corresponds with the frequency of data points. The adjusted p values were calculated with Šidák’s multiple comparisons. All plotted data points are provided in Source Data. Number of scored cells, which are randomly chosen from at least 10 testes for each experiments, is shown for each data point. Scale bars in (a) represent 10 μm. Scale bars in b represent 2 μm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271046-1-41467_2022_31737_Fig3_HTML.jpg"
}
|
008840
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Representative scanning electron micrographs of A. baumannii on the working electrode area only (A) cells not treated with any of the tested compounds—Control; (B) cells treated with Gen; (C,D) cells treated with ZnL1. Red arrows showing point of ell rupture and shrinkage.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271062-7-41598_2022_16047_Fig8_HTML.jpg"
}
|
008841
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Representative contrast enhanced MR images overlaid with ADC maps, cell number estimates, proliferation maps, and proliferation histograms are shown for time point combinations from a patient with pCR (RCB 0). This patient exhibited robust initial response with full response by mid-treatment (T2).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271064-2-41598_2022_15801_Fig4_HTML.jpg"
}
|
008842
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Patient No. 1 showed slightly decreased density and dilatation (arrowhead) of capillaries (A), and Patient No. 6 had few capillaries because of extensive architecture damage, and hemorrhage (arrow) in the nailbed area (B). These were taken from the bilateral second and fourth fingers. (× 400 magnifications; Olympus SZ-PT, Olympus, Tokyo, Japan; R: right, L: left, 2: second finger, 4: fourth finger.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271069-0-41598_2022_15779_Fig1_HTML.jpg"
}
|
008843
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Characterization of FveATHB-OE transgenic lines.a Plant and fruit phenotype of FveATHB-OE transgenic lines. Fruits of three FveATHB29b-OE lines and two FveATHB30-OE lines are shown. b Mock- and NAA-treated fruits of FveATHB29b-OE and FveATHB30-OE lines. c Fruit size measurement of WT, three FveATHB29b-OE lines, and two FveATHB30-OE lines. Significant difference from WT is marked by ** (n = 20, P < 0.01 by two-tailed Student’s t-test). The elements of boxplots and source data are provided in a Source Data file. d, e Relative transcript level (Y-axis) of auxin biosynthetic genes FveYUC10 and FveTAA1 in stage 2 seeds of WT and FveATHB29b-OE (d) and FveATHB30-OE (e) lines. Significant difference (two-tailed Student’s t-test) from WT is marked with ** (P < 0.01) and * (P < 0.05). Error bars indicate standard deviation. Three biologically independent experiments gave similar results. f Confocal laser scanning microscopy reveals extensive cell death (red arrowheads) and precocious cellularization (white arrows in enlarged inserts) in the endosperm of stage 2 seeds in FveATHB-OE lines. Scale bars, 1 cm (a, b), 100 μm (f).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271072-1-41467_2022_31656_Fig6_HTML.jpg"
}
|
008844
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Characterization of F. vesca fveagl62 mutant seedcoat.a Vanillin-stained F. vesca WT and fveagl62 mutant seeds at the pre-fertilization stage 1 and post-fertilization stages 2–3. The proanthocyanidins in the endothelium layer stains red with the vanillin. b Confocal laser scanning microscopy images of WT and fveagl62 seeds at stage 2. The enlarged box highlights the three integument cell layers (red arrows) exterior to the endothelium. Scale bars, 500 μm (a), 100 μm (b).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271072-3-41467_2022_31656_Fig4_HTML.jpg"
}
|
008845
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Arabidopsis atagl62 endosperms have reduced auxin when compared with WT.a Confocal image of auxin reporter R2D2 in WT (Col-0) and atagl62-2 seeds at 2 DPA. Absence of DII-VENUS nuclear signal in the WT endosperm contrasts with strong DII-VENUS nuclear signals in the atagl62-2 endosperm. The scatter graph Y-axis indicates the ratio between DII-VENUS and mDII-Tdtomato signal per endosperm nucleus. A second independent experiment gave a silimar result. The elements of boxplots and source data are provided in the Source Data file. Significant difference indicated by ** (P = 7.55e-12 by two-tailed Student’s t-test) is found between WT and atagl62. b Confocal image of ProAtYUC10::3xnGFP signal in WT and atagl62 endosperms. Note the strong nuclear GFP signals in the WT endosperm and almost undetectable GFP signals in the atagl62 endosperm. c Confocal image of WT and atagl62 mutant seeds at 2 DPA either mock-treated or auxin (2,4-D)-treated. Different extent of endosperm cellularization is observed. Arrows indicate cell walls between endosperm cells. d Quantification of mock- or 2,4-D-treated seeds derived of atagl62-2 (−/+) parents. Y-axis is the percentage of endosperms with one of the three phenotypes: no cellularization, partial cellularization, and complete cellularization. Significant difference (two-tailed Fisher’s exact test) is indicated by ** (P = 0.0006) for complete cellularization or * (P = 0.0416) for no cellularization between mock and 2,4-D treatments of each phenotypic category. e Confocal image of Arabidopsis seeds at 2 DPA. Precocious endoserpm cellularization is absent in transgenic atagl62 plants containing the strawberry FveAGL62 gene. Scale bar in a–e: 50 μm.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271072-4-41467_2022_31656_Fig3_HTML.jpg"
}
|
008846
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "F. vesca fveagl62 mutant seeds show reduced auxin biosynthesis.a Hierarchical clustering of auxin biosynthesis gene expression in WT and fveagl62 stage 2 seeds. b Hierarchical clustering of GA biosynthesis gene expression in WT and fveagl62 stage 2 seeds. c RT-qPCR analysis of five auxin biosynthesis genes in WT and fveagl62 stage 2 seeds. Gene IDs are indicated in a. Y-axis indicates the relative expression level against the control gene FvePP2a (FvH4_4g27700). Significant difference by two-tailed Student’s t-test is indicated by ** (P < 0.01) or * (P < 0.05) between WT and fveagl62 mutant seed. Error bars indicate standard deviation. Similar results were obtained in three biologically independent experiments. d\nDR5ver2::GUS reporter expression in WT and fveagl62 stage 2 seeds. e\nDR5ver2::GUS expression in individual stage 2 seeds. f Confocal laser scanning microscopy images of WT and fveagl62 seeds at stage 2. Precocious cellularization of fveagl62 endosperm (arrows) is observed in stage 2 seeds. g Confocal laser scanning microscopic images of WT and fveagl62 stage 2 seeds mock- or NAA-treated. Scale bars: 1 mm (d), 120 μm (e), 100 μm (f–g).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271072-6-41467_2022_31656_Fig2_HTML.jpg"
}
|
008847
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Pneumonia changes after SARS-CoV-2 Delta VOC infection.a–f Representative CT images with pneumonia volume. a, b Non-vaccinated group, (c, d) 1-dose vaccine group, (e, f) 2-dose vaccine group. g Peak pneumonia volume for each patient. Two-tailed p values (Kruskal–Wallis test) are indicated. Data are the median (IQR). h Pneumonia absorbance time. Two-tailed p values (Tukey’s multiple comparisons test) are indicated. Data are the median (IQR). i Overall changes in pneumonia during the whole hospitalization. Each point represents one measurement. Fitted curves of pneumonia absorbance volume distribution are shown, smooth curves and shaded regions indicate 95% CIs. Non-Vac nonvaccinated group (black circle). 1-dose 1-dose vaccine group (blue square). 2-dose 2-dose vaccine group (red triangle). Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271076-3-41467_2022_31693_Fig3_HTML.jpg"
}
|
008848
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "NEMEP deletion leads to early defects in mouse embryo chimeras.a Scheme of blastocyst injection, transfer to pseudopregnant mouse, and collection of embryos at E7.5 (Created with BioRender.com). b Brightfield and green fluorescence (GFP) images of embryo chimeras including WT and Nemep−/− ESCs recovered at E7.5. Scale bars, 100 µm. Confocal microscopy images of serially sectioned embryo chimeras, with WT ESCs and Nemep−/− mESCs dissected at E7.5 depicting GFP (green), FOXA2 expression (red) (c) or T expression (red) (d), and nuclear (Hoechst33342, blue) localization. Scale bars, transverse section, 100 µm; high-magnification view, 20 µm. b–d: Data are representative of three independent experiments with similar results. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271079-3-41467_2022_31762_Fig4_HTML.jpg"
}
|
008849
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Sagittal SPGR 3D FS knee MRI of the immature and mature pigs after MASI. In the immature knee joint (a–c), at 2 weeks after MASI (a), MRI demonstrates MSC implants (dashed lines) in full-thickness cartilage defects (arrows). On follow-up imaging scans at week 4 (b), the knee joint demonstrates associated subchondral edema (asterisks) and bone defect in the subchondral bone (arrows). The follow-up imaging study of the immature joint at 12 weeks after MASI (c) demonstrates a persistent size of the cartilage defect and increasing size of the subchondral bone defect (arrows). In the mature knee joint (d–f), at 2 weeks after MASI (d), MSC implants (dashed lines) in full-thickness cartilage defects and intact subchondral endplate (arrows) are appreciated. In contrast to the immature joint, on follow up MR imaging of the mature joint, the knee joint demonstrates limited subchondral edema (asterisks) and the size of the cartilage defects and subchondral bone defects (arrows) decreases at week 4 (e), and week 12 (f) after MASI, consistent with progressive healing.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271080-5-41598_2022_15721_Fig1_HTML.jpg"
}
|
008850
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Intestinal villus tip endothelial cell polarization is VEGFA-dependent.a, b Villus tip endothelial cells display high VEGFA signaling. Staining for (a) VEGFR3 (red) and PECAM1 (green) and (b) ESM1 (green) and VEGFR2 (red) of adult (a) C57BL/6 and (b) mTomato small intestinal villus tip vessels. L, lymphatic vessel. c Endothelial cell nuclei are polarized to the villus core side of villus tip vessels. Staining for ERG (green) and VEGFR2 (red) in C57BL/6 adult mice. Box denotes villus tip area. Quantification of endothelial cell nuclei positioning in the villus tip vessel; n = 3 mice. d Pericytes are positioned on the villus core side of villus tip vessels. Staining for NG2 (red, arrowhead) and PECAM1 (green). e Villus tip vessels consist of unicellular endothelial tubes. Cartoon representing differences in cell-cell junction patterning (black lines) between multicellular and unicellular vessels. Villus tip vessels (PECAM1, green) display lumenized endothelial cells based on cell-cell junction immunostaining (VE-cadherin, red) and “open faces” (arrowheads) towards epithelial cells. f VEGFA is concentrated to the epithelial side of villus tip vessels. Staining for VEGFA (red) and PECAM1 (green); bottom, 3D rendering of top image. g Villus tip endothelial cells do not proliferate. Staining for VEGFR2 (blue) and Ki67 (red) in C57BL/6 adult mice. Quantification of Ki67+ endothelial cells in the crypts, villus body (arrowhead) and villus tips; n = 4 mice. h Villus tip endothelial cell nuclei polarization is VEGFA-dependent. Staining for VEGFR2 (red) and ERG (green). Quantification of endothelial cell nuclei position on the villus core (arrowheads), middle, or epithelial sides (arrows) of the villus tip vessel in control- and DC101-treated adult C57BL/6 mice; n = 3 mice. i Unicellular arrangement of villus tip blood vessels is VEGFA-dependent. Staining for endothelial cell nuclei (green, ERG) and endothelial cell junctions (red, VE-cadherin). j Villus tip endothelial nuclei are positioned on the villus core side of the vessel, aligning with pericytes, while the endothelial membrane with fenestrations faces the epithelium. VEGFA is sequestered on the epithelium-facing part of the vessel (created with biorender.com). All microscopic images were generated by whole-mount immunostaining. Scale bars: 50 μm: a, b, c, d, g, h; 20 μm: e, g (inset), i; 10 μm: f. All values shown as mean ± SD. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271081-0-41467_2022_31571_Fig1_HTML.jpg"
}
|
008851
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "ADAMTS18 promotes villus tip vessel and epithelial cell integrity.a Villus tip endothelial cell fenestration extends to the villus core side in Adamts18−/− mice. Electron micrographs of villus tip vessels from wild-type and Adamts18−/− mice. Zoomed areas from the epithelial side (black box) or villus core side (red box) of villus tip vessels are shown below. Quantification for the percentage of fenestra observed on each side of the vessels (p = 0.0017, n = 4 mice). b, c Increased villus tip vessel leakage in Adamts18−/− mice. b 100 nm fluorescent beads were injected i.p. and visualized in the intestine by wholemount imaging. In wild-type animals beads (red) accumulated sparsely throughout the villus but were concentrated around venules (green) in villi and the submucosal layer. c Analysis of bead distribution in the villus tip of wild-type and Adamts18−/− mice. Quantification of the bead area/villus tip vessel area (p = 0.001, n = 4–5 mice). d Amino acid concentration is increased in blood of Adamts18−/− mice. Blood was sampled from the (left) portal vein of fasted mice or (right) hearts of mice gavaged with high protein solution. (Left, Tyr, p = 0.0051; Met, p = 0.0011; Ser, p = 0.0063; n = 5–9, right, Tyr, p = 0.0188; Gln, p = 0.0005; Glu, p = 0.0046; Asp, 0.0018; n = 3–5 mice; 2 technical replicates/sample displayed). e Villus tip “holes” in Adamts18−/− mice. LAMA5 staining (red) allows visualization of holes in the basement membrane. Quantification of percentage of villi with basement membrane holes in adult Adamts18−/− mice or littermate wild-type controls (p = 0.0112, n = 5–6 mice). f Holes run completely through the basement membrane (red, LAMA5) at the villus tips and are covered by epithelial cells (green, EpCAM). Cross-sectional view of a villus tip hole in an Adamts18−/− mouse; white, VEGFR2; blue, DAPI. Quantification of hole location along the villus/crypt axis, 100 denotes the villus tip. g Bifurcated villi are more abundant in adult Adamts18−/− mice than littermate wild-type controls. Whole-mount immunostaining for LAMA5 (red) and VEGFR2 (green). Quantification of percentage of villi with split villi in adult Adamts18−/− mice or littermate wild-type controls (p = 0.0147, n = 5–6 mice). h Scheme for proposed mechanism of VTT-derived ADAMTS18 limiting fibronectin and VEGFA to maintain the polarized endothelial cell phenotype at the intestinal villus tip (created with biorender.com). Scale bars: 50 μm: b (villus) e, g; 20 μm: b (submucosal), c, f; 2 μm: a. All values shown as mean ± SD. Source data are provided as Source Data and Supplementary Data files.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271081-1-41467_2022_31571_Fig6_HTML.jpg"
}
|
008852
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "VTTs are a distinct subepithelial cell population.a Strategy used for single cell RNAseq (scRNAseq) of wild-type small intestinal fibroblasts by Smartseq2 and 10X Genomics technologies. b UMAP plot of 10 fibroblast clusters from integrated Smartseq2 and 10X Genomics scRNAseq libraries. c Dot plot displaying defining genes for each fibroblast cluster, color coded by expression level with dot size denoting the percent of cells in each cluster expressing the given gene. d VTTs are a subset of the PDGFRα+ subepithelial stromal network. Staining for PDGFRα (red), GFP (green) and, VEGFR2 (blood vessels, cyan). Inset: Magnification of the boxed area from (d), PDGFRα+ VTTs are highlighted by arrowheads; whole-mount immunostaining. e F3 (red) is expressed in all subepithelial stromal cells while TNC (green) is limited to villus fibroblasts. Paraffin section immunostaining; blue, DAPI. f TNC (green) and periostin (red) are expressed in the villi and crypts, respectively. Paraffin section immunostaining; blue, DAPI. g Dot plot of representative transcripts from subepithelial clusters A and B. h Desmin is produced by both subepithelial cells and villus smooth muscle cells. Staining for desmin (red) PECAM1 (blue) and αSMA (green). i\nLgr5+ VTTs do not express desmin. Staining for GFP (green), desmin (red) and VEGFR2 (blue). (j) High LAMA5 expression is limited to the villus tip and VTTs. Staining for GFP (green) and LAMA5 (red). Inset, magnification of villus tip, white arrowheads denote LAMA5+ VTTs. Whole-mount immunostaining; blue, VEGFR2. k VTTs secrete POSTN at villus tip. Whole-mount immunostaining for Lgr5+ VTTs (green, GFP), POSTN (red) and TNC (blue) at the villus tip. l Cartoon summarizing phenotypic and typical genes expressed by villus SMCs and cells in subepithelial clusters A and B. Scale bars: 50 μm: d, e, f, h, j; 20 μm: d (inset), i, j (inset), k. Source data are provided as Source Data and Supplementary Data files.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271081-2-41467_2022_31571_Fig4_HTML.jpg"
}
|
008853
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "VTTs constrain villus tip VEGFA signaling.a Reduced number of VTTs in Lgr5DTA mice. Quantification of VTTs/villus in control Lgr5-GFP-CreERT2 and Lgr5DTA mice after 1 week of deletion (p = 0.0112, n = 3–4 mice). b VTT depletion increases villus tip endothelial VEGFA signaling. Staining for PECAM1 (blue) and VEGFR3 (red, top) or ESM1 (red, bottom). L, lymphatic vessel. Quantification of distance at which ESM1+ vessels are observed from the villus tip in either control or Lgr5DTA mice after 1 week of deletion (p = 0.0011, n = 3-4 mice). c–f VTT depletion disturbs villus tip vessel polarization and phenotype. c Endothelial cell nuclei are polarized towards the villus core (white arrowheads, perinuclear VEGFR2 staining) or epithelial side (yellow arrowheads) of villus tip vessels. Endothelial cells displaying filopodia (yellow arrows). Staining for VEGFR2 (red) and GFP (green). d–f Quantification of the (d) percentage of villus tip endothelial cells displaying filopodia (p = 0.0123), (e) percentage of endothelial cells on the villus core side of the vessel (p < 0.0001) and (f) the number of endothelial cells/villus tip in control and Lgr5DTA mice; n = 3–4 mice. g Scheme of VEGFA signaling phenotype in the presence (left) or absence (right) of VTTs. The presence of VTTs confines VEGFA signaling to villus tip vessels and promotes villus tip endothelial cell nucleus polarization. VTT depletion increases VEGFA signaling and disturbs villus tip endothelial cell polarization (created with biorender.com). All microscopic images were generated from whole-mount immunostaining. Scale bars: 50 μm. *P < 0.05, **P < 0.01, ****P < 0.0001 2-tailed unpaired Student’s t test. All values shown as mean ± SD. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271081-3-41467_2022_31571_Fig3_HTML.jpg"
}
|
008854
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "VTT-specific ADAMTS18 is necessary for constraining villus tip VEGFA signaling by limiting fibronectin accumulation.a ADAMTS18 expression is restricted to the villus tips in the human small intestine. Chromogenic immunostaining for ADAMTS18 (brown) of human jejunum villus tips (above) and crypts (below); H + E counterstained. b Co-localization of Lgr5, Vegfa and Adamts18. RNAscope fluorescent in situ hybridization of the intestine for Vegfa (red), Lgr5 (green) and Adamts18 (white). The white box delineates zoomed villus tip area shown in the right two panels. c Loss of villus tip endothelial cells and nucleus polarization in adult Adamts18−/− mice. Whole-mount immunostaining showing decreased number of villus tip endothelial cells (white arrowheads, green perinuclear VEGFR2 immunostaining) and increased number of endothelial cell nuclei on the epithelial side of villus tip vessels (bottom). Dotted lines, epithelium. Quantification of (d) the number of endothelial cells/villus tip (p = 0.0005), (e) percentage of endothelial cells on the villus core side of the vessel (p < 0.0001), and (f) percentage of villus tip endothelial cells displaying filopodia in Adamts18−/− mice and littermate wild-type controls (p = 0.0022); n = 5-6 mice. g–i Increased villus tip endothelial VEGFA signaling in Adamts18−/− mice. Whole-mount immunostaining of villus tip vessel for PECAM1 (green) and (g) VEGFR3 (red, top) or (h) ESM1 (white bottom). i Quantification of distance (a.u.) at which ESM1+ vessels are observed from the villus tip in adult Adamts18−/− mice or littermate wild-type controls (p = 0.0001, n = 5-6 mice). j Increased VEGFA at the villus tip in Adamts18−/− mice. Wholemount immunostaining for VEGFA (red) and PECAM1 (green) at the intestinal villus tip in wild-type and Adamts18−/− mice. Images show Imaris-generated 3D surfaces. Quantification of the VEGFA volume at the villus tip (p = 0.0142, n = 4 mice. k Increased deposited fibronectin at the villus tips of Adamts18−/− mice. Wholemount immunostaining for fibronectin (red) and VEGFR2 (green) in wild-type and Adamts18−/− mice. Scale bars: 200μm: a; 50 μm: b, c, g, h; 20μm: b (inset), j, k. *P < 0.05, **P < 0.01, ***P < 0.001 2-tailed unpaired Student’s t test. All values shown as mean ± SD. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271081-4-41467_2022_31571_Fig5_HTML.jpg"
}
|
008855
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Change in cell ultrastructure in the leaves of S. caninervis along with Hg stress concentration by measured using transmission electron microscopy (TEM). (A) control; (B) 20 µM Hg concentration; (C) 30 µM Hg concentration; (D) 50 µM Hg concentration. Chl chloroplast, CN cell nucleus, CW cell wall, CM cell membrane, SG starch grain.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271083-0-41598_2022_15822_Fig1_HTML.jpg"
}
|
008856
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Artificial labelling of E. coli membranes.a fnet and CARE predictions of diffraction-limited (i) and PAINT super-resolution (SR) (ii) membrane labels obtained from bright field (BF) images. GT = ground truth. Values represent averages from five test images and the respective standard deviation b Pseudo-dual-colour images of drug-treated E. coli cells. Nucleoids were super-resolved using PAINT imaging with JF646-Hoechst64. Membranes were predicted using the trained fnet model. CAM = Chloramphenicol. Scale bars are 2 µm (a) and 1 µm (b).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271087-0-42003_2022_3634_Fig5_HTML.jpg"
}
|
008857
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Segmentation of bacterial images using open-source deep learning approaches.a Overview of the datasets used for image segmentation. Shown are representative regions of interest for (i) S. aureus bright field and (ii) fluorescence images (Nile Red membrane stain), (iii) E. coli bright field images and (iv) fluorescence images of B. subtilis expressing FtsZ-GFP47. b Segmentation of S. aureus bright field and membrane-stain fluorescence images using StarDist9. Bright field and fluorescence images were acquired in the same measurements and thus share the same annotations. Yellow dashed lines indicate the cell outlines detected in the test images shown. c Segmentation of E. coli bright field images using the U-Net type network CARE14 and GAN-type network pix2pix18. A representative region of a training image pair (bright field and GT mask) is shown. d Segmentation of fluorescence images of B. subtilis expressing FtsZ-GFP using U-Net and SplineDist42. GT = ground truth. e Segmentation and tracking of E. coli cells during recovery from stationary phase. Cells were segmented using StarDist and tracked with TrackMate45,46. f Plots show the mean (line) and standard deviation (shaded areas) for all cells in seven different regions of interest (colour-coded). Morphological features were normalised to the first value for each track. Scale bars are 2 µm (a, d), 3 µm (b, c) and 10 µm (e).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271087-1-42003_2022_3634_Fig2_HTML.jpg"
}
|
008858
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Overview of the DL tasks and datasets used in DeepBacs.a We demonstrate the capabilities of DL in microbiology for segmentation (1), object detection (2), denoising (3), artificial labelling (4) and prediction of super-resolution images (5) of microbial microscopy data. A list of datasets can be found in Supplementary Table 1, comprising different species such as B. subtilis (1), E. coli (2–4) and S. aureus (5) and imaging modalities (widefield (1,2) and confocal (2,3) fluorescence microscopy, bright field imaging (1,2,4) or super-resolution techniques (4,5)). NN: neural network output. CAM = Chloramphenicol. Scale bars: 2 µm. b Schematic workflow of applying a DL network. Users select a ZeroCostDL4Mic notebook based on the image analysis task to be performed. Custom annotated or publicly available datasets are used to train and validate DL models. The user can train the DL model from scratch or load a pretrained model from public repositories (e.g., Zenodo or BioImage Model Zoo77) and fine tune it. After model accuracy assessment, trained models can be applied to new experimental data.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271087-4-42003_2022_3634_Fig1_HTML.jpg"
}
|
008859
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Prediction of SIM images from widefield fluorescence images.Widefield-to-SIM image transformation was performed with CARE for a live E. coli (FM5-95) and b\nS. aureus (Nile Red) cells. Shown are diffraction-limited widefield images (i) and the magnified regions (ii) indicated by yellow rectangles in (i). WF = widefield; NN = neural network output. (iii) Line profiles correspond to the red lines in the WF images and show a good agreement between prediction and ground truth (bottom panel). Scale bars are 10 µm (i), 1 µm (ii) and 0.5 µm (iii).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271087-5-42003_2022_3634_Fig6_HTML.jpg"
}
|
008860
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "The SEM images for (a) PPMM, (b) PPMM@PVA, and (c) PPMM@PDA, as well as (d) PPMM@PDA/PVA(1/2), (e) PPMM@PDA/PVA(1/4), and (f) PPMM@PDA/PVA(1/8), respectively. The insets are their respective high magnification images.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271090-2-41598_2022_15961_Fig1_HTML.jpg"
}
|
008861
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "The SEM images for PPMM@PDA/PVA(1/8)@Au in (a) low and (b) high magnification views, as well as PPMM@PDA/PVA(1/8)@Au@IrO2 in (c) low and (d) high magnification views.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271090-7-41598_2022_15961_Fig4_HTML.jpg"
}
|
008862
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "MOF films with anisotropic fluorescence and controlled micropore alignment.a Schematics showing DMASM dye molecules (orange rods) selectively recruited on (002) facets of MIL-96 particles (Step 1). The molecular structure of the dye is shown, and its transition dipole moment is labeled with black double arrow. The randomly oriented dye molecules in solution are encapsulated in the ellipsoidal pores of MIL-96 (structure shown) and their transition dipole moments are aligned to the pore (the [002] direction, purple double arrow). The dye-encapsulated particles (MIL-96-2) with random orientations are assembled to form MOF films with mutually oriented dye arrays (Step 2). The side view of dye orientation (angle with respect to substrate is 42°) and their spatial arrangement in a centered rectangular lattice are shown. b, c Fluorescence microscope images of dye-encapsulated MIL-96-2 particles before (b) and after (c) self-assembly. Inset (b) shows a large MIL-96 particle with fluorescence located at the (002) faces; inset c is the zoomed-in MOF film. d Illustration of the angle-dependent emission of MIL-96-2 films excited by linearly polarized light (blue double arrows). The direction of polarization is parallel (left) and perpendicular (right) to the dye orientation to turn on and off the emission. e Azimuthal plot of the fluorescence intensities (IFl) of MIL-96-2 films as a function of θ, angle between polarization direction and dye orientation (also c axis of MIL-96). f Representative fluorescence images show strong, intermediate, and weak fluorescence of the MIL-96-2 film in response to the polarized light at θ of 0°, 45° and 90°. g Fluorescence image displays grains of MIL-96-2 film with diverse orientations and their boundaries (yellow dotted lines). Scale bars: 5 μm (b, c, f, g), 2 μm (b, inset), and 1 μm (c, inset).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271095-2-41467_2022_31651_Fig7_HTML.jpg"
}
|
008863
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Anisotropic and directional assembly of UiO-66 particles.a–e 2D hexagonal superlattice (hp) assembled on a smooth substrate. Optical microscope image of the UiO-66 films is shown in (a). Cartoon in (b) shows particles sitting on the substrate by the triangular (111) face within the assemblies. They contact via their faces in an antiparallel fashion (shown in purple). Laser diffraction pattern of the resulting hexagonal lattice c. The (111) facet arrays are highlighted by reflected-light confocal microscopy (d) and SEM (e). f–h, Anisotropic quasi-1D stripe-like superstructure assembled from UiO-66 octahedra on a rough substrate. Optical image f shows the supercrystals; inset shows a crystal stripe and its long and short axes. Cartoons in (g) highlight the interparticle bonding within (along the short axis) and between hexagonal layers (along the long axis), featuring antiparallel (top right) and full facet overlap (bottom right), respectively. SEM images in (h) show the (110)- and (112)-oriented UiO-66 superstructures. Scale bars: 3 μm (a), 1 μm (d, e, h), 5 μm (f), and 2 μm (f, inset).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271095-3-41467_2022_31651_Fig4_HTML.jpg"
}
|
008864
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Self-assembly of MIL-88A particles.a–d 1D top-down alternating chain of MIL-88A particles formed on a smooth substrate. a Cartoon (left) shows the particle orients its (100) face towards the substrate by depletion attraction. Cartoon (right) shows the particles in the upper layer (light brick red) bind with those at the bottom (dark brick red) by the side faces (purple, n = 2). b Optical image of MIL-88A chains. Inset is the zoomed-in optical and reflected-light confocal image of the chains, both showing an alternating pattern. Optical images and cartoon in (c) show a microscope focus series of the chain. Snapshots from a movie (d) show the chain formation process. e–h 2D snowflake-like network of MIL-88A particles, formed on a rough substrate (gray plate with yellow dots). Schematic in (e) shows two short chains bind via (100) faces to form a branch, which flips over and stands on the substrate by their pyramidal tips ([001] direction). Cartoons in (f) compare the fully coordinated structure (n = 6, left) with the actual unsaturated network structure (n ≤ 6, right). Optical images in (g) show the flipping and branching process. Optical image in (h) shows the snowflake-like networks and the angles of branch junctions (inset). Scale bars: 5 and 1 μm (inset) for (b), 1 μm for (c, d), 2 μm for (g), 5 and 2 μm (inset) for (h).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271095-4-41467_2022_31651_Fig3_HTML.jpg"
}
|
008865
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Self-assembly of ZIF-8 particles and dimension control.a, b Quasi-3D superstructures assembled from 0.9-µm ZIF-8 RD particles on a rough substrate. For each particle, the coordination number n = 12. Large-view optical microscope image of the assembled crystals with a face-centered cubic structure (FCC) is shown in (a). Cartoons, zoomed-in optical images and SEMs in (b) show (100)-, (111)-, and (110)-oriented colloidal crystals; the axial angles are labeled. c–f 1D chains (n = 2) by assembling ZIF-8 RD (c–e) or truncated rhombic dodecahedra (TRD) (f) particles on a smooth substrate. Reflected-light confocal microscopy image in (c) reveals the well-arrayed rhombic faces (inset, orange dashed lines) within the RD chain. Cartoon in (d) illustrates that the particles stand on the substrate by their (110) faces and contact with one another by virtual patches (purple) to form a chain. Cartoon and SEM image in (e) show the top view of a colloidal chain. f Cartoon and bright-field optical image of chains assembled by TRD particles. g–j 2D chain bundles (n = 2~6). Optical (g) and SEM images (h) show the structure of ZIF-8 chain bundles and highlight the crosslinker particles (in blue). Cartoons in (i) illustrate the binding and the corresponding particle facets (purple) between the chains (at bottom layer) and the crosslinkers (at upper layer). A gap with a width of δ is observed between the bridged chains of TRD particles. Optical images in (j) show the flexible and rigid chain bundles according to the number density of crosslinkers. Color of chain segment denotes the deviation in angles from straight chain (white line). Scale bars: 5 µm for microscope images in (a, b), 2 μm for SEMs in (b), 5 and 2 µm (inset) for (c), 1 µm for (e, h), 10 µm for (f), 10 and 5 µm (inset) for (g), and 3 µm for (j).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271095-6-41467_2022_31651_Fig2_HTML.jpg"
}
|
008866
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Epithelial inhibition of ACC1-mediated de novo FAS reduces inflammation-associated tumor formation.a Experimental setting. Deletion of ACC1 was achieved through 5 consecutive days of tamoxifen injection (i.p). Mice were subsequently subjected to 3 cycles of DSS (2% w/v in drinking water) and 2 injections of AOM (10 mg/kg, i.p) before the 1st and 3rd DSS cycle. Analysis was performed on day 16 after the last DSS cycle, as depicted. b Pictures of the colons of ACC1lox/lox and ACC1∆/∆IEC mice are shown for one representative out of 3 independent experiments. c Numbers of macroscopically counted colonic tumors. d Representative H&E images of colonic tumors. Bar graph shows the distribution of colonic tumors identified in individual mice classified according to their size. Bar = 200 µm. e Measurement of colon length and the histopathological score. Data was pooled from 3 experiments with n = 19 (ACC1∆/∆IEC) and n = 13 (ACC1lox/lox) mice (c, d) and n = 18 (ACC1∆/∆IEC) and n = 13 (ACC1lox/lox) mice (e). Statistical analysis was performed using unpaired two-tailed Student’s t-test with *p < 0.05, **p < 0.01, ***p < 0.001. ****p < 0.0001. Exact p values provided as Source Data. Bar graphs represent mean and error bars indicate SD (c, e) or SEM (d). Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271096-1-41467_2022_31725_Fig6_HTML.jpg"
}
|
008867
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "ACC1 deletion interferes with PPARδ/β-catenin activation in intestinal organoids.a Transcription levels of genes associated with intracellular de novo fatty acid synthesis. CPM values were derived from RNA-seq of organoids from ACC1∆/∆IEC and ACC1lox/lox mice at day 4 after 4-OHT treatment. RNA-seq was performed in triplicates from 3 independent experiments. b\n13C labeled glucose was added to organoids derived from ACC1∆/∆IEC and ACC1lox/lox mice directly after 4-OHT treatment. Organoids were harvested at indicated time points and incorporation (δ) of 13C into de novo synthesized fatty acids was measured by mass-spec. Data pooled from N = 3 independent experiments. c Accumulation of neutral lipids in organoids. LipidTox green was added 30 min prior to analysis of mean fluorescence intensity (MFI) by flow cytometry. Data is representative for 4 independent experiments. d Western blot analysis of nuclear PPARδ and β-catenin protein was performed at indicated time points in organoids derived from ACC1lox/lox and ACC1∆/∆IEC mice. Anti-histone H3 was used as loading control. Representative data is shown from one out of 2 independent experiments with similar results. e ACC1Δ/ΔIEC and ACC1lox/lox control mice were injected with tamoxifen and treated daily (i.p.) with PPARδ agonist GW501516 or vehicle (veh) until analysis on day 14. H&E stainings of ileum sections are representative of 2 independent experiments with n = 3–5 mice per group. Scale bar represents 100 µm. f–i Organoids from ACC1∆/∆IEC mice were cultured in the absence or presence of 4-OHT for 24 h to induce ACC1 deletion. PPARδ agonist GW501516 or vehicle control (DMSO) were added for the whole culture period of 5 days. f Representative pictures of organoids and quantification of crypt domains. More than 30 organoids per group were analyzed. GW = GW501516. Bar = 200 µm. g qPCR analysis of Lgr5 expression. h Western blot analysis of nuclear PPARδ and β-catenin protein. GW = GW501516. Representative data is shown from one out of 2 independent experiments with similar results. i Number of secondary organoids per dissociated crypt-derived primary organoids. Primary organoids from ACC1∆/∆IEC mice were cultured +/− 4-OHT for 24 h. GW501516 or DMSO were added directly after plating. Primary organoids were subcloned on day 4. Data was pooled (N = 3) g, i or is representative (f) for 3 independent experiments with similar results. Statistical significance was analyzed using Bonferroni-Dunn method (b), unpaired two-tailed Student’s t-test (c, Benjamini–Hochberg procedure (a) or One-way ANOVA with Tukey’s multiple comparison test (f, g, i) with *p < 0.05, **p < 0.01, ***p < 0.001. ****p < 0.0001. Exact p values provided as Source Data. Bar graphs represent mean and error bars indicate SD. Boxes in boxplots denote 25th to 75th percentiles with whiskers representing min-max, and the central line the median. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271096-2-41467_2022_31725_Fig4_HTML.jpg"
}
|
008868
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "External lipid delivery compensates for the lack of ACC1-mediated de novo FAS.a–d Crypts were isolated from ACC1∆/∆IEC mice and grown in organoid cultures in the absence or presence of 4-OHT for 24 h to induce ACC1 deletion. Palmitate was added into cultures with 100 µM on day 3 and analyzed 48 h later. a Organoids were imaged and the number of crypt domains was quantified. Crypt domain formation was calculated from >30 organoids per group. (Bar = 200 µm). b qPCR analysis of Lgr5 expression. c Western blot analysis of nuclear PPARδ and β-catenin protein. d Secondary culture of organoids from palmitate-treated primary culture. e Organoid cultures of crypts isolated from ACC1∆/∆IEC and ACC1lox/lox mice were treated with Etomoxir (Eto, 10 µM) and palmitate (palm, 100 µM) or vehicle directly after 4-OHT treatment. Crypt domain formation was calculated at day 4 from >30 organoids per group. Data was pooled (N = 3) (a, b, d, e) or is representative (c) for 3 independent experiments with similar results. f ACC1∆/∆IEC mice were injected with tamoxifen and fed with a high fat (HFD) or control diet as indicated in the schematic overview. H&E stainings of ileum sections and expression of Lgr5 gene in IECs isolated from the small intestine. Data shown are representative of 3 independent experiments with n = 3–5 mice per group. Scale bar represents 100 µm. Statistical significance was analyzed using unpaired two-tailed Student’s t-test (f) or One-way ANOVA with Tukey’s multiple comparison test (a, b, d, e) with *p < 0.05, **p < 0.01, ***p < 0.001. ****p < 0.0001. Exact p values provided as Source Data. Bar graphs represent mean and error bars indicate SD. Boxes in boxplots denote 25th to 75th percentiles with whiskers representing min-max, and the central line the median. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271096-4-41467_2022_31725_Fig5_HTML.jpg"
}
|
008869
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "IEC-specific ACC1-inactivation results in a specific loss of Lgr5+ ISCs.ACC1Δ/ΔIEC and ACC1lox/lox control mice were analyzed on day 9 after a 5 day period of tamoxifen treatment. a Expression of Lgr5 gene in IECs isolated from the small intestine. Data was pooled from 3 independent experiments with a total of n = 12 and 13 mice per group. b Immunohistochemical staining of the small intestine (ileum) with anti-Olfm4 antibody. For quantification >10 crypts were examined per mouse. Data is shown from one representative out of 3 independent experiments with n = 5 mice per group, bar = 50 µm. c Expression of Tert, Muc2, Lyz1 and Chgb in IECs isolated from the small intestine. Data was pooled from 3 independent experiments with a total of n = 12 and 13 mice per group. d Immunohistochemical staining of small intestinal paneth cells in the ileum of ACC1Δ/ΔIEC and ACC1lox/lox control mice with anti-MMP-7 antibody (upper panel) and PAS staining of neutral and acidic mucins (in pink), representing goblet cells (lower panel), bar = 200 µm. For quantification >10 crypts were examined per mouse. Data was pooled from 2 independent experiments with a total of n = 3 and 4 mice per group. e Frequency of DAPI-Epcam+Lgr5high ISCs and DAPI-Epcam+Lgr5int progenitor cells within total DAPI-Epcam+ epithelial cells isolated from the duodenum/jejunum or the ileum of Lgr5-EGFP-IRES-creERT2 (Lgr5-EGFP) control and ACC1∆/∆Lgr5 mice one day upon the last tamoxifen injection. Data pooled from 2 independent experiments with a total of n = 7 mice per group. Statistical significance was analyzed using unpaired two-tailed Student’s t-test (a–e) with *p < 0.05, **p < 0.01, ***p < 0.001. ****p < 0.0001. Exact p values provided as Source Data. Bar graphs represent mean and error bars indicate SD. Boxes in boxplots denote 25th to 75th percentiles with whiskers representing min-max, and the central line the median. Source data are provided as a Source Data file.",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271096-5-41467_2022_31725_Fig2_HTML.jpg"
}
|
008870
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Port implantation in the left forearm in a 16-year-old girl with a rhabdomyosarcoma. a Posteroanterior fluoroscopy confirms correct placement of the port catheter at the level of the central superior vena cava, just above the right atrium. b Oblique projection fluoroscopy image shows an implanted port chamber, with the port-puncture needle inserted in the proximal lateral forearm distal to the cubital fossa. Injection of a small volume of contrast agent proved the correct placement and connection of the port system",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271099-0-247_2022_5321_Fig1_HTML.jpg"
}
|
008871
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Axial MR images in a 10-year-old girl (patient 13) with an aneurysmal bone cyst (ABC) of the posterior half of the C3 ring. a Axial MR image 2 weeks before the first treatment shows expansion and replacement of spinous process and bilateral lamina at C3. More aggressive ABCs tend to have innumerable tiny cysts, as depicted in this case. b Axial MR image at the same level 3 months later shows near doubling in size of this very aggressive lesion, now with effacement of the canal",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271102-0-247_2022_5328_Fig3_HTML.jpg"
}
|
008872
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Computed tomography images in a 16-year-old boy (patient 5) with an aneurysmal bone cyst (ABC) involving C5, C6 and C7. a Diagnostic axial CT at C6 level before first treatment shows ABC expanding and replacing the entire right half of the vertebral ring at that level. b Diagnostic axial CT at same level 5 years after last treatment shows sclerotic bone has replaced the entirety of the ABC. This appearance was similar at all the other levels",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271102-1-247_2022_5328_Fig2_HTML.jpg"
}
|
008873
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Cross-sectional images from a 14-year-old boy (patient 9) with a C6 aneurysmal bone cyst (ABC). a Axial pre-treatment supine T1-W MR image following contrast administration shows a destructive and exophytic multilocular cystic mass replacing the right half of the C6 ring and surrounding the vertebral artery (arrow). b Axial supine CT image during biopsy and first treatment at the same level as (a) shows a 14-gauge (G) guiding needle (single arrow) through which passes a 15-G biopsy needle (double arrows). c Axial supine CT on the same date and at the same level as in (a and b) shows three separate needles within different portions of the ABC with doxycycline foam (appearing black from air in foam) throughout the different loculations of the lesion. d Diagnostic axial CT at same level 3 years after last treatment shows healing of the ABC",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271102-2-247_2022_5328_Fig1_HTML.jpg"
}
|
008874
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Ecchordosis physaliphora in a 24-year-old male patient with headache. MRI shows a midline, intradural, cystic lesion located in the retroclival prepontine region (black arrows) with intraosseous extension into the dorsal aspect of the clivus (white arrows). It shows T2 high (a, sagittal; b, axial), T1 low SI (c, sagittal), and lack of enhancement after gadolinium contrast media intravenous injection (d, e, axial). CT (f) reveals a bony defect in the dorsal clivus representing the stalk (white dotted arrow) connecting the retroclival and intraosseous components of the lesion. Note the well-marginated and scalloped bone margins of the lesion in the dorsal clivus",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-0-234_2022_2986_Fig1_HTML.jpg"
}
|
008875
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Nasopharyngeal carcinoma in a 28-year-old male patient. MRI shows a lesion of the right Rosenmüller fossa (white dotted arrows) invading the clivus posteriorly. Bony invasion (white arrows) is better depicted on axial T1W non-CE image as a focal area of low SI in the clivus next to the primary tumour (a). Bony involvement is less noticeable on axial T2W (b), axial (c), and sagittal (d) T1W CE images",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-1-234_2022_2986_Fig14_HTML.jpg"
}
|
008876
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Sphenoid epidermoid cyst as an incidental finding in a 74-year-old female patient. Axial CT images (a and b) reveal a rounded lytic lesion in the right greater sphenoid wing (white arrows) with sclerotic margins and homogenous density similar to cerebrospinal fluid. Axial MRI images show that the lesion has high SI on T2W (c), heterogeneously low/dirty SI on fluid attenuated inversion recovery (d), and high SI on DWI b1000 sequences (e) due to the restricted water movements. Epidermoid cyst has similar features as arachnoid cyst on CT. Arachnoid cysts would have demonstrated homogeneous low SI on fluid attenuated inversion recovery MRI — as low as cerebrospinal fluid — and facilitated diffusion on DWI",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-10-234_2022_2986_Fig4_HTML.jpg"
}
|
008877
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Arrested pneumatisation of the sphenoid sinus as an incidental finding in a 51-year-old female patient with headache. The sphenoid sinus is replaced by a non-expansile solid lesion (white arrows) showing high SI on MRI axial T1W (a) and T2W images (b), and homogeneous low SI on sagittal T1W fat-saturated sequence (c). Axial bone algorithm reconstruction CT image (d) shows a lesion with sclerotic margins, internal curvilinear calcifications, foci of fat, and loss of bone trabeculae (white dotted arrow). Note the absence of a cortical bone breach",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-11-234_2022_2986_Fig3_HTML.jpg"
}
|
008878
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Clival metastasis in a 58-year-old female patient with known breast cancer and focal retro-orbital uptake on scintigraphy (not shown here). Axial T2W (a), axial fluid attenuation inversion recovery (b), sagittal T1W (c), and axial T1W fat-saturated CE (d) MRI images show a hypervascular clival metastasis (white arrows)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-12-234_2022_2986_Fig19_HTML.jpg"
}
|
008879
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Right spheno-ethmoidal ossifying fibroma as an incidental finding in a 79-year-old female patient. Coronal CT image (a) shows a well-demarcated expansile lesion with central fibrous density areas (white arrow), surrounded by an ossified rim (white dotted arrow). MRI (b, c, and d) shows a lesion with intermediate central SI (fibrous areas, white arrows) and a peripheral rim of low SI (ossified area, white dotted arrows). The central fibrous areas have low SI on axial T1W image (b), mixed SI on axial T2W image (c), and inhomogeneous SI on sagittal T1W fat-saturated CE image (d). The peripheral ossified rim and internal septa appear hypointense in all MRI sequences",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-14-234_2022_2986_Fig10_HTML.jpg"
}
|
008880
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Fibrous dysplasia in a 20-year-old male patient with right atypical trigeminal neuralgia. Coronal CT image (a) reveals an expansile lesion in the middle cranial fossa extending into the right sphenoid sinus, pterygoid plates, sphenoid wings, and parietal bone with a “ground glass” appearance representing fibrous tissue (white arrow). Notice the narrowing of the right foramen rotundum (white dotted arrow) compared to the contralateral (black dotted arrow). Sagittal CT image (b) shows expansion of the clivus (arrow). At MRI, the lesion shows low SI on coronal T1W image (c, arrow) and highly inhomogeneous enhancement on sagittal T1W CE image (d, arrow)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-15-234_2022_2986_Fig5_HTML.jpg"
}
|
008881
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Neurenteric cyst of the clivus as an incidental finding in a 56-year-old female patient with headache. MRI shows an oval, intramedullary cystic lesion of the clivus (arrows). Compared to the cerebrospinal fluid, this lesion is characterised by intermediate-to-high SI on sagittal (a) and axial (b) T1W images, and high SI on sagittal (c) and axial (d) T2W images, thus reflecting high protein content",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-16-234_2022_2986_Fig2_HTML.jpg"
}
|
008882
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Primary lymphoblastic lymphoma of the left sphenoid sinus in a 79-year-male patient with headache. MRI reveals a homogeneous soft tissue mass in the left sphenoid sinus (white arrows) showing intermediate SI on sagittal T1W (a) and axial T2W (b) images and moderate homogeneous enhancement after intravenous gadolinium contrast agent on axial T1W fat-saturated images (c). The right sphenoid sinus is filled by partially dehydrated mucus due to the drainage obstruction (c, black dotted arrow). Bone algorithm reconstruction CT obtained one month later (d) shows a rapid growth of the lesion with massive destruction of the clivus (*)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-17-234_2022_2986_Fig17_HTML.jpg"
}
|
008883
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Sphenoid localization of multiple myeloma in an 82-year-old male patient. Coronal (a) and axial (b) CT images show a lytic lesion in the left greater sphenoid wing (white arrows) surrounded by bone sclerosis (white dotted arrows). MRI reveals a lesion in the left greater sphenoid wing characterised by low SI on sagittal T1W image (c, white arrow) and vivid enhancement after intravenous gadolinium contrast agent injection on axial T1W fat-saturated image (d, white arrow)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-18-234_2022_2986_Fig18_HTML.jpg"
}
|
008884
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Chordoma of the clivus in a 41-year-old male patient with headache. The lesion appears as a destructive, multilobulated, well-circumscribed, expansile mass located in the midline next to the spheno-occipital synchondrosis. At MRI, high SI on sagittal T2W image due to the fluid content (a, black arrow) and honeycombing enhancement on axial T1W fat-saturated CE image (b, white arrow) are found. Axial CT images well depict a massive bony erosion of the clivus (c and d, white dotted arrows)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-2-234_2022_2986_Fig13_HTML.jpg"
}
|
008885
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Fungus ball of the left sphenoid sinus (black arrows) in a 61-year-old female patient complaining of headache. CT shows a soft tissue density mass within the left sphenoid sinus with peripheral foci of calcific deposit due to fungal hyphae (black dotted arrows). Complete sinus opacification indicates obstruction of the ipsilateral spheno-ethmoidal drainage recess (a). MRI shows a mass in a completely mucous-filled left sphenoid sinus: the lesion is characterised by intermediate-to-low T1W (b) and T2W (c) SI and intralesional calcified foci with very low SI (black dotted arrows) similar to the air signal. Peripheral rim enhancement is seen on the axial T1W image obtained after gadolinium contrast injection (white arrow, d). The fungus ball shows intralesional areas of low SI on b800 DWI trace (e), and very low ADC values (f) due to the presence of calcifications and paramagnetic metals of fungal hyphae (black dotted arrows). These findings are suggestive for non-invasive fungal infection",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-3-234_2022_2986_Fig6_HTML.jpg"
}
|
008886
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Sphenoid haemangioma as an incidental finding in a 70-year-old female patient with sarcoidosis and chronic rhinosinusitis. CT shows a small osteolytic lesion (white arrows) in the left greater sphenoid wing characterised by well-defined sclerotic margins and a “sunburst appearance” on axial (a) and coronal (b) images. The fatty component is found on axial (c) and coronal (d) soft tissue reconstruction algorithm images",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-4-234_2022_2986_Fig9_HTML.jpg"
}
|
008887
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Neuroendocrine carcinoma of the sphenoid sinus in a 42-year-old female patient complaining of headache. CT with bone algorithm reconstruction shows massive opacification of both sphenoid sinuses (white arrows) with partial reabsorption of the intersphenoid septum on axial section (a, white empty arrow), and erosion of the floor of the sella turcica on sagittal section (b, white dotted arrow). MRI shows a solid mass replacing the right sphenoid sinus (white arrows) with low SI on T2W (c) and vivid enhancement on T1W fat-saturated CE images (d). Notice the right spheno-ethmoidal recess enlargement on sagittal section (b and c, white arrowheads) and the mucous retention in the right nasal fossa (c, *). An incidental osteoma in the right sphenoid sinus is found (a, c, and d, white curved arrows)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-5-234_2022_2986_Fig15_HTML.jpg"
}
|
008888
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Inverted papilloma of the right sphenoid sinus in a 71-year-old male patient. MRI shows a solid expansive lesion in the right nasal fossa in correspondence to the spheno-ethmoidal recess (white arrows). That lesion has similar SI to the grey matter on axial T2W images (a and b) with focal “cerebroid” appearance (b, white curved arrow) and moderate enhancement on T1W fat-saturated CE image (c). Axial bone reconstruction algorithm CT reveals a focal plaque-like hyperostosis in the anterior wall of the right sphenoid sinus (d, white dotted arrow), as the likely site of tumour origin",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-6-234_2022_2986_Fig12_HTML.jpg"
}
|
008889
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Sphenoid osteomyelitis in a 67-year-old male patient with chronic rhinosinusitis. Axial (a) and coronal (b) CT with bone algorithm reconstruction show maxillary sinusitis, osteolysis of the right greater sphenoid wing (white arrows) without cortical involvement, and thickening of maxillary sinus walls on both sides (dotted white arrows). Axial MRI images show inflammatory bony changes of the right greater sphenoid wing characterised by low SI on T1W image (c, white arrow) and mild enhancement after gadolinium contrast agent injection on T1W fat-saturated image (d, white arrow)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-7-234_2022_2986_Fig8_HTML.jpg"
}
|
008890
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Left sphenoid sinus mucocele with high protein content in a 53-year-old male patient with headache. MRI shows a large mass (white arrows) displacing the ipsilateral internal carotid artery posteriorly (white dotted arrow) on T2W axial image (a) and the pituitary gland superiorly (white dotted arrow) on T2W sagittal image (b). Sphenoid sinus is markedly enlarged with mucous content and peripheral rim enhancement on axial (c) and sagittal (d) T1W fat-saturated CE images. No sign of superimposed infection or invasion of the adjacent structures is observed",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-8-234_2022_2986_Fig7_HTML.jpg"
}
|
008891
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Invasive pituitary macroadenoma in a 60-year-old male patient with visual field defect. A huge pituitary macroadenoma (white arrows) extending into the suprasellar region through the pituitary stalk that invades the sella turcica and clivus. The “snowman” sign (white dotted arrows) is nicely depicted on coronal (a)—sagittal (b) CT sections and sagittal MRI T1W CE image (c) since the soft tumour is indented by the diaphragm sellae. This sign helps in differentiating macroadenomas from pituitary fossa meningiomas. Notice the focal erosion of the dorsal aspect of the clivus on the sagittal bone algorithm reconstruction CT image (d, white curved arrow)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271108-9-234_2022_2986_Fig11_HTML.jpg"
}
|
008892
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "a CT template (512 × 512 × 26 voxel), b MRI-CT template (512 × 512 × 26 voxel), c MRI template (160 × 240 × 256 voxel).",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271109-1-234_2021_2875_Fig2_HTML.jpg"
}
|
008893
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Validation of alignment with the newly developed registration pipeline (*)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271109-2-234_2021_2875_Fig3_HTML.jpg"
}
|
008894
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Examples of images following data augmentation in the starting dataset (original image is in the top left corner)",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271110-0-234_2022_2921_Fig2_HTML.jpg"
}
|
008895
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Example of a Chiari MRI misclassified as normal",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271110-1-234_2022_2921_Fig5_HTML.jpg"
}
|
008896
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Example of a normal MRI misclassified as Chiari",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271110-3-234_2022_2921_Fig4_HTML.jpg"
}
|
008897
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Examples of an image cropped to 64 × 64 pixels of the craniocervical junction without skull stripping",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271110-4-234_2022_2921_Fig1_HTML.jpg"
}
|
008898
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
|
{
"caption": "Representative T2 sagittal imaging showing eAFMS; see Table 1 for a description of the findings in each grade. Sagittal (a-d, f-i) and axial (e) T2 magnetic resonance images: a A 23-month-old girl with a normal CCJ. b A 30-month-old girl with AFMS 1 stenosis. c An 8-month-old girl with AFMS 2a stenosis. d A 4-year-old boy with AFMS 2b stenosis. e An 8-month-old girl with AFMS 2c stenosis. f A 7-year-old girl with AFMS 3a stenosis. g A 12-month-old boy with AFMS 3b stenosis. h A 7-year-old girl with AFMS 4a stenosis. i A 9-month-old boy with AFMS 4b stenosis. AFMS achondroplasia foramen magnum score, CCJ craniocervical junction, eAFMS extended achondroplasia foramen magnum score",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_124_46-PMC9271114-0-247_2022_5348_Fig1_HTML.jpg"
}
|
008899
|
hf://datasets/vector-institute/open-pmc-18m@b5bf5b815f7ed24176e14a861ca062afe8d8775d/data_00028.tar
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.