Open-PMC-18M
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json dict | jpg image | __key__ string | __url__ string |
|---|---|---|---|
{
"caption": "Rescuing Molecular Oscillations within the LNvs Is Not Sufficient to Rescue Locomotor Activity RhythmsThe rescued mutant genotype is y w;pdf–GAL4;UAS–CYC,cyc01/cyc01. The flies were entrained in standard LD conditions and timepoints taken. Molecular oscillations were examined by whole-mount in situ hybridization of the tim gene. Double staining with a Pdf probe was used to label the LNvs neuronal group.(A and B) These show representative duplicate experiments. No tim mRNA signal is detectable in the dorsal region of the brain. The lower arrows point to the s-LNvs and the upper arrows to the l-LNvs. (A) Brain taken at timepoint ZT3. Panels shown from left to right are Pdf (green, FITC labeled), tim (red, Cy3 labeled), and an image overlay. (B) Brain taken at timepoint ZT15. Panels shown from left to right are Pdf (green, FITC labeled), tim (red, Cy3 labeled), and an image overlay.(C) The double-plotted actograms of rescue mutant and control flies in a standard LD:DD behavior assay. The colors on the background indicate the lighting conditions of the behavior monitors (white, lights on; light blue, lights off). In the actogram, the average locomotor activity of the group of flies is plotted as a function of time. The left panel shows the actogram of the rescued mutant flies (y w;pdf–GAL4/+;UAS–CYC,cyc01/cyc01, n = 30). RI (rhythm index; Levine et al. 2002a) = 0.14. The right panel shows the actogram for the rescued wild-type (control) flies (y w;pdf–GAL4/+;UAS–CYC/+, n = 32, RI = 0.61).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC193604-0-pbiop0000013pg001.jpg",
"summary": "The subfigure shows a brain taken at timepoint ZT3, where no tim mRNA signal is detectable in the dorsal region. The lower arrows point to the small LNvs (s-LNvs) and the upper arrows to the large LNvs (l-LNvs). The tim gene is a direct target of the circadian oscillator transcriptional feedback loop, and its expression levels cycle robustly in wild-type flies, with a trough at ZT3. The rescue of the cyc01 mutation specifically in the LNvs using CYC overexpression restored tim mRNA cycling within these cells, indicating successful rescue of the molecular oscillator within the LNvs."
} | 000000 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "All Brain Clock Neuronal Groups Maintain Robust Oscillations of tim RNA Levels in DDWild-type flies were entrained for at least 3 days and then released into DD. tim RNA was assayed at trough (left panels) and peak (right panels) timepoints by whole-mount in situ hybridization. Wild-type flies in LD (A) were compared with the eighth day of DD (B). On the eighth day of DD, the locomotor activities of the fly population were still in close synchrony, without any obvious phase spreading (data not shown). Left panels, brains at ZT3 (A) or CT3 (B); right panels, brains from ZT15 (A) or CT15 (B). Both (A) and (B) are representative of three replicate experiments.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC193604-3-pbiop0000013pg002.jpg",
"summary": "The subcaption and full caption indicate that tim RNA levels in different neuronal groups of fly brains were assayed after 8 days in constant darkness (DD). The context passage highlights that all tim-expressing brain cell groups, including l-LNvs, s-LNvs, LNds, and DNs, maintain robust oscillations of tim RNA levels even after 8 days in DD. This contrasts with previous findings where l-LNvs initially fail to maintain oscillations but adapt to become rhythmic again after about 2 days in DD. These results suggest that multiple brain neuronal groups might act together to support robust rhythms."
} | 000001 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A PDF Peptide Binds to Many Cells, Including Several Clock Neuronal GroupsIn vitro biontinylated PDF peptide was used to visualize the peptide binding locations (middle panels, with Cy3) in the brain (see Materials and Methods for details). We used membrane-bound GFP (green panels on the left) to label specific circadian neurons as well as their projections (right panels show the overlay of both channels).(A) The brain is from flies with labeled LNvs (y w,UAS–mCD8iGFP;pdf–GAL4). Numerous cells at the periphery of the medulla have the vast majority of the bound PDF peptide signal within the brain. This region receives widespread dendritic arborizations from the l-LNvs.(B) Bound PDF peptide was also detected on the surface of LNvs at a lower intensity. LNv cell bodies were labeled using UAS–mCD8iGFP;pdf–GAL4. Since the signal from the Cy3 channel was much weaker than the GFP signal, we reduced the output gain from the GFP channel. Sequential scanning was used to prevent cross-talk between the two channels.(C) y w,UAS–mCD8iGFP;tim–GAL4/+ flies were used to label all circadian neurons. In the dorsal region shown in this series, the arrow points to a group of DN3 neurons.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC193604-4-pbiop0000013pg005.jpg",
"summary": "The bound PDF peptide was detected coincident with DN3 clock neurons within the superior protocerebrum region, as shown in Figure 5C. The peptide colocalized with GFP in brains from a strain with GFP-labeled clock neurons. The staining intensity was temporally constant, and the results were consistent with two differently biotinylated PDF peptides."
} | 000002 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Electron micrograph of Proteobacteria in eukaryotic cell",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC193607-0-pbiop0000031pg001.jpg",
"summary": ""
} | 000003 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A. Real time image of the translocation of ARF1-GFP to the plasma membrane. HeLa cells that had been stably transfected with ARF1-GFP were transiently transfected with myc-ARNO, serum starved overnight, and treated with 100 nM insulin. Images were collected every 30 seconds using a Molecular Dynamics 2001 confocal microscope. The time intervals that were indicated on the upper right hand corner of each panel represent the time after the addition of insulin. B. The translocation of ARF1-GFP to the plasma membrane by the effects of insulin requires ARNO. ARF1-GFP/HeLa cells were transfected with myc-ARNO, treated, fixed, and stained for myc-epitope as described in the Materials and Methods section. Images displaying ARF1-GFP (green) and myc-ARNO (red) were merged us ing Adobe Photoshop software.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212319-1-1471-2121-4-13-3.jpg",
"summary": "The translocation of ARF1-GFP to the plasma membrane in response to insulin requires ARNO. HeLa cells stably transfected with ARF1-GFP were transiently transfected with myc-ARNO, serum-starved overnight, and treated with insulin. Cells were then fixed, stained for the myc-epitope, and imaged. The merged images show ARF1-GFP (green) and myc-ARNO (red). Without ARNO, a significant accumulation of ARF1-GFP on the plasma membrane was not observed."
} | 000004 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A Constellation of NeuronsImage courtesy of Miles Herkenham.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212696-0-pbiop0000017pg001.jpg",
"summary": ""
} | 000005 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Expression of Dll in Bacteriocytes and the Pattern of Bacteriocyte Development Are Conserved in Parthenogenetic Females of P. spyrothecae\nConfocal micrographs of P. spyrothecae parthenogenetic embryos stained with anti-Dll antibody (red).(A) Dll is first detected in stage 6 embryos in one or two nuclei posterior to the cellular blastoderm (arrow).(B) By stage 8, the bacteria have been transferred to and entirely fill the embryo (red arrowhead). The Dll-expressing nuclei (arrow) have become highly polyploid.(C and D) At stage 12, only the original bacteriocyte nuclei are observed expressing Dll (white arrow), but by stage 14 (D) additional nuclei (blue arrow) closely apposed to the dorsal germband express Dll.(E) By stage 15, these new nuclei surround the original bacteriocyte, and at later stages the bacteria are divided into individual cells.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212699-0-pbiop0000021pg004.jpg",
"summary": "In P. spyrothecae, one or two nuclei are originally determined as bacteriocytes and become highly polyploid prior to bacterial invasion. By stage 8, the bacteria have been transferred to and entirely fill the embryo, and the Dll-expressing nuclei are highly polyploid."
} | 000006 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Elimination of B. aphidicola by Treatment with Antibiotics Has No Effect on the Determination and Maintenance of the Bacteriocyte Cell Fate in A. pisum\n(A–C) Confocal micrographs of control embryos stained with anti-Dll antibody (red) show expression of Dll, as described in Figure 1. Enlarged views of the bacteria within the broken white boxes in each embryo are shown in (A′)–(C′).(D–F) Embryos within aposymbiotic aphids at comparable stages as the controls in (A)–(C) express Dll in bacteriocyte nuclei. No bacteria are observed within these embryos, as seen in the enlarged views of (D′)–(F′).",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212699-1-pbiop0000021pg003.jpg",
"summary": null
} | 000007 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The Second Wave of Bacteriocyte DeterminationIn (A)–(D), the embryos, which are normally folded in upon themselves in a pretzel shape within the ovariole (Miura et al. 2003), have been dissected flat, stained with anti-Dll antibody (red) and phalloidin (green), and examined with a confocal microscope.(A) Dll expression (red) in a stage 14 embryo is detected in the labrum (La) and all developing limbs on the ventral surface except the mandibular segment (Mn). (Other abbreviations: An, antenna; Mx, maxilla; Lb, labium; T1, T2, T3, first, second, and third thoracic leg, respectively.) The dorsal surface of the abdomen of the same embryo is shown illustrating Dll expression in the original bacteriocytes (white arrow) and in a more posterior population of nuclei or cells (blue arrow). Germ cells (gc) are labeled.(B) Dll expression is first observed in the new bacteriocyte nuclei at stage 13.(C) By stage 15, many of the new bacteriocytes have migrated to and begun intercalating between the original bacteriocytes.(D) By stage 16, all of the new bacteriocytes have intercalated between the original bacteriocytes.(E) The migration of the new bacteriocytes is seen in a confocal section of an undissected stage 14 embryo.Embryos in (A)–(D) are oriented with the anterior of the germband towards the left.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212699-2-pbiop0000021pg002.jpg",
"summary": "At stage 13, a second population of approximately 40–60 cells located near the posterior end of the dorsal germband begins to express Dll. These cells are inferred to be new bacteriocyte nuclei based on their Dll expression."
} | 000008 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Bacteriocytes Are Retained in One Species That Has Evolutionarily Lost Bacteria, but Not in Males of Another Species That Do Not Inherit Bacteria(A and B) Confocal micrographs of embryos of T. styraci stained with anti-Dll antibody (red). In T. styraci, in which B. aphidicola has been evolutionarily lost (Fukatsu and Ishikawa 1992a), embryos still contain nuclei that express Dll in the correct time and place to be bacteriocyte nuclei. (A) Dll expression is first detected in posterior nuclei at blastoderm at approximately stage 6 (arrow). (B) By stage 14, the original nuclei have divided once or twice and become polyploid (original bacteriocytes), and new cells begin to express Dll (new bacteriocytes; blue arrow) and migrate towards the original bacteriocytes.(C–F) Confocal micrographs of embryos of P. spyrothecae stained with anti-Dll antibody (red). (C) Stage 16 male embryos of P. spyrothecae do not contain B. aphidicola, and no Dll-expressing cells are observed in the expected location for bacteriocytes. We believe that the cells in this location are sperm (marked with an asterisk). Sexual female embryos within the same ovary do contain Dll-expressing original and new bacteriocyte nuclei (white and blue arrows, respectively). (D and E) Transient expression of Dll in putative bacteriocytes is observed in stage 7 male embryos (arrow in male embryo of [D]), but this expression does not persist into stage 10 male embryos (E), where no Dll-expressing nuclei are observed. By contrast, stage 6 female embryos (D) contain polyploid Dll-expressing nuclei (arrow in female embryo of [D]). The sex of each embryo could be determined because males develop synchronously and earlier than females (Lampel 1958, 1968). (F) In stage 14 male embryos, we observe transient Dll expression in nuclei (blue arrow) adjacent to the germ cells (gc) in the correct location to be the second wave of bacteriocyte nuclei. This Dll expression does not persist (see stage 16 male in [C]), and the fate of the cells is unknown.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212699-3-pbiop0000021pg005.jpg",
"summary": "In stage 14 male embryos of P. spyrothecae, weak Dll expression is observed in nuclei adjacent to the germ cells, which are in the correct location to be the second wave of bacteriocyte nuclei. However, this expression does not persist into later stages (stage 16), and the fate of these cells remains unknown."
} | 000009 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Expression of Three Transcription Factors during Early Bacteriocyte Development(A) Drawings of some stages of pea aphid embryonic development, approximately to scale. Embryos develop viviparously within a follicular epithelium of the ovariole (data not shown). For a complete description, see Miura et al. (2003). Bacteria are transferred at stage 7. Embryos are labeled with bacteria (b), head (h), thoracic (t), and abdominal (a) regions. The three thoracic segments (t1, t2, t2) and germ cells (gc) are indicated in the stage 14 embryo.(B) A drawing of a stage 7 embryo illustrates transovarial transfer of the bacteria (red arrowhead) to the embryo and the presumptive bacteriocyte nuclei (arrow).(C) Confocal micrograph of a stage 6 embryo stained with anti-Dll antibody (red, indicated by arrow). Anti-Dll labels syncytial nuclei (presumptive bacteriocyte nuclei) in the posterior of the embryo.(D) Confocal micrograph of stage 7 embryo stained with anti-Dll and FP6.87 antibodies. Soon after the bacteria begin to invade the embryo, we observe staining with the FP6.87 antibody localized to the nucleoli (blue), which recognizes both Ubx and Abd-A in diverse arthropods, in the same nuclei that are already expressing Dll (red). The region outlined with a broken white box is enlarged in (D′) to show the bacteria, and only the green channel is shown in monochrome. The red arrow indicates one bacterium.(E and F) In these two panels of the same focal plane from the same stage 9 embryo, Ubx/Abd-A staining (blue) is observed throughout the entire nucleus of all nuclei that also express Dll (red).(G) Confocal micrograph of a stage 8 embryo stained with anti-En (yellow). As the transfer of bacteria (arrowhead) is being completed, the bacteriocyte nuclei begin to express En (yellow, indicated with arrow).In (C)–(G), confocal micrographs show only one focal plane of the embryo, so not all bacteriocyte nuclei in each embryo can be seen. In all figures, F-actin is stained with phalloidin (green). Embryos in all figures, except Figure 2, are oriented with anterior of the entire embryo (towards the germarium) to the left.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212699-4-pbiop0000021pg001.jpg",
"summary": "We tested five cross-reacting antibodies and found that three of them stained nuclei that form bacteriocytes of A. pisum. These antibodies recognize the homologues or possibly paralogues of their respective target proteins. Specifically, we observed that the Distal-less (Dll) protein is expressed in syncytial nuclei at the posterior of the blastoderm embryo just prior to the invasion of bacteria into the embryo. As the bacteria enter the embryo, these nuclei start to express a second protein, Ultrabithorax (Ubx) or Abdominal-A (Abd-A) or both, detected by the FP6.87 antibody. By stage 9, Ubx/Abd-A staining (blue) is observed throughout the entire nucleus of all nuclei that also express Dll (red)."
} | 000010 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Caenorhabditis elegans worms",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC212701-0-pbiop0000026pg001.jpg",
"summary": ""
} | 000011 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "ARK and DRONC Are Required for Spermatid Individualization(A and C) Testis from β2tub-Ark-RNAi and β2tub-Dn-DRONC males, respectively. Active DRICE-positive cysts are present, but cystic bulges and waste bags are largely absent.(B and D) Investment cone movements in testis from β2tub-Ark-RNAi and β2tub-Dn-DRONC, respectively, are uncoordinated.(E, G, and H) EM images of an elongated cyst from a β2tub-Ark-RNAi male. Some individualization failures are observed (E, G, and H), two of which are highlighted by the dashed lines in (G) and (H). In addition, many spermatids that have apparently undergone individualization still contain large amounts of excess cytoplasm (E and G).(F) EM image of a cyst from a β2ub-Dn-DRONC male. A large region in which individualization did not occur is outlined.(I) Western blot from wild-type (Wt) and β2tub-Ark-RNAi (DArki) testis probed with anti-ARK and anti-DRICE antibodies. ARK, but not DRICE, levels are greatly reduced in β2tub-Ark-RNAi testis.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-0-pbiop0020015pg002.jpg",
"summary": "ARK and DRONC are required for spermatid individualization. Decreasing ARK levels specifically in the male germline using β2tub-Ark-RNAi and expressing a dominant-negative version of DRONC (Dn-DRONC) under the β2tub promoter resulted in active DRICE-positive cysts, but cystic bulges and waste bags were largely absent. This indicates that while DRICE is still activated, the normal process of individualization is disrupted."
} | 000012 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The bln1 P-Element Insertion, Which Inhibits Cyt-c-d Expression, Results in Pleiotropic Defects in Spermatogenesis(A) Genomic organization of the cyt-c-d region. Upper half of the panel illustrates the structure of the region, as described by Arama et al. (2003). The lower half of the panel indicates the relative locations of several other genes in the region, as annotated by the Berkeley Drosophila Genome Project (http://flybase.bio.indiana.edu/search/) as of August 2002. The bln1 P element is inserted within the cyt-c-d transcription unit. This P element is also inserted within the transcription unit of a second gene, CR31808-RA (RE70695). Both of these genes and the bln1 P element reside within the intron of a third gene, CG31782.(B and D) Wild-type and bln1 testis, respectively, stained with anti-active DRICE antibodies. Active DRICE immunoreactivity is eliminated in bln1 testis, as described in Arama et al. (2003).(C and E) Wild-type and bln1 testis, respectively, stained with AXO49 antibodies (blue), which recognize polyglycylated β2tub present in axonemal microtubules, and phalloidin (red). Polyglycylation occurs prior to individualization (Bressac et al. 1995). Axonemes of elongated cysts from wild-type flies stain with AXO49 (C), while those from bln1 males do not (E).(F–I) EMs of cysts of different developmental stages from wild-type (F and G) and bln1 (H) testis. (F) Wild-type cyst prior to individualization. Note the structures of the major and minor mitochondrial derivatives, in particular the fact that the major mitochondrial derivative is increased in size and is electron dense. (G) Wild-type cyst following individualization. (H) Representative example of the most mature cysts found in bln1 testis. Note the dramatically increased cell size and the lack of differentiation of the major and mitochondrial derivatives, as compared to wild-type.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-1-pbiop0020015pg005.jpg",
"summary": "Males homozygous for a P-element insertion (bln1) in the cyt-c-d gene were sterile and lacked active DRICE staining in testis, as described in Arama et al. (2003). This suggests that cyt-c-d may be required for DRICE activation, although the bln1 insertion also causes multiple defects in spermatogenesis prior to individualization."
} | 000013 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "HID, dFADD, and DREDD Participate in Individualization(A) HID protein (green) is concentrated in the region of the cystic bulge, which is marked by the presence of the phalloidin-stained individualization complex (red).(B) HID immunoreactivity is absent in testis from hid 05014/H99 flies.(C) Active DRONC (green) is associated with the trailing edge of the individualization complex in a wild-type cyst.(D) Active DRONC is absent from the individualization complex in cysts from hid 05014/H99 males.(E) EM section from hid 05014/H99 testis. Essentially all spermatids have failed to individualize.(F) Higher magnification view of boxed area in (E). Multiple spermatid units sharing a common cytoplasm are outlined by the dashed line.(G) Representative EM section of cyst from dFadd f02804/dFadd f02804 testis. Essentially all spermatids have failed to individualize.(H) EM section of cyst from Dredd B118/Dredd B118 testis in which individualization has failed to occur. In some other cysts from this same male, individualization proceeded apparently normally (data not shown).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-3-pbiop0020015pg004.jpg",
"summary": "Cysts from dFadd f02804/dFadd f02804 testis showed a range of phenotypes at the EM level, with almost all cysts (greater than 90%) displaying defects in individualization similar to those observed in β2tub-DIAP1 and β2tub-p35 flies. This indicates that dFADD participates in individualization, likely independent of promoting DREDD activation."
} | 000014 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "DRONC Activation Occurs in Association with Individualization Complexes and Is ARK-Dependent(A and B) Wild-type testis stained for active DRICE (green), phalloidin-stained filamentous actin (red), and TOTO-3-stained DNA (blue). (A) Active DRICE is present throughout the length of cysts undergoing individualization. (B) Higher magnification of the testis in (A). The arrowhead points to a cyst in which the individualization complex has assembled around the spermatid nuclei, but DRICE activation has not occurred. The arrow points to a neighboring cyst in which the individualization complex has just begun to move away from the spermatid nuclei. Active DRICE is now present throughout the length of this cyst, indicating that DRICE activation within a cyst occurs rapidly and globally.(C) Active DRONC (green) is initially present in a punctate pattern, apical to the individualization complex (red) at the base of the testis (arrowheads). The individualization complex then moves through the region containing active DRONC (arrow).(D) Subsequently, active DRONC is found associated with the trailing edge of the individualization complex as it moves apical within the cyst. A higher magnification view of active DRONC staining in the left-most cyst is shown in the inset.(E and F) Active DRONC is eliminated in cysts from β2tub-Ark-RNAi and β2tub-Dn-DRONC testis, respectively.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-4-pbiop0020015pg003.jpg",
"summary": "Active DRONC was initially observed in a punctate pattern just apical to the juxtanuclear individualization complex (arrowhead in Figure 3C). The individualization complex then moved through this region (arrow in Figure 3C)."
} | 000015 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Active DRICE Is Eliminated from the Cytoplasm of Wild-Type Spermatids Following Passage of the Individualization Complex, but Not from Spermatids in Which Caspase Activity Has Been Inhibited(A) Cystic bulge from a wild-type cyst stained with active DRICE (red). The cystic bulge (arrowhead) is moving to the left. Active DRICE staining is absent in areas of the spermatid bundle that the individualization complex has passed through and in which excess cytoplasm has been eliminated (arrow).(B) Cystic bulge from a β2tub-p35 cyst. The cystic bulge (arrowhead) is decreased in size, and active DRICE is present in areas of the spermatid bundle through which the individualization complex has moved (arrows). These observations suggest caspase inhibition results in at least a partial failure to eliminate excess cytoplasm, but that this is not necessarily associated with lack of movement of the individualization complex.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-5-pbiop0020015pg007.jpg",
"summary": "Active DRICE was not effectively swept up into the stunted cystic bulges in the presence of caspase inhibitors such as p35 or in other contexts where caspase activity was inhibited. This suggests that caspase inhibition results in a partial failure to eliminate excess cytoplasm, while the movement of the individualization complex is not necessarily affected."
} | 000016 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "driceless Males Lack Active Drice Staining and Show Defects in Individualization(A) Testis from driceless male stained with active DRICE. Active DRICE staining is eliminated.(B) Elongated cysts from driceless male. AXO49 staining (blue) outlines the location of three cystic bulges. Individualization complexes (arrows) are marked with phalloidin (red).(C) Example of a cyst from a driceless male in which individualization has proceeded normally.(D) Example of a cyst from a driceless male in which individualization has failed to occur.(E) Boxed area in (D) shown at higher magnification. A region in which individualization has failed is outlined with a dashed line.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-6-pbiop0020015pg006.jpg",
"summary": "We serendipitously identified a line of flies carrying an X chromosome mutation (driceless) in which DRICE activation during spermatid individualization was completely eliminated. Testis from these flies contained large cystic bulges in which individualization complexes were present as a coordinated front, similar to wild-type. Some cysts from driceless males underwent individualization normally (approximately 50%), as illustrated in the subfigure."
} | 000017 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Caspase Activity Is Required for Spermatid Individualization(A–C) Testis of different genotypes were visualized with antibodies specific for activated Drice (green). (A) Wild-type testis. Active DRICE is present in multiple elongated cysts. Cystic bulges (cb) and waste bags (wb) are indicated by arrows. (B and C) Testes from β2tub-DIAP1 and β2tub-p35 males, respectively. Active DRICE is present in elongated cysts, but cystic bulges and waste bags are reduced in number and size.(D–F) Phalloidin-stained investment cones from testes of different genotypes (red). Spermatid axonemes in (D)–(F) are highlighted by the AXO49 antibody, which recognizes polyglycylated β2tub (Bressac et al. 1995) (blue). (D) In wild-type testes, investment cones move as a coordinated group. (E and F) Coordinated investment cone movement is disrupted in cysts from β2tub-DIAP1 and β2tub-p35 males, respectively.(G–L) EM sections of elongated cysts of different genotypes. (G) A cyst from a wild-type male that has undergone individualization. The boxed region is shown at higher magnification in (J), along with the locations of the major mitochondrial derivative (mj), minor mitochondrial derivative (mi), and axoneme (ax). A single spermatid unit is outlined with a dashed line. (H and I) In cysts from β2tub-DIAP1 and β2tub-p35 males, respectively, many spermatid units are present in a common cytoplasm that contains organelles, often including an enlarged minor mitochondrial derivative. Boxed regions of β2tub-DIAP1 and β2tub-p35 cysts shown in (H) and (I) are shown at higher magnification in (K) and (L), respectively. Several examples of multiple spermatids present in a common cytoplasm are outlined by the dashed line in (K) and (L). Scale bar for EM micrographs = 1 μm.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300883-7-pbiop0020015pg001.jpg",
"summary": "To determine whether caspase activity is required for spermatid individualization, flies expressing the broad-specificity Drosophila caspase inhibitor DIAP1 or the baculovirus caspase inhibitor p35 under the control of the male germline-specific β2-tubulin promoter were generated. In cysts from β2tub-DIAP1 and β2tub-p35 flies, spermatids failed to separate from each other and contained excess cytoplasm, often including an enlarged minor mitochondrial derivative. These phenotypes were observed at higher magnification in EM sections (Figures H, I, K, and L)."
} | 000018 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Developing spermatids in a normal Drosophila testis",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC300886-0-pbiop0020034pg001.jpg",
"summary": ""
} | 000019 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Histological Architecture of CSR Gene Expression in Breast CancerRepresentative ISH of LOXL2 and SDFR1 and IHC of PLOD2, PLAUR, and ESDN are shown (magnification, 200×). Panels for LOXL2, PLAUR, PLOD2, and ESDN represent cores of normal and invasive ductal breast carcinoma from different patients on the same tissue microarray. Panels for SDFR1 demonstrate staining in adjacent normal and carcinoma cells on the same tissue section. Arrows highlight spindle-shaped stromal cells that stain positive for SDFR1 and PLOD2. No signal was detected for the sense probe for ISH or for control IHC without the primary antibody.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314300-0-pbiop0020007pg005.jpg",
"summary": "SDFR1 was expressed at a low level in normal breast epithelial cells and was induced in a significant fraction of invasive ductal carcinomas of the breast. SDFR1 mRNA was detected in breast carcinoma cells and in a small but consistent fraction of peritumor stroma cells. Arrows in the subfigure highlight spindle-shaped stromal cells that stain positive for SDFR1."
} | 000020 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Effect of deH on Agouti ExpressionComparable sections from at/at; deH/deH and at/at; +/+ littermates.(A) At E14.5, deH/deH embryos have a smaller body cavity and loose skin within which Agouti expression appears to be shifted dorsally, as marked by arrows (scale bars = 500 μm).(B) At P4.5, Agouti expression in both dorsal and ventral skin is similar in deH/deH compared to nonmutant, but in the midflank region, there is increased Agouti expression in deH/deH, especially in the upper dermis (scale bars = 200 μm). Sections shown are representative of two mutant and two nonmutant samples examined at each time.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314463-0-pbiop0020003pg006.jpg",
"summary": "At E14.5, the normal ventral-to-dorsal gradient of Agouti expression appeared to extend more dorsally in deH/deH embryos, as shown in Figure 6A. This dorsal extension of Agouti expression is not observed at earlier stages such as E12.5 or E13.5."
} | 000021 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Embryonic Establishment of Dorsoventral Skin PatterningPieces of skin from dorsal, flank, and ventral regions of at/a E12.5 embryos were transplanted into the testes of congenic animals as described in the text. Hair color of the grafts was examined 3 wk later. Grafts of ventral embryonic skin (n = 3) produced yellow hairs, dorsal embryonic skin (n = 4) produced black hairs, and flank embryonic skin produced mostly (13 out of 15) black and yellow hairs in distinct regions as shown. In parallel, in situ hybridization studies revealed that the embryonic flank contains the boundary of expression between Agouti and Tbx15 (scale bars = 1 mm for hairs and 200 μm for in situ hybridization results).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314463-4-pbiop0020003pg007.jpg",
"summary": "Previous studies by Silvers and colleagues showed that ventral skin isolated from at/at embryos produces yellow hair when transplanted into testis. In this study, ventral skin from at/a embryos at E12.5 was transplanted into testes and produced yellow hair in 3 out of 3 grafts. This indicates that dorsoventral identity for adult pigmentation is established by E11.5–E12.5."
} | 000022 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Developmental Expression of Tbx15\n(A) At E12.5, transverse sections at different levels show expression in head mesenchyme (a and b); myotome, occipital, and periocular mesenchyme (b); palatal shelf, cervical sclerotome, and nasal cartilage (c); maxillary and mandibular processes (d); limbs (e); and myotome and lateral mesenchyme (e and f) (scale bars = 500 μm).(B) Transverse sections through the flank at different times show expression in lateral mesenchyme (E11.5), expanding dorsally at E12.5, and both ventrally and dorsally at E13.5, detectable in loose mesenchyme underlying the dermis and the abdominal and subcutaneous muscles (scale bar = 500 μm). At P3.5, Tbx15 is expressed in the entire dermis and is most strongly expressed in dermal sheaths (scale bar = 200 μm).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314463-5-pbiop0020003pg004.jpg",
"summary": "At E12.5, Tbx15 expression is observed in the myotome and lateral mesenchyme, as detailed in the transverse sections of the compound figure. This expression is part of a broader pattern of Tbx15 expression in multiple mesenchymal tissues of the head, trunk, and developing limbs, which is consistent with the reported skull, cervical vertebrae, and limb malformations in mice with the droopy ear allele."
} | 000023 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Embryonic Expression of Tbx15 Compared to Agouti in at/at Mice(A and C) Tbx15. (B and D) Agouti. At E12.5, expression of Tbx15 in dorsal skin is approximately complementary to that of Agouti in ventral skin. At E14.5, the levels of expression for both genes are lower, but Tbx15 expression has expanded ventrally and overlaps extensively with that of Agouti. In all four panels, arrows mark the approximate ventral limit of Tbx15 and the approximate dorsal limit of Agouti (scale bars = 500 μm).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314463-8-pbiop0020003pg005.jpg",
"summary": "At E12.5, expression of Tbx15 in dorsal skin is approximately complementary to that of Agouti in ventral skin. By E14.5, Tbx15 expression expands ventrally and overlaps extensively with Agouti expression. This pattern is observed in adjacent sections hybridized with probes for Tbx15 and Agouti, indicating that dorsoventral identity for adult pigmentation is established by E11.5–E12.5 and maintained throughout later stages of skin development."
} | 000024 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Centrosome-independent spindle assembly",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC314476-0-pbiop0020026pg001.jpg",
"summary": null
} | 000025 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Centriole Migration in Primary Spermatocytes(A) Time-lapse series of confocal images from a wild-type primary spermatocyte expressing GFP-PACT (centrioles) and His2AvD–GFP (chromosomes). The centrioles (arrows) can be seen moving away from the plasma membrane (0) towards the nucleus (N) and then migrating diametrically apart as the chromatin condenses. The chromosomes are fully condensed at timepoint 121 min.(B–D) The two centriole pairs (green) projected over the phase-contrast view (grey) can be seen close to the fenestrated NE and away from the plasma membrane (pm) in control cells (B), while they remain plasma membrane-bound in asp (C) and in colcemid-treated wild-type cells (D). In asp spermatocytes (C), the position of the membrane-bound centrioles correlates tightly with the pointed end of phase-dark protrusions (arrows) that are not present in colcemid-treated cells. These reflect the distribution of phase-contrast membranes known to overlap microtubules in these cells.(E–J) XY projections (E–G) and their corresponding optical sections (H–J) of control (E and H), asp (F and I), colcemid-treated spermatocytes (G and J) expressing an endogenous GFP–α-tubulin confirm that the two major MTOCs in control cells are close to the nucleus, but remain near the plasma membrane in the two experimental conditions. MTOC activity in colcemid-treated spermatocytes was assayed following a 1-s pulse of 350 nm light to inactivate the drug, thus allowing microtubule regrowth. The yellow bar in the XY projections (E–G) marks the position of the corresponding XZ optical sections (H–J).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC317275-2-pbiop0020008pg001.jpg",
"summary": "In asp mutant spermatocytes, the centrioles remain at the plasma membrane and are associated with phase-dark protrusions, which are not present in colcemid-treated cells. These protrusions reflect the distribution of phase-contrast membranes overlapping microtubules. The centrioles in asp mutant cells retain MTOC activity, as evidenced by the presence of γ-Tub23C around the membrane-bound centrioles."
} | 000026 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Time-Lapse Series of Meiosis Progression in Control, asp, and Colcemid-Treated SpermatocytesTimepoint 0 coincides with the time of NEB revealed by the sudden entry of GFP signal into the nucleus. In control cells (Video 2), microtubules are mainly organised around the centrosomes (arrows). However, when centrosomes are kept away from the nuclear region by mutation in asp (Video 3) or colcemid treatment (Video 4), microtubule nucleation and growth are clearly revealed over the nuclear region (N), well away from the centrosomes. Such noncentrosomal microtubules may form bundles that eventually are sorted into spindlelike bipolar microtubule arrays. Microtubules were labelled with an endogenous GFP–α-tubulin fusion.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC317275-3-pbiop0020008pg002.jpg",
"summary": "At the onset of prometaphase, the nuclear envelope becomes fenestrated, allowing GFP–α-tubulin to enter the nucleus, marking the time of nuclear envelope breakdown (NEB). In control cells, microtubule polymerisation is centrosome-dependent, making it difficult to observe noncentrosomal activity. However, in asp mutant and colcemid-treated cells, centrosomes are kept away from the nuclear region, allowing clear observation of noncentrosomal microtubule nucleation and growth within the nuclear region. These microtubules can form bundles and eventually organise into spindle-like bipolar arrays."
} | 000027 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Chromosome Segregation in Anastral Spindles in Drosophila Spermatocytes(Control [Video 5]) At metaphase I (0), the bivalents (revealed by a His2Avd–YFP fusion, shown by double arrowheads) are aligned in the middle of the spindle (revealed by a GFP–α-tubulin fusion), at the metaphase plate. At the onset of anaphase (3 min), the homologue chromosomes start to migrate towards opposite poles (single arrowheads) and to decondense. During anaphase B (4 min and 6 min), the spindle poles move apart from each other and the two sets of decondensed chromosomes become further separated.(asp [Video 6]) At timepoint 0, the bivalents align at the metaphase plate. Homologue chromosomes split apart at the onset of anaphase I (4 min). However, anaphase A migration is highly impaired. By the time the chromosomes start to decondense, they have barely moved towards the spindle poles (8 min and 14 min), and often homologue chromosomes end up included in the same daughter nucleus.(Colcemid [Video 8]) As in asp spermatocytes, the asters (arrows) remain at the plasma membrane at metaphase I in colcemid-treated cells, and the bivalents align in a metaphase plate-like within the acentrosomal spindles (0 min). Homologue chromosomes split apart at the onset of anaphase (upper cell, 6 min) and significantly segregate from one another (upper cell, 8 min; lower cell, 3 min). Further separation of the daughter nuclei during anaphase B is very limited in these cells (8 min), and cytokinesis does not occur.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC317275-4-pbiop0020008pg005.jpg",
"summary": "In contrast to asp cells, in half of the anastral spindles assembled following transient colcemid treatment, homologue chromosomes segregate from one another. However, anaphase in these cells is incomplete, as only the chromosome-to-pole movement (anaphase A) is observed, and the further separation achieved in wild-type cells by the extension of the spindle (anaphase B) is very limited."
} | 000028 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The Place of Noncentrosomal Microtubule NucleationThe initial stages of noncentrosomal microtubule nucleation revealed by an endogenous GFP–α-tubulin fusion (left) and phase contrast (right). Following the corresponding videos, it is possible to unmistakably tell the chromosomes (arrows) apart form the other phase-dark objects that are present over the nuclear region (asterisks). The cell in (A) is shown as a single timeframe and the cell in (B) as a time-lapse series. In both cells, noncentrosomal microtubule nucleation (arrowheads) takes place close to the remains on the NE and does not overlap with the major chromosomes. Nucleation sites can be clustered (A) or dispersed (B). In the time-lapse series (B), only the chromosomes that are in focus are labelled. Timepoint 0 min in these series corresponds to the first sign of noncentrosomal microtubule nucleation, around 11 min after NEB. A white bar marks the growing end of a microtubule bundle that at timepoint 93 min reaches one of the bivalents.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Ultrasound",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC317275-5-pbiop0020008pg004.jpg",
"summary": "The initial stages of noncentrosomal microtubule nucleation were observed using time-lapse microscopy, revealing that nucleation sites can be clustered or dispersed. No significant correlation was found between the site of microtubule nucleation and the chromosomes. Nucleation occurs in close proximity to the remnants of the nuclear envelope (NE) in all observed cells."
} | 000029 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "SIRT-1 Deacetylase—the Human Enzyme That Promotes Cell Survival—in a Dividing Human CellThe enzyme is marked in red, and the image is superimposed on acetylated proteins (green) and condensed chromosomes (blue). (Image courtesy of David Sinclair.)",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC322746-0-pbiop0020012pg001.jpg",
"summary": "SIRT-1, the human enzyme that promotes cell survival, is a member of the Sir-2 family of proteins. Resveratrol is a potent activator of SIRT-1, which is associated with health benefits in humans, including the mitigation of age-related defects such as neurodegeneration, carcinogenesis, and atherosclerosis."
} | 000030 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Expression of ArmΔArm Leads to the Nuclear Localization of Endogenous ArmProtein(A) Wild-type Arm protein appears in stripes that correspond to cells responding to Wg signaling.(B) Expression of ArmΔArm in an armF1a background leads to the nuclear localization of endogenous Arm.(C and D) Dark-field images reveal that expression of both ArmΔArm and ArmS10 leads to similar naked cuticle phenotypes.(E) An anti-Arm Western blot showing a faster-migrating band, which correlates with endogenous Arm's being active, and a slower-migrating band, which correlates with Arm's being inactive.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC338072-0-pbiop0020095pg004.jpg",
"summary": "Expression of ArmΔArm in an armF1a background leads to the nuclear localization of endogenous Arm protein. This effect is observed in subfigure B of the compound figure, which shows that ArmΔArm can drive both wild-type and point mutant forms of Arm into the nucleus. This nuclear localization is consistent with the activation of Wg signaling and is similar to the response seen when negative components of the Wg pathway are removed, resulting in a downshift of the Arm protein on Western blots, indicating a change in its phosphorylation state."
} | 000031 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "C-Terminally Truncated Arm Can Signal If Its Levels Are Increased(A) armXM19 shows a wg mutant phenotype.(B) Expression of GAL4/UAS-driven ArmXM19 protein in armXM19 mutant background rescues this to a wild-type pattern.(C) The same is true of expression of an endogenous promoter-driven truncation ArmS8.(D) Removal of Zw3 has no effect on armXM19 cuticle pattern.(E) However, when ArmS8 is introduced into armXM19, zw3 mutants, the cuticle is naked.(F) Wild-type embryo is shown for comparison.(G–I) Arm stainings reveal that expression of UAS–ArmXM19 (stained for the HA tag [G]) and ArmS8 (stained for Arm [H]) is present in stripes corresponding to Wg striping, whereas removal of Zw3, along with ArmS8 expression, leads to uniform and high levels of Arm throughout the epidermis (I).",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC338072-1-pbiop0020095pg003.jpg",
"summary": null
} | 000032 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "ΔArm Functions through Endogenous Arm(A) Embryonic cuticle of armF1a mutant showing a weak loss-of-function phenotype.(B) Cuticle of armLM134 mutant embryo showing a strong loss-of-signaling phenotype.(C) Embryo mutant for armF1a expressing ArmΔArm showing relatively normal segment polarity.(D) armLM134 mutant expressing ArmΔArm also shows segment polarity.(E and F) Both alleles in combination with a null zw3 allele and expressing ArmΔArm show a complete lack of denticles.(G and H) Both alleles expressing the activated but nontethered form of stabilized Arm, ArmS10, show the naked cuticle phenotype.(I–L) In both missense alleles, the mutant protein is expressed in stripes (I and J), corresponding with Wg expression (data not shown), which is abolished when the key degradation kinase Zw3 is removed (K and L).",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC338072-3-pbiop0020095pg005.jpg",
"summary": "The armF1a allele produces a partial loss-of-function phenotype, resulting in some residual naked cuticle in germline clone embryos. This allele retains the phosphorylation sites required for degradation and accumulates in stripes in response to Wg signal. When ArmΔArm is expressed in embryos with the armF1a mutation, the cuticle pattern shows periodic denticle belts and regions of intervening naked cuticle, indicating that ArmΔArm functions through the endogenous Arm protein."
} | 000033 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Relief of C-Terminal Repression through the Elimination of Cby Leads to Uniform Activation of Signaling(A) A wild-type cuticle shown for comparison.(B) Expression of ArmΔArm in the armF1a background.(C) Expression of a Cby RNAi construct along with ArmΔArm in the armF1a background.(D) Expression of a Cby RNAi construct in an armF1a background.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC338072-4-pbiop0020095pg006.jpg",
"summary": "The expression of a Cby RNAi construct in an armF1a background (in the absence of ArmΔArm) has no visible effect on the cuticle. However, when ArmΔArm is present, reducing Cby levels leads to increased naked cuticle, characteristic of Wnt pathway activation. This suggests that Cby's effect on armF1a protein is dependent on ArmΔArm relocalizing Arm to the nucleus."
} | 000034 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "ArmΔArm Requires Endogenous ArmEndogenous allele indicated at top; ectopically expressed transgenes indicated at left.(A) The wild-type cuticle of a Drosophila embryo.(B) The armXM19 “weak” allele phenotype, similar to wg mutations in which the entire cuticle is covered with denticles.(C) The armO43A01 “medium” allele phenotype shows disintegrated embryos in which cells delaminate owing to an inability to form adherens junctions.(D) armXK22 “strong” allele does not produce embryos, owing to an oogenesis defect.(E) A wild-type embryo expressing ArmS18 shows a wild-type cuticle.(F) armXM19 mutant expressing ArmS18 is rescued to a wild-type cuticle.(G) armO43A01 mutant expressing ArmS18 shows rescued adhesion, but a wg mutant signaling phenotype.(H) armXK22 mutant expressing ArmS18 also shows rescued adhesion, as well as a wg mutant signaling phenotype.(I) Coexpression of ArmΔArm and ArmS18 in wild-type embryos leads to naked cuticle or the uniform Wg active phenotype.(J) Coexpression of ArmΔArm and ArmS18 leads to naked cuticle or the uniform Wg active phenotype in an armXM19 mutant background.(K) Coexpression of ArmΔArm and ArmS18 in armO43A01 mutant embryos leads to naked cuticle or the uniform Wg active phenotype.(L) However, coexpression of ArmΔArm and ArmS18 in “strong” mutant armXK22 background shifts embryos back to the wg mutant phenotype. Expression of the membrane-tethered, stabilized form of Arm (ArmΔArm) leads to uniform activation of signaling in all cells. This effect is independent of whether the cell is exposed to Wg signal or not, because ArmΔArm functions independently of Wg ligand. The membrane-tethered, unstabilized form of Arm (ArmS18) leads to pathway activation only in cells that receive Wg signal, because this form of Arm is still subject to Wg-dependent phosphorylation and phosphorylation-dependent degradation.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Ultrasound",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC338072-5-pbiop0020095pg001.jpg",
"summary": "The \"weak\" class of arm gene mutants, represented by armXM19, shows a phenotype similar to wg mutations, where the entire cuticle is covered with denticles. Expression of the membrane-tethered, stabilized form of Arm (ArmS18) rescues the signaling defects of armXM19, leading to a wild-type cuticle pattern. However, coexpression of ArmΔArm and ArmS18 in an armXM19 mutant background leads to a naked cuticle or the uniform Wg active phenotype, indicating that ArmΔArm can uniformly activate signaling in all cells, independent of Wg ligand."
} | 000035 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Tumor MorphologiesHemotoxylin and eosin staining of WAP-T121 (C and D) and WAP-T\n121\np53+/− (A and B) (also representative of WAP-T121) tumor sections shows that terminal stage adenocarcinomas have varied morphologies. Poorly differentiated solid tumors were comprised of nests (A) or cords of epithelial cells (Tu) that infiltrate a fibrous stroma and were accompanied by necrosis (arrow) and strong immune response (arrowheads). Moderately differentiated glandular tumors (B) consisted of irregular, disorganized glands. In animals of wild-type p53 background, four pilar tumors (C), distinguished by swirls of laminar acellular keratin (arrow), and a single spindle cell carcinoma (D) were also observed. For comparison, a lactating gland from a wild-type animal is shown in Figure 3A. The percentage of animals displaying each of the phenotypes is summarized in (G). Since many tumors shared multiple morphologies, the sum exceeds 100%.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340938-3-pbiop0020022pg006.jpg",
"summary": "Poorly differentiated solid tumors (Figure 6A) are composed of nests or cords of epithelial cells that infiltrate a fibrous stroma. These tumors are characterized by necrosis and a strong peripheral immune response."
} | 000036 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Mammary-Specific Inactivation of the pRb Pathway Induces Extensive AbnormalitiesHistologic comparisons of nontransgenic (A–D), mosaic (F0 line 2 [E–H]), and transgenic (F1, line 3 [I–L]) lactating mammary glands reveals that T121 expression results in increased proliferation and apoptosis. Hemotoxylin and eosin staining shows acini of the normal lactating gland are composed of a single layer of secretory epithelial cells (A) with milk-filled lumen. Consistent with atrophy, transgenic animals have a lower density of acini demonstrated by the presence of lipid-filled adipocytes (asterisk in [K]). Acini composed of T121-expressing cells are atypical. Many are collapsed and composed of tall columnar epithelia of large hyperchromatic cells with papillary tufting (arrows in [I]). Transgene-expressing cells have large pleomorphic nuclei (open arrows in [G]) as compared to nuclei of nonexpressing cells (arrows in [G]). Staining for T121 expression (blue in [B]–[J]) indicates the line 2 F0 animal is mosaic, showing localized expression (F), whereas the transgene expresses throughout the gland of an F1 line 3 animal (J). Increased proliferation assayed by PCNA staining (red) is also localized in the mosaic founder (G), but found throughout the F1 transgenic gland (K). Similarly, TUNEL staining (brown) demonstrates increased apoptosis in transgenic animals (H and L); moreover, the regionalized apoptosis in the mosaic gland (H) strongly suggests that transgene expression and not precocious involution is the cause. All samples are from primiparous females on lactation day 1.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340938-6-pbiop0020022pg003.jpg",
"summary": "Representative histological analysis of lactating mammary glands from transgenic animals shows that acini composed of T121-expressing cells are often atypical, with many being collapsed and composed of tall columnar epithelia of large hyperchromatic cells with papillary tufting (arrows in [I]). T121-positive mammary epithelial cells were associated with these abnormalities."
} | 000037 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "EGF-CFC Coreceptor Depen-dence Determines Susceptibility to Antagonism by Lefty(A–L) Embryos were injected with 75 pg of SqtActβB[loopβ8] mRNA (A–C), 75 pg of SqtActβA[loopβ8] mRNA (D–F), 200 pg of Vg1ActβB[loopβ8] mRNA (G–I), or 200 pg ActSqt[Finger1-loopβ8] mRNA (J–L). Embryos were further double-injected with either 500 pg of LacZ mRNA (A, D, G, and J), 100 pg of lefty1 and 400 pg LacZ mRNAs (B, E, H, and K), or 500 pg of lefty1 mRNA (C, F, I, and L). gsc mRNA expression in wild-type zebrafish embryos is shown at shield stage, animal pole view. Note that both levels of Lefty1 cannot inhibit the ectopic gsc expression induced by SqtAct\nβ\nB[loop\nβ\n8] (B and C), SqtAct\nβ\nA[loop\nβ\n8] (E and F), and Vg1Act\nβ\nB[loop\nβ\n8] (H and I). In contrast, Lefty1 can inhibit ActSqt[Finger1-loop\nβ\n8] (K and L).(M) Wild-type embryos were injected with 75 pg of either SqtAct\nβ\nB[loop\nβ\n8], SqtAct\nβ\nA[loop\nβ\n8], Vg1Act\nβ\nB[loop\nβ\n8], or 200 pg of ActSqt[Finger1-loop\nβ\n8] mRNA. Embryos were further double-injected with 500 pg of LacZ mRNA, 100 pg of lefty1, and 400 pg of LacZ mRNAs, or 500 pg of lefty1 mRNA. Smad2 pathway activation was measured by an Activin response element luciferase reporter, A3-luc. Values are folds over wild-type control injected with 500 pg of LacZ mRNA and A3-luc reporter. An asterisk indicates a significant difference from the level of activation with ligand and LacZ expression alone (Student's t-test, p < 0.05).",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340941-2-pbiop0020030pg008.jpg",
"summary": "Our genetic and biochemical studies suggested that Lefty blocks Nodal and Vg1 signaling via EGF-CFC coreceptors, while coreceptor-independent signaling by Activins cannot be inhibited by Lefty. This implies that EGF-CFC-independent chimeric ligands such as SqtActβB[loopβ8], SqtActβA[loopβ8], and Vg1ActβB[loopβ8] should be resistant to Lefty inhibition. As predicted, Lefty1 did not inhibit signaling by SqtActβB[loopβ8], SqtActβA[loopβ8], or Vg1ActβB[loopβ8], but it did antagonize ActSqt[Finger1-loopβ8]."
} | 000038 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "EGF-CFC Coreceptors Genetically Interact with LeftyLive wild-type zebrafish embryos at 30 h postfertilization (hpf).(A1, B1, and C1) Ventral views of the head.(A1′, B2, B3, and C1′) Lateral views, with anterior to the left, dorsal up.(A1, A1′, B1, B2, and B3) Wild-type embryos were injected with 20 pg of lefty1 mRNA. Embryos were further double-injected with either 200 pg of LacZ mRNA (A1 and A1′) or 200 pg of Cripto mRNA (B1, B2, and B3).(C1 and C1′) Wild-type embryos injected with 200 pg of Cripto mRNA and 20 pg of LacZ mRNA.Misexpression of Lefty1 results in cyclopia and other head and trunk mesoderm defects ([A1 and A1′] 32 of 32 embryos had the phenotype shown; arrow shows cyclopia). Coexpression of Cripto with Lefty in embryos leads to rescue of two eyes ([B1] four of 50; arrows show two eyes), notochord ([B2] 20 of 50; inset shows trunk somites and notochord, red bar delineates notochord), and trunk somites ([B3] 50 of 50). Embryos injected with Cripto mRNA only show normal wild-type phenotype ([C1 and C1′] 30 of 30; arrow in [C1] shows two normal eyes, and inset in [C1′] shows normal notochord and trunk somites, red bar delineates notochord).",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340941-8-pbiop0020030pg002.jpg",
"summary": null
} | 000039 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Solid Tumor Growth Is Inhibited by Systemic RI-TATp53C′ Peptide Administration(A) Delivery of RI-TATp53C′-biotin to subcutaneous TA3/St tumors after IP administration to immune competent A/J mice.(B) Reduction of solid TA3/St tumor growth in immune competent mice as a result of systemic administration of RI-TATp53C′. TA3/St cells were injected subcutaneously into A/J mice and allowed to grow to an average size of approximately 100 mm3. Mice were then sorted into treatment groups that received eight daily injections of vehicle (open circle) (n = 17), 650 μg of mutant peptide (open diamond) (n = 7), or 650 μg of wild-type RI-TATp53C′ peptide (open triangle) (n = 11). Final mean tumor volumes were 573 mm3 for vehicle-treated mice, 550 mm3 for mice treated with mutant peptide, and 268 mm3 for the wild-type RI-TATp53C′ peptide group.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340944-1-pbiop0020036pg003.jpg",
"summary": "IP administration of RI-TATp53C′ peptide in immune competent mice resulted in significant inhibition of TA3/St tumor growth. Tumors in mice treated with wild-type RI-TATp53C′ peptide reached a final mean volume of 268 mm3, which was less than 50% of the mean volume (573 mm3) in vehicle-treated mice (p = 0.01)."
} | 000040 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Decreased Fiber CoherenceDecreased fiber coherences, as observed with DTI, in persistent developmental stutterers compared with a fluent control group. A red dot indicates the peak difference in a coronal (top left), axial (top right), and a sagittal (bottom) slice.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340949-2-pbiop0020046pg003.jpg",
"summary": "Using a new MRI technique, diffusion tensor imaging (DTI), investigators observed an area of decreased white matter tract coherence in the Rolandic operculum, which is adjacent to the primary motor representation of tongue, larynx, and pharynx and the inferior arcuate fascicle linking temporal and frontal language areas. This finding suggests that disturbed signal transmission through fibers passing the left Rolandic operculum may impair the fast sensorimotor integration necessary for fluent speech production."
} | 000041 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "PhageNegative stain electron micrograph of the gamma phage from which the PlyG lytic enzyme was cloned for use to control B. anthracis. (Photograph courtesy of Vincent Fischetti and Raymond Schuch, The Rockefeller University.)",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340955-1-pbiop0020053pg002.jpg",
"summary": null
} | 000042 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Transgene expression is associated with increased cell proliferation and cell death (apoptosis)",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC340959-0-pbiop0020059pg001.jpg",
"summary": ""
} | 000043 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A Taste Bud in a MouseThis taste bud was taken from a transgenic mouse in which the marker green fluorescent protein is being driven by the T1R3 promoter; 20%–30% of the cells in the taste bud are expressing T1R3. (Photograph courtesy of Sami Damak, Mount Sinai School of Medicine, New York, New York, United States.)",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC368160-0-pbiop0020064pg001.jpg",
"summary": "Taste buds are onion-shaped structures on the tongue and elsewhere in the mouth, containing up to 100 taste receptor cells. In the tongue, these taste buds are innervated by the chorda tympani (a branch of the facial nerve) and the glossopharyngeal nerve, which carry taste messages to the brain."
} | 000044 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Non-Taster or Supertaster?(A) Top surface of the tongue of a non-taster.(B) Tongue of a supertaster. The small circles are fungiform papillae, each of which contains about six taste buds.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC368160-1-pbiop0020064pg002.jpg",
"summary": "Supertasters have more fungiform papillae on their tongues than non-tasters, each containing about six taste buds. Supertasters find vegetables, particularly brassicas like Brussel sprouts, bitter, leading them to consume fewer vegetables and potentially affecting their health."
} | 000045 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Transmission electron micrograph of Wolbachia within an insect cell (Image courtesy of Scott O'Neill)",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC368170-0-pbiop0020076pg001.jpg",
"summary": null
} | 000046 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Localization of Puf ProteinsTAP-tagged Puf proteins were visualized in fixed cells. DNA was costained with 4′,6-diamidino-2-phenylindole dimethylsulfoxide (DAPI).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC368173-2-pbiop0020079pg006.jpg",
"summary": "The TAP-tagged Puf proteins were predominantly localized to multiple discrete foci in the cytoplasm, consistent with previous reports for S. cerevisiae Puf3p and Puf5p and homologous proteins in higher eukaryotes. The distribution of these foci was not obviously related to distinct cellular organelles, except for Puf1p and Puf2p, which localized near the cell periphery. The multifocal cytoplasmic distribution suggests that mRNAs associated with each Puf protein may be colocalized, potentially aiding in the assembly of complexes and coordinated control of translation or RNA turnover."
} | 000047 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "MRIs of a normal individual (bottom left) and a patient with microcephaly caused by an ASPM mutation (bottom right). Primate skulls provided courtesy of the Museum of Comparative Zoology, Harvard University",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC374245-0-pbiop0020134pg001.jpg",
"summary": "Elucidating the molecular mechanisms that account for the expansion of the human brain and cerebral cortex will provide insight into brain evolution. This includes identifying changes in the human genotype that generated the complex phenotype distinguishing humans from nonhuman primates and early hominids."
} | 000048 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Time-Lapse Imaging of Astrocytes In VivoFour astrocytes, from which fluorometric Ca2+ imaging (0.5 Hz) was made, are outlined. A blood vessel, outlined by the astrocyte end feet, runs diagonally across the viewed area. White arrows show the end foot connected to the imaged astrocyte.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC387267-2-pbiop0020096pg002.jpg",
"summary": "Fluorometric Ca2+ imaging was performed on four astrocytes, which were identified based on their morphological appearance and S100B immunoreactivity. The astrocytes were labeled using Fluo-4 AM, and their somata and processes, including vessel-contacting end feet, were clearly visualized. The blood vessel outlined by the astrocyte end feet runs diagonally across the viewed area."
} | 000049 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "FMRI Signal in RH aSTG during Initial Solving Efforts(A) Voxels in right temporal lobe showing baseline-to-peak event-related FMRI signal when subjects first encounter problems, overlaid on the averaged normalized structural image of all subjects. The cluster is in RH aSTG, with a volume of 469 mm3, with peak t value of 4.37 at 41, −6, −12 in Talairach space, clearly overlapping with the cluster showing an insight effect at solution.(B) Group average signal change following problem onset (time = 0), for the cluster defined by signal at the problem onset (green line) and the cluster (illustrated in Figure 2A) showing the insight effect at solution (white line). Error bars show the standard error of the mean of the difference at each time point.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC387268-0-pbiop0020097pg003.jpg",
"summary": "The RH aSTG shows increased neural activity when subjects first encounter problems, indicating its involvement in initial problem processing. This area is robust, with a peak signal difference of 0.25% across a 6-s window and 0.30% at a single TR. The cluster in RH aSTG overlaps with the area showing an insight effect at solution, suggesting its role in both initial problem processing and solution insight."
} | 000050 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "FMRI Insight Effect in RH aSTG(A) Voxels showing greater FMRI signal for insight than noninsight solutions, overlaid on the averaged normalized structural image of all subjects. The active area has a volume of 531 mm3 (peak t = 4.89 at 44, −9, −9 in Talairach space).(B) and (C) Group average signal change following the solution event, for insight (red line) and noninsight (blue line) solutions (yellow arrow indicates button press): (B) over entire LH aSTG region; (C) over entire RH aSTG region.(D) Insight solution signal change minus noninsight solution signal change, in RH aSTG (error bars show the standard error of the mean of the difference at each timepoint).",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC387268-5-pbiop0020097pg002.jpg",
"summary": null
} | 000051 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "CAP Mutant ClonesFollicle cells lacking CAP accumulate actin (red) in their apical region. Ena (blue in the bottom panel), also accumulates apically in the mutant cells (looks pink in the clone of cells due to overlap with F-actin in red). The mutant cell clones are identified by the absence of GFP (green in the top panel). Using this technique the cytoskeleton of mutant cells can be analysed in the context of a wild type epithelium. (Image kindly supplied by Buzz Baum.)",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC387270-0-pbiop0020100pg001.jpg",
"summary": null
} | 000052 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Astrocyte in the cerebral cortex",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC387279-0-pbiop0020115pg001.jpg",
"summary": "Hajime Hirase and his colleagues at Rutgers University focused their microscope on the brains of living rats to examine how astrocytes function in vivo."
} | 000053 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The Blastula Dorsal Animal Cap Is Specified to Form CNS(A) Experimental diagram showing embryos injected with CerS mRNA from which three regions of the animal cap were dissected at blastula, cultured until stage 26, and processed for RT-PCR. The size of the explants was 0.3 mm by 0.3 mm in these samples. Abbreviations: A, animal pole; D, dorsal region; V, ventral animal cap.(B) RT-PCR analysis of animal cap fragments; note that anterior brain markers were expressed in the dorsal fragments in the absence of mesoderm (α-actin) and endoderm (endodermin, Edd) differentiation. Abbreviations: A, animal pole; D, dorsal region; V, ventral animal cap.(C) Experimental diagram of the small animal cap sandwich experiments; these embryos were not injected with CerS. In this case, the size of the explants was 0.15 mm by 0.15 mm leaving a 0.15-mm gap from the floor of the blastocoel to avoid contamination from mesoderm-forming cells. Fragments from two explants were sandwiched together (explants are too small to heal by curling up) and cultured in 1× Steinberg's solution until stage 40. Abbreviations: VSW, ventral sandwich; DSW, dorsal sandwich.(D) Histological section of dorsal animal cap explant (dorsal sandwich). These sandwiches differentiated into histotypic forebrain tissue including white and gray matter (4/17). Abbrevations: DSW, dorsal sandwich; gm, gray matter; wm, white matter.(E) Histological section of a ventral animal cap sandwich. All sandwiches differentiated into atypical epidermis (n = 20). Abbreviations: ae, atypical epidermis; VSW, ventral sandwich.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406387-5-pbiop0020092pg003.jpg",
"summary": "Ventral animal cap explants, when cultured in isolation, differentiated into atypical epidermis, as shown in Figure 3E. This indicates that ventral animal cap cells are not specified to form neural tissue at the blastula stage."
} | 000054 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The BCNE Center Contributes to Forebrain and Midline Structures(A) Method used for lineage tracing of the BCNE center with biotin-dextran amine (BDA) labeled grafts.(B) Sagittal section of a recently grafted BCNE at stage 9.(C) Chd mRNA expression at stage 9.(D) BCNE descendants at stage 10.5.(E) Chd mRNA expression at stage 10.5.(F) BCNE center descendants at stage 11.(G) Dorsal view of BCNE descendants at neural plate stage 14.(H) Double staining of transplanted BCNE region with nuclear lacZ mRNA and epidermal ectoderm of the host with epidermal cytokeratin (epi) probe in light red at stage 14.(I) Transverse section at the level of the trunk at stage 16. Abbreviations: fp, floor plate; no, notochord.(J–L) Transverse sections at stage 40. Abbreviations: fp, floor plate; hb, hindbrain; he, heart; le, lens; mb, midbrain; no, notochord; ov, otic vesicle; re, retina.(M) Dorsal view of 6-d embryo transplanted with a BCNE graft from CMV-GFP transgenic embryos. Abbreviations: br, brain; fp, floor plate; on, optic nerve; op, olfactory placode.(N) Side view at 4 d showing labeled retina and brain. Abbreviation: br, brain.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406387-6-pbiop0020092pg002.jpg",
"summary": "At neural plate stage 14, BCNE center descendants were found in a wide region in the anterior neural plate and, more posteriorly, in a narrow stripe in the midline. Double staining using nuclear lacZ mRNA as a lineage tracer in combination with an epidermal cytokeratin marker confirmed that BCNE cells give rise to anterior neural plate. The midline staining in the trunk region corresponded to floor plate and notochord in histological sections."
} | 000055 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Embryos with Defective Myocardial Function Do Not Form AV ECs(A–C) Fluorescence micrographs of embryos carrying a tie2::GFP transgene, visualized at 48 hpf. In (A), the endocardial ring is visible as a collection of GFP-positive cells at the AV boundary in wild-type (wt) embryos (red arrow). In (B), sih−/− embryos fail to form an AV ring at 48 hpf. In (C), cfk−/− embryos fail to form an AV ring at 48 hpf.(D and E) Cushion development remains defective in cfk−/− embryos. In (D), a 5 μm hematoxylin and eosin-stained plastic section shows the initial stages of cushion development at the AV boundary (red arrows) in a 72 hpf wild-type embryo, with the ECs being two to three cell layers thick at this stage. In (E), a cfk\n−/− embryo at 72 hpf shows dilation of both chambers of a blood-filled heart with no evidence of cushion formation at the AV boundary (red arrows).(F and G) cfk−/− embryos fail to form ECs at late stages. Embryos were visualized at identical magnification after counter-staining with rhodamine phalloidin. Red blood cells (RBCs) are seen in the atria of the hearts. In (F), confocal microscopy of a 96 hpf wild-type heart from a tie2::GFP line shows triangular ECs at the AV boundary (blue arrows). In (G), cfk−/− embryos at 96 hpf lack cushion formation and clustering of GFP-positive cells at the AV boundary (blue arrows).(H) At 72 hpf, wild-type embryos have narrow hearts with forward blood flow through the embryo.(I) At 72 hpf, cfk−/− embryos have dilated hearts filled with blood that regurgitates freely from the ventricle to the atrium.(J and K) The initial phenotype in cfk−/− embryos is cardiac dilation at 36 hpf. In (J), wild-type embryos have a narrow ventricle and generate pulsatile flow at 36 hpf. In (K), cfk−/− embryos have an increased end-diastolic diameter (on average 1.18× wild-type, p < 0.01) and do not generate blood flow at 36 hpf.(L and M) Increased bmp-4 expression at the AV boundary (red arrow) is observed in wild-type (L) and cfk−/− (M) embryos at 42 hpf in anticipation of endocardial ring formation.(N) Orientation of the embryos shown in (L) and (M).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406391-0-pbiop0020129pg001.jpg",
"summary": "In zebrafish, the endocardial ring, a structure formed by clustering of endocardial cells at the atrioventricular (AV) boundary, is crucial for EC development. Confocal microscopy at 96 hpf shows that wild-type embryos have well-developed cushions and triangular ECs at the AV boundary (blue arrows). In contrast, cfk−/− embryos at the same stage lack cushion formation and clustering of GFP-positive cells at the AV boundary (blue arrows), indicating a failure in EC formation."
} | 000056 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Sequence and Expression Analysis of cfk\n(A) cfk encodes a sarcomeric actin highly homologous to zebrafish α-cardiac and α-skeletal actins. Cfk differs from zebrafish α-cardiac actin at six residues and from zebrafish α-skeletal actin at four residues, but from zebrafish β-actin at 28 residues. Residues in red are those that differ from Cfk. Dots above the sequence indicate residues that universally distinguish sarcomeric from cytoplasmic actins. The arrow at R177 indicates the location of histidine in Cfks11.(B) The arginine at position 177 is universally conserved in all actin proteins examined.(C and D) cfk is expressed in the myocardium during development. In (C), whole-mount in situ hybridization on a cmlc2::GFP embryo at 36 hpf shows that cfk is expressed throughout the AP extent of the heart tube. Blue staining indicates areas of cfk expression; green is the region of cmlc2 expression. The red arrow indicates the heart tube. In (D), a plastic section of stained embryo shows cfk expression in the myocardium of the heart (blue arrow), but not in the endocardial cells (red arrow). From the onset of its expression in the heart region (around the 16-somite stage), cfk does not appear to be expressed in endothelial and endocardial cells. Weak cfk expression is also seen in the somites (data not shown).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406391-4-pbiop0020129pg003.jpg",
"summary": "To determine the expression pattern of cfk, in situ hybridization was performed on zebrafish embryos from 24 to 48 hpf. The results showed that cfk is expressed in the myocardial but not in the endocardial cells, indicating a nonautonomous role in endocardial cell (EC) formation."
} | 000057 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "CDSC-Pax7 Cells Become Myogenic ProgenitorsMyf5 (A–C) and MyoD (D–F) protein (green) are expressed in proliferating CDSC-Pax7 cells. Exposure of CD45+:Sca1+ cultures to low mitogen medium induced the formation of multinucleated myotubes and expression of myogenic differentiation markers including MyHC (red) (G–I) and myogenin (red) (J–L). Sustained expression of Pax7 (red) (M–O) in these cultures did not interfere with their differentiation. DAPI staining (blue) was used to visualize all nuclei.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406392-1-pbiop0020130pg003.jpg",
"summary": "CDSC-Pax7 cells, which constitutively express Pax7, differentiated efficiently into multinucleated myotubes expressing terminal differentiation markers such as MyHC and myogenin. The sustained expression of Pax7 (red) in these cultures did not interfere with their differentiation, as shown in (M–O)."
} | 000058 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "CDSC-Pax7 Cells Efficiently Contribute to the Repair of Dystrophic Muscle(A) Wild-type muscle expressed dystrophin at the plasmalemma of all myofibers.(B) Dystrophin protein was not detected in muscle sections from dystrophin-deficient mdx:nude mice (mdx:nu).\n(C–F) CDSC-Pax7 cells differentiated in vivo after transplantation, readily forming large numbers of dystrophin-expressing myofibers (green) in mdx:nude muscle (C and D). Serial cross sections showing the viral expression of Pax7 protein in central nuclei of regenerated fibers (red staining in [E]) confirmed the donor origin of dystrophin-positive myofibers (red staining in [F]).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406392-3-pbiop0020130pg005.jpg",
"summary": "CDSC-Pax7 cells were transplanted into dystrophin-deficient mdx:nude mice, and two months later, dystrophin-expressing myofibers were observed. The expression of Pax7 protein (from retrovirus) in central nuclei within these dystrophin-positive fibers confirmed the contribution of CDSC-Pax7 donor cells to the recipient muscles."
} | 000059 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Adenovirus-Pax7 Significantly Improves Regeneration In Vivo(A and B) Infection of ctx-damaged Pax7\n −/− muscles with Ad-Pax7 resulted in markedly improved muscle integrity and a significantly increased number of Desmin immunoreactive (green) regenerated fibers (B) relative to muscles treated with Ad-LacZ (A).(C and D) Hematoxylin and Eosin staining similarly showed an increased number of centrally nucleated fibers in Ad-Pax7-treated Pax7\n −/− muscles.(E) In three separate experimental trials, the number of regenerated fibers was markedly increased in Ad-Pax7-treated muscles relative to Ad-LacZ; however, the response was biologically variable between groups. On average, Ad-Pax7 infection resulted in a 4.1 ± 0.72–fold increase in regenerated Pax7\n −/− myofibers (F).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406392-4-pbiop0020130pg008.jpg",
"summary": "To assess the effect of Pax7 expression in damaged tissue, TA muscles were analyzed for regeneration 12 days after infection, with the newly regenerated status of centrally nucleated fibers confirmed by Desmin and embryonic MyHC immunoreactivity. Ad-Pax7 induced a markedly enhanced regenerative response relative to Ad-LacZ in Pax7\n −/− muscle, as evidenced by the increased number of centrally nucleated fibers. In three independent experiments, ctx-damaged TA muscle from Pax7\n −/− mice typically contained an average of 46 surviving or regenerated fibers following regeneration, whereas infection of regenerating Pax7\n −/− TA with Ad-Pax7 resulted in the generation of an average of 192 myofibers, demonstrating the ability of virally transduced Pax7 to direct the de novo generation of myogenic progenitors capable of forming new myofibers and participating in regenerative myogenesis."
} | 000060 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Pax7-infected stem cells rescue dystrophin expression",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406395-0-pbiop0020135pg001.jpg",
"summary": "Some researchers are finding that adult stem cells could perform similar duties in certain tissues and are responsive to genetic manipulation. This genetic manipulation could involve infecting adult stem cells with Pax7 to rescue dystrophin expression."
} | 000061 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "tie2::GFP+ cells form the endocardial cushions",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406396-0-pbiop0020138pg001.jpg",
"summary": "In the process of dissecting the early steps of heart valve formation, Thomas Bartman et al. use zebrafish genetics to provide evidence for a causal relationship between the early function of the heart and its final structure."
} | 000062 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Spindle Cell Tumors Resembling MPNSTs in Zebrafish Heterozygous for Mutations in RP Genes(A and B) Fish with apparent masses, as indicated by the arrows, or other evident pathology were selected for histological analysis: (A) a hi2582 fish, (B) a hi1034B fish.(C–H) Histopathology of representative tumors stained with hematoxylin and eosin reveals patterns consistent with the diagnosis of MPNST in hi10 fish (C and D), hi1974 fish (E–G), and hi1807 fish (H).(C) Tumors typically filled the entire abdomen (sb, swim bladder; br, brain) (80×).(D) A large tumor with central necrosis is seen emanating from the optic nerve (n) (e, eye) (20×).(E) Tumors consist of spindle cells that stack into short fascicles, typically organizing into whorls (400×).(F) Tumor is aggressively invading muscle (m) and gill (g) (br, brain) (100×).(G) Mitotic figures (arrows) are evident (1000×).(H) Areas of focal necrosis (arrows) are frequently seen (200×).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406397-1-pbiop0020139pg001.jpg",
"summary": "Histological analysis of the tumors revealed a high mitotic index, with mitotic figures evident in the tissue samples, as shown in subfigure G at 1000× magnification."
} | 000063 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Reversal Learning and the Orbitofrontal Cortex(A) Lateral and ventral views of the surface reconstructions of the lateral and medial orbitofrontal cortex lesions in monkeys (adapted from Iversen and Mishkin 1970), with the former monkeys having difficulty with the reversal task.(B) A ventral view of the human brain, with the cerebellum removed. Red activations in the lateral orbitofrontal cortex indicate the maximal activation for reversal compared to stable acquisition events. Blue activations indicate the main effects of facial expression (adapted from Kringelbach and Rolls 2003).",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Visible Light Photography",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406398-0-pbiop0020140pg001.jpg",
"summary": "The study by Iversen and Mishkin (1970) demonstrated that lesions in the lateral orbitofrontal cortex of monkeys significantly impaired their ability to reverse rewarding associations in an object reversal task. Monkeys with these lesions continued to respond to an object that was no longer rewarded, indicating difficulty with the reversal task."
} | 000064 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Zebrafish kugelig MutantsThe image shows live one-week-old zebrafish embryos. The embryos around the outside are wild-type fish. Those in the middle are a mutant called kugelig and have a homozygous mutation in a gene called cdx4. Loss of the proper functioning of this gene causes the obvious trunk and tail defects but also causes a reduction in the number of haematopoietic stem cells in the embryos, which therefore become severely anaemic. Studies on this mutant might lead to the discovery of molecules that can drive stem cell differentiation, for example, or could help improve understanding of human haematological malignancies. (Image courtesy of Alan Davidson, Harvard Medical School, Boston, Massachusetts, United States.)",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406403-0-pbiop0020148pg004.jpg",
"summary": "Zon and his colleagues are using zebrafish models, including cell-cycle mutants, to screen for small molecules that can suppress the cell-cycle phenotype. These molecules may have potential as anticancer drugs."
} | 000065 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Zebrafish Hindbrain(Left) Dorsal view of GFP-expressing neurons in the hindbrain of a one-day-old zebrafish embryo. (Right) Antibody-labelled axons. (Image courtesy of Dave Lyons, University College London.)",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406403-1-pbiop0020148pg003.jpg",
"summary": "In the ZF-MODELS project, zebrafish expressing GFP in specific cells or tissues are generated and characterized. These GFP lines allow for the easy imaging of developing structures over time in living embryos. The subfigure shows antibody-labelled axons, which can be studied in these GFP-expressing zebrafish to understand their development."
} | 000066 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A Zebrafish Pigment MutantThe mutant called bleached blond was produced by insertional mutagenesis. The embryos in the picture are four days old. At the top is a wild-type embryo, below is the mutant. The mutant lacks black pigment in the melanocytes because it fails to synthesise melanin properly. (Image courtesy of Adam Amsterdam, Massachusetts Institute of Technology, Boston, Massachusetts, United States.)",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406403-2-pbiop0020148pg002.jpg",
"summary": "The mutant called bleached blond was produced using insertional mutagenesis, where mutations are caused by the random insertion of viral DNA throughout the fish genome. This method allows for straightforward cloning of mutated genes. The bleached blond mutant lacks black pigment in the melanocytes because it fails to synthesize melanin properly."
} | 000067 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Ras at the plasma membrane of S. cerevisiae",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC406405-0-pbiop0020151pg001.jpg",
"summary": null
} | 000068 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Different Activation Patterns in the Brains of Dyslexics As Compared to Normal Subjects in a Rhyming Task(Images courtesy of John Gabrieli, Stanford University.)",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Magnetic Resonance",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC423132-0-pbiop0020150pg002.jpg",
"summary": "John Gabrieli has shown that distinct activation patterns in the brains of dyslexic children normalize as they improve their reading skills. However, fMRI is not yet reliable for interpreting individual scans based on group data, making it currently among the most useless things to do for a schoolchild struggling in the classroom."
} | 000069 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "In Vivo Two-Photon Imaging Through the Thinned SkullYellow cameleon 3.12 at different depths (MTH-YC3.12-8) (A) and with high resolution (MTH-YC3.12-7) (B). (C) IP at different depths (MTH-IP-1).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC423138-2-pbiop0020163pg005.jpg",
"summary": "To evaluate the achievable signal levels in intact animals, we performed in vivo two-photon imaging through the thinned skull in adult anesthetized mice (MTH-YC3.12-7). Densely packed neurites were clearly visible, consistent with the staining patterns seen in acute slices, demonstrating that FCIP fluorescence is sufficiently strong for high resolution in vivo morphological imaging."
} | 000070 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Doxycycline and tTA-Dependent FCIP ExpressionImmunohistochemical assay (A–F) using rabbit polyclonal GFP antibodies/peroxidase-DAB system: (A) YC3.12, single-positive (MTH-YC3.12-7), double-positive (MTH-YC3.12-7, αCamKII-tTA), and Dox-treated double-positive (MTH-YC3.12-7, αCamKII-tTA).(B) Cg2, single-positive (MTH-Cg2-7) and doubles-positive (MTH-Cg2-7, αCamKII-tTA).(C) IP, single-positive (MTH-IP-12) and double-positive (MTH-IP-12, αCamKII-tTA).(D) Moderate-expression line of Cg2 (MTH-Cg2-14, αCamKII-tTA).(E) Low-expression line (MTH-Cg2-15, αCamKII-tTA).(F) FCIP distribution in various brain areas.(G) Fluorescence in fixed brain slices from the accessory and the main olfactory bulb.(H–K) Two-photon images of acute, living brain slices. (H) Neurons in both CA1 and striatum usually show nuclear exclusion. (I) punctate expression in low-expressing lines (also see Figure 2B, open circles); example from CA1 and cortex. Maximum intensity projection of two-photon 3D stacks taken from a brain slice (J) and a whole-mount retina (K).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC423138-4-pbiop0020163pg003.jpg",
"summary": "Expression of FCIPs was apparent only in double-positive animals and in the absence of Dox, with strong to moderate levels in several lines, including MTH-IP-12. Expression levels varied by line, with high expression in MTH-IP-12 and MTH-IP-1, and low expression in other lines. In high-expressing lines, cytosolic fluorescence was smooth with occasional bright spots, and nuclei were usually less fluorescent. In low-expressing lines, fluorescence was punctate. FCIP-positive cells included hippocampal and neocortical pyramidal cells, vomeronasal and main olfactory receptor neurons, granule cells, and a few mitral cells in the olfactory bulb."
} | 000071 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Light-Evoked Ca2+ Responses in Retinal Ganglion Cells(A) Intact, light-sensitive retinal whole mount with Sulforhodamine 101 (red) in the extracellular space. Blood vessels are red; IP-positive (MTH-IP-12) retinal ganglion cells are green; and unstained ganglion cells are dark. (Scale bar: 50 μm).(B) Projection of an image stack reveals the IP-labeled primary dendrites of the retinal ganglion cells.(C) Time course of Ca2+ response measured by high repetition rate image scan (62.5 Hz) of a soma: The cell responds with a decrease in fluorescence to the onset of the laser (asterisk) and to the repeated light stimulation (arrows).(D) Averaged (four repetitions) light-stimulus-evoked Ca2+ response (black trace; gray traces are single trials) measured in the soma (above) and in the primary dendrite (below) of a retinal ganglion cell.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC423138-5-pbiop0020163pg007.jpg",
"summary": "In one of two IP-expressing mice tested (MTH-IP-12), the fluorescence levels were high enough to follow axons and primary dendrites. Blood vessels are red, and IP-positive retinal ganglion cells are green, while unstained ganglion cells are dark. This subfigure illustrates the intact, light-sensitive retinal whole mount with Sulforhodamine 101 in the extracellular space."
} | 000072 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "In Vivo Imaging of Odor-Evoked Ca2+ Signals with Transgenic Indicators in the Olfactory Bulb(A–C) IP (MTH-IP-12). (A) Raw fluorescence image. (B) Time course of fluorescence signal in the corresponding regions outlined in (C) (matching line colors). The black trace shows respiratory activity. (C) Color-coded map showing the relative change in fluorescence evoked by different odors in each pixel during the first second of the odor response.(D–F) Cg2 (MTH-Cg2-19). (D) Raw fluorescence image. (E) Time course of fluorescence signal in the corresponding regions outlined in (F) (matching line colors). (F) Color-coded maps showing the relative change in fluorescence evoked by different odors in each pixel during the first second of the odor response.",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_0-PMC423138-7-pbiop0020163pg008.jpg",
"summary": "Odor-evoked fluorescence changes were observed in the olfactory bulb, with widespread signals in MTH-IP-12 and more localized signals in MTH-Cg2-19. Each odor evoked a unique activity map, and the spatial patterns of Ca2+ signals were more diffuse than maps of afferent glomerular activity. This diffuseness is likely due to the expression of FCIP in granule cells, which receive input from secondary dendrites of mitral cells. The largest fluorescence changes were −8% for IP and +3% for Cg2."
} | 000073 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "In Situ Protein Localization(A) IF studies of glomerular protein expression in Actn4\n+/+, Actn4K228E/+ , and Actn4\nK228E/K228E mice. As indicated, expression of α-actinin-4, ZO-1, and nephrin is shown, as is a merged image of α-actinin-4 and ZO-1 expression.(B) Glomerular expression of α-actinin-4 in normal human kidney and in an individual heterozygous for a K228E mutation.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423141-0-pbiop0020167pg007.jpg",
"summary": "The appearance of α-actinin-4 is more punctate in the kidney from a K228E heterozygous individual compared to a control, suggesting the presence of aggregates in heterozygous humans. This subtle effect is consistent with the lack of any detectable renal phenotype in humans carrying disease-associated ACTN4 mutations."
} | 000074 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "In Vivo PhenotypeElectron micrographs from Actn4 wild-type (A) and Actn4\nK228E/K228E mice (B–D). As shown, Actn4\nK228E/K228E mice were found to have abnormalities that were typically focal, with some areas of podocyte foot process effacement (B), as well as areas that appeared essentially normal (C). Bottom image ([D] using tannic acid counterstaining) illustrates electron-dense deposits observed in several podocyte cell bodies in Actn4\nK228E/K228E mice. No such deposits were observed in wild-type or heterozygous mice.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Electron microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423141-3-pbiop0020167pg005.jpg",
"summary": "In Actn4 K228E/K228E mice, electron microscopy revealed the presence of abnormal electron-dense structures in podocyte cell bodies, which were not observed in wild-type or heterozygous mice. These structures are highlighted in Figure 5D using tannic acid counterstaining."
} | 000075 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Mutant α-Actinin-4 Behavior in Cells(A) Mutant and wild-type α-actinin-4 show different localization and dynamics when expressed in a conditionally immortalized differentiated mouse podocyte cell line. Differentiated podocytes were injected in the nucleus with equal concentrations of expression plasmid for GFP fusions of mutant and wild-type actinins. At 2–4 h after injections, cells were imaged and both phase and fluorescence images recorded as described in the Materials and Methods. To illustrate changes in distribution of the fluorescence signal, three fluorescence images each 1 min apart were overlaid as red, green, and blue panes. Areas of fluorescence that were the same in all panes show as white, while dynamic areas are indicated by the color. The top panel indicates the initial phase and overlain dynamic fluorescence images of wild-type α-actinin-4, while the bottom two panels illustrate characteristic results for mutants K228E and T232I at 3 min time intervals. (See Videos S1–S3.)(B) Transfections in podocytes derived from mutant and wild-type mice. When transfected into conditionally immortalized podocytes of all three α-actinin-4 genotypes (+/+, K228E/+, or K228E/K228E), wild-type GFP–α-actinin-4 shows diffuse cytoskeletal localization. Mutant GFP–α-actinin-4 shows a similar alteration in localization when expressed in these three cells types.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423141-4-pbiop0020167pg002.jpg",
"summary": "Video microscopy was used to observe the behavior of GFP–α-actinin-4 after nuclear injection of the cDNA in a conditionally immortalized podocyte cell line. The wild-type protein showed normal diffuse cytoskeletal localization, while mutants K228E and T232I formed localized aggregates and were less dynamic. These results were consistent across multiple experiments and time intervals, as illustrated in the subfigure."
} | 000076 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Mean Component Cluster Equivalent Dipole LocationsThe mean scalp map for each of the nine component clusters could be well fit by a single equivalent dipole (mean residual variance: 4.8%). The figure shows the locations and orientations of these dipoles, as determined by BESA, plotted on the spherical head model, with ellipses showing the spatial standard deviations of the locations of the equivalent dipoles for the individual components in the cluster.",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423146-7-pbiop0020176pg005.jpg",
"summary": "The mean scalp map for each of the nine component clusters was modeled as a projection of an equivalent dipole, with residual variances being relatively small (mean: 4.93%). The equivalent dipole locations for individual components were not tightly clustered, as indicated by the spatial standard deviation ellipses. For the P3b cluster, the equivalent dipole locations were scattered across parietal and central cortex, leading to an unnaturally deep mean equivalent dipole location. The P3f cluster's equivalent dipole was mislocalized below the orbitofrontal brain surface due to the complicated geometry of the frontal skull, which cannot be well fit to the spherical head model."
} | 000077 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Four Different Species of Volvocales Algae(A) Gonium pectorale, (B) Eudorina elegans, (C) Pleodorina californica, and (D) Volvox carteri. These are unicellular organisms that live in colonies and have both large and small gametes. Photo courtesy of Aurora M. Nedelcu, from the Volvocales Information Project (http:\\\\www.unbf.ca\\vip\\index.htm).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423151-1-pbiop0020183pg004.jpg",
"summary": "The variation in gamete size within each species of Volvocales matches its degree of complexity. For example, the unicellular species Gonium pectorale, Eudorina elegans, Pleodorina californica, and Volvox carteri, which are shown in the subfigure, exhibit different levels of complexity, with some having both large and small gametes while others remain isogamous."
} | 000078 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Scars of Sex(A) Streaks of sperm (St) received after a mating interaction in the hermaphroditic flatworm, Pseudobiceros bedfordi. (B) Received sperm appears to “burn” holes (H) in the receiver. Some (unknown) component of the ejaculate dissolves the skin tissue. Sc, scar tissue. (C) Exceptional case where an individual received a large amount of sperm somewhere in the middle of the body, resulting in a large hole (asterisk). The the body subsequently tore in two. Individuals like these are occasionally found in the field and can regenerate much of their body. Photo courtesy of Nico Michiels.",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423151-2-pbiop0020183pg002.jpg",
"summary": null
} | 000079 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Zooming in on mitochondria (Image by Peter Seibel, design by Shayna Roosevelt)",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423160-0-pbiop0020193pg001.jpg",
"summary": null
} | 000080 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Mutant α-actinin-4 is mislocalizes and aggregates in renal glomeruli",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC423161-0-pbiop0020194pg001.jpg",
"summary": "Focal segmental glomerulosclerosis (FSGS) causes inflammation and irregular scarring in the glomeruli, which are clusters of blood vessels in the kidney that filter toxins from the blood. This condition leads to lesions that allow protein and blood to escape into the urine, causing progressive kidney failure."
} | 000081 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A Cell Culture Screen Identifies Novel Regulators of the Innate Immune Response(A) LPS induces an increase of about 10-fold in the number of Dipt-lacZ cells that stain positively for β-galactosidase. Ecdysone sensitizes the cells and promotes the response.(B) Dipt-lacZ induction by LPS requires known Imd signaling components, but not Tl pathway members. The fraction of β-galactosidase-positive cells was normalized to the induced control (normalized %), and influence of RNAi of Tl pathway members (dif, spz, and tub) or Imd pathway members (PGRP-LC, Imd, Ird5, and Dredd) is shown.(C–H) Activity stain (X-Gal) for β-galactosidase.(C) Untreated cells.(D) Cells treated with ecdysone alone.(E) Cells treated with ecdysone and LPS. About 10% of cells express detectable β-galactosidase.(F) RNAi against the DDRi sick reduces Dipt-lacZ expression in response to LPS.(G) RNAi of a representative EDRi, the Ras signaling pathway component Cnk, enhances Dipt-lacZ induction by LPS.(H) RNAi of a representative CDRi, the actin regulator SCAR induces Dipt-lacZ in the absence of LPS.(I–J) Immunofluorescence of S2 cells with actin in red, tubulin in green, and DNA in blue. Scale bars in (I) and (J) indicate 10 μm.(I) Wild-type cells have a characteristic rounded morphology.(J) RNAi against many CDRi genes disrupts morphological features of wild-type S2 cells. S2 cells are shown treated with MESR4 dsRNA. Cells are significantly larger in appearance and less round, with irregular tubulin and actin networks.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC434151-1-pbiop0020203pg001.jpg",
"summary": "The subfigure shows S2 cells treated with ecdysone and LPS, where about 10% of the cells express detectable β-galactosidase. This result is consistent with previous studies indicating that ecdysone enhances the induction of Dipt-lacZ by LPS, which requires an intact Imd signaling pathway."
} | 000082 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "A GFP-Relish Reporter Cell Line Subdivides DDRi dsRNA into Three Categories(A–B) Immunofluorescence of GFP-Relish cells with GFP-Relish in green, DNA in blue, and actin in red. Relish is predominantly cytoplasmic in untreated control cells and rapidly translocates to the nucleus of cells incubated with LPS.(C) An anti-GFP Western blot of lysates harvested from GFP-Relish cells treated with LPS for different periods. GFP-Relish rapidly shifts from a full-length form to a shorter processed form after exposure to LPS, and full-length Relish gradually reaccumulates.(D–E) Immunohistochemistry of GFP-Relish cells incubated with GFP-expressing E. coli (arrowheads) and treated with (E) or without (D) dsRNA against PGRP-LC. Imd pathway inactivation prevents bacterial-induced Relish nuclear translocation.(F) Shows effects of treatment of GFP-Relish cells with DDRi dsRNAs for 4 d prior to LPS treatment. GFP-Relish was scored as cytoplasmic (uninduced), nuclear (induced), or reduced in amount (abnormal).(G) Shows an epistatic analysis of the DDRi, sick. Suppression of sick interferes with Dipt-lacZ induction by Group III, IV, and V CDRi dsRNAs, but not those of Groups I and II, suggesting that Sick acts downstream of Imd and Dredd, but upstream of Relish in signal transduction.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC434151-9-pbiop0020203pg003.jpg",
"summary": "The GFP-Relish cell line is a reliable reporter for Relish activation, with GFP-Relish predominantly cytoplasmic in untreated cells and rapidly translocating to the nucleus upon treatment with LPS or exposure to E. coli. Inactivation of PGRP-LC by RNAi prevents the bacterial-induced nuclear translocation of GFP-Relish, indicating that the reporter can be used to assay the function of Imd pathway genes."
} | 000083 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Malaria infecting red blood cells",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC434155-0-pbiop0020251pg001.jpg",
"summary": null
} | 000084 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Fate of Membrane Protein during Lysosomal FusionLysosomal membranes in MEFs were labeled by transfecting cells with a vector encoding a CD63–GFP fusion protein, and expression was allowed for 48 h. For simultaneous labeling of lysosomal membrane and lumen, the CD63–GFP transfected cells were labeled with 70 kDa TRITC–dextran as described in Figure 1.(A) Following ionophore-induced calcium increase in WT MEFs, when the TRITC–dextran was released completely (left), CD63–GFP (right) was delivered to the plasma membrane, but it remained in multiple puncta near the site of fusion rather than diffuse away. The panels are pseudocolor surface plots, with the x and y axis representing the coordinates and the z axis representing the fluorescence intensity of individual pixels.(B) In the event of partial release of TRITC–dextran (top row), the CD63–GFP (bottom row) did not appear to be delivered to the plasma membrane. The lower panel shows the plot of fluorescent intensity of lumenal and membrane label (within the dotted circle) of the lysosome shown in (B).(C and D) Analysis of CD63–GFP-labeled lysosomes in WT MEFs (C) and in Syt VII KO MEFs (D) indicates that while CD63–GFP is retained in puncta in the WT MEFs, it diffuses freely in the plasma membrane in the SytVII KO MEFs. The lower panel shows the total and peak intensity plots of CD63–GFP-labeled lysosome in (D).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC439782-1-pbiop0020233pg002.jpg",
"summary": "In WT MEFs, during complete release of lumenal content (TRITC–dextran), CD63–GFP (membrane protein) is delivered to the plasma membrane but remains in multiple puncta near the site of fusion rather than diffusing away. This behavior is observed in the context of Ca2+-triggered lysosomal exocytosis, where the membrane proteins do not diffuse freely into the plasma membrane."
} | 000085 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Presence of Syt VII Restricts the Size of the Fusion PoreThe lumen of lysosomes was loaded simultaneously using different-sized FITC- and TRITC-labeled dextran, using the approach described in Figures 1 and 2. Representative plots shown here demonstrate the fate of both dextran populations in individual lysosomes following the increase in intracellular calcium by addition of calcium ionophore. In WT MEFs, exocytosing lysosomes that released 70 kDa TRITC–dextran also simultaneously released 70 kDa FITC–dextran (A and B), 250 kDa FITC–dextran (C and D), but not 500 kDa FITC–dextran (E and F). In Syt VII KO MEFs, lysosomes that released 70 kDa TRITC–dextran also released 500 kDa FITC–dextran (G and H). In all cases the plots represent the normalized fluorescence intensity of the region marked in the images by dotted circles.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC439782-2-pbiop0020233pg003.jpg",
"summary": "In WT MEFs, lysosomes that released 70 kDa TRITC–dextran also did not release 500 kDa FITC–dextran, indicating that the fusion pore opened large enough to release the smaller but not the larger cargo. This suggests that the presence of Syt VII restricts the size of the fusion pore, preventing the release of larger dextrans."
} | 000086 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Overexpression of Apically Localizing Fz1/2 Chimeras Has an Inhibitory Effect on Canonical Wnt Signaling(A–D) show adult wings of the respective genotypes. Anterior is up and distal to the right.(A) Adult wing of an en-Gal4/+; UAS-fz1–1-1/+ fly (en>fz1–1-1). en-Gal4 drives UAS reporter genes only in the posterior compartment. Inset shows high magnification of region marked by arrowhead. Some wing margin bristles are missing (arrow) in the posterior compartment. The border between anterior (“a”) and posterior (“p”) compartments is marked with black line.(B) dshV26/+; en>fz1–1-1 adult wing. Note enhancement of the margin bristle phenotype: all margin bristles are missing from the area between the arrows in the posterior compartment.(C) en>fz2–1-1 wing. Most of the wing margin bristles are missing in the posterior compartment. Note also that the posterior compartment is smaller.(D) en>fz2–2-1 wing. Again the posterior compartment is smaller and most of the margin is missing.(E–G) show that Fz1–1-1 expression increases apical localization of Dsh-GFP and reduces Dsh-GFP in more basolateral areas of wing cells. (E) and (F) are xy-horizontal optical sections, and (G) is an xz-cross section. The positions of (E) and (F) sections are indicated in (G).(E) Apical xy-optical section of a third instar wing disc. Fz1–1-1 (red) is overexpressed by en-Gal4 in the posterior compartment (anterior–posterior border is labeled by white line, and the corresponding compartments are labeled “a” and “p,” respectively). Dsh-GFP (green) accumulates at higher levels apically in the posterior compartment. Single-channel Dsh-GFP staining is shown at right. In wild-type disc, Dsh-GFP is evenly distributed with no anterior–posterior bias (not shown).(F) A more basal xy-section of the same disc as in (E). Note reduction of Dsh-GFP staining in the posterior compartment, except at the apical junctions as seen in folds (arrowhead). In the anterior compartment, where Fz1–1-1 is not overexpressed, Dsh-GFP is only slightly enriched in the apical folds (arrow).(G) xz-section of the same wing disc shown in (E) and (F), with top panel showing double labeling for anti-Myc (red) and anti-Dsh-GFP (green) and bottom panel showing single channel of Dsh-GFP staining.(H) xz-section of a comparable disc expressing Fz2–1-1 in the posterior compartment. Fz2–1-1 overexpression (red) also causes accumulation of Dsh-GFP in apical junctions and reduction of Dsh-GFP along the basolateral region.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449784-0-pbiop0020158pg007.jpg",
"summary": "In wing epithelia with overexpressed Fz1–1-1 or Fz2–1-1, much more Dsh-GFP is recruited apically in cells expressing the Fz chimeras, while Dsh-GFP levels are reduced in basolateral regions of these cells. This suggests that Fz in adherens junctions (apical) is trapping Dsh there, depleting it away from Wnt/βcat signaling components located more basally and thus reducing canonical Wnt signaling."
} | 000087 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Subcellular Localization of Fz1–1-1 in fmi− Mutant ClonesFz1–1-1 (Myc-tagged; shown in green) is expressed with omb-Gal4 (in large parts of the third instar wing pouch). fmiE59 clones were labeled by the absence of anti-βGal staining (red). A projection of several horizontal sections in the apical region (A) and the corresponding xz-section (B) across the clone (as indicated by a white line in A) are shown. Fz1–1-1 is localized apically inside and outside the clone, indicating that initial apical Fz recruitment is independent of Fmi.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449784-2-pbiop0020158pg006.jpg",
"summary": "Fz1–1-1 is localized apically in fmiE59 mutant cells in third instar imaginal discs, indistinguishable from its localization in wild-type tissue. This indicates that Fmi is not required for the initial apical localization of Fz1–1-1, which happens prior to the initiation of PCP signaling."
} | 000088 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "The Cytoplasmic Region of Fz Regulates Subcellular LocalizationAll Fz1/2 chimeras shown are Myc-tagged (the tag being inserted right after the CRD of Fz1 or Fz2; see Materials and Methods; Boutros et al. 2000). The respective Fz1/2 chimeras, with their schematic structure shown under each photomicrograph, were expressed under dpp-Gal4 (expression domain marked with UAS-EGFP in example in [A]) and analyzed by confocal microscopy xz-sections (perpendicular to the stripe of expression in the wing pouch region).(A) Subcellular localization of wild-type Fz-Myc (Fz1–1-1, in green; red channel shows coexpressed GFP to mark expressing cells). Single-channel black-and-white staining of Fz-Myc is shown on right.(B–F) Anti-Myc staining of different Fz1/2 chimeras: (B) Fz1–2-2, (C) Fz1–1-2, (D) Fz2–1-1, (E) Fz1–2-1, and (F) Fz2–2-1.(G) Fz2–2-2. Note the correlation of apical Fz localization with the presence of the Fz1 C-tail.",
"domain": "Medical",
"primary_modality": "Radiology",
"secondary_modality": "Ultrasound",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449784-4-pbiop0020158pg002.jpg",
"summary": "The hybrid Fz1/2 proteins carrying the C-tail of Fz1 were enriched apically, comparable to wild-type Fz1, while chimeric Fz receptors carrying the Fz2 C-tail, including Fz2–2-2, were localized evenly along the apical–basal axis, comparable to wild-type Fz2. This indicates that the C-tails of Fz receptors are responsible for their specific subcellular localization."
} | 000089 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Rescue of the fz− Eye Phenotype with tub-Promoter-Driven Fz ChimerasTangential eye sections with corresponding schematic in lower part of panel reflecting ommatidial polarity (respective genotypes are also marked below each panel). Black arrows, dorsal chiral form; red arrows, ventral chiral form; green arrows, symmetric ommatidia; black circles, ommatidia with missing photoreceptors. Anterior is to the left, dorsal is up, and an area around the equator is shown for each genotype.(A) Section of a wild-type eye (equator is indicated by yellow line).(B) fzP21/fzR52 (fz null). Note random orientation of ommatidia.(C) fzP21/fzR52; tub-fz1–1-1. The fz− phenotype is fully rescued (100% with respect to chirality; only a minor rotation wobble is rarely seen).(D) fzP21/fzR52; tub-fz1–1-2. Note partial rescue with respect to polarity (approximately 83%) and occasional photoreceptor loss representative of Wg/β-cat signaling.(E) fzP21/fzR52; tub-fz1–1-2S. Note 100% rescue, identical to wild-type Fz1 (compare with [C]).(F) fzP21/fzR52; tub-fz1–2-1. No rescue due to the presence of the Fz2 7-TM region. This chimera actually shows a mild dominant negative behavior as apparent by the increased percentage of symmetric clusters (approximately 50% as compared to fz− [approximately 15%]).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449784-5-pbiop0020158pg005.jpg",
"summary": "The tub-Fz1–1-2 receptor, which contains the Fz1 7-TM region but is localized throughout the cellular membrane, partially rescues the fz− eye phenotype with approximately 83% rescue of chirality. However, it also causes defects related to canonical Wg/β-cat signaling, such as photoreceptor loss. This suggests that proper apical enrichment is critical for a clean PCP readout, but a ubiquitously distributed Fz1 chimera might still be present at apical adherens junctions to allow for partial rescue."
} | 000090 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Effects of Fz1/2 C-Tail Mutations on Subcellular Localization and PCP Activity(A) Sequence alignment of Fz1 and Fz2 C-tails. Note high degree of conservation within the membrane proximal shared portion of the Fz1 and Fz2 C-tails. The respective mutations generated and analyzed are indicated above the sequence (see also Table 1 for complete data set). As in Figures 2 and 3, dpp-Gal4 was used to drive expression of the respective mutants, and these were detected by anti-Myc staining in third instar wing discs. Examples for Fz1–1-1V559E (V to E substitution) are shown in (B) (localization) and (F) (function). All other mutants analyzed as shown in (A) are listed in Table 1. (C–E, G, and H) show the effects of the Fz2 C-tail-specific sequences. The Fz2 C-tail was truncated at the position of the Fz1 stop codon (amino acid L633), yielding a short Fz2 C-tail (2S). The localization (C and D) and GOF PCP function (G and H) of the respective chimeras, Fz1–2-2S and Fz1–1-2S, is shown. Note that both chimeras localize apically (C and D), and Fz1–1-2S shows a strong PCP GOF phenotype (H), very similar to Fz1–1-1 (see Figure 3B). Fz1–2-2S shows only a very weak PCP phenotype (G), mainly occurring at an anterior distal region of the wing (marked by arrow; the rest of the wing is wild-type). (E) Subcellular localization of Fz1–1-1C2. Fz1–1-1C2 is Fz1 with the addition of the Fz2-specific tail extension (see Materials and Methods). Note ubiquitous protein localization within the apical–basal axis (E) and a much reduced PCP activity, as compared to wild-type Fz1–1-1, in the functional assay (I). The phenotype is much weaker than in wild-type Fz1 (compare with [F] and [H] and Figure 3B).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449784-6-pbiop0020158pg004.jpg",
"summary": "The Fz2 C-tail was truncated at the position of the Fz1 stop codon (amino acid L633), generating chimeras Fz1–1-2S and Fz1–2-2S. Both chimeras localized apically to adherens junctions, similar to Fz1–1-1 and Fz1–2-1. Fz1–1-2S showed a strong PCP GOF phenotype, similar to Fz1–1-1, while Fz1–2-2S showed only a weak PCP phenotype, similar to Fz1–2-2 or Fz1–2-1. These results suggest that the Fz2 C-tail extension interferes with apical localization and affects PCP signaling."
} | 000091 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Epigenetic Imprints at the Initiation of X Inactivation(A–H) Indirect immunofluorescence and subsequent DNA FISH analysis on mitotic chromosomes prepared from undifferentiated clone 36 ES cells after 3 d of Xist induction. H3K27m3 (A), H4K20m1 (B), and Ezh2 (D) are enriched on the arms of Chromosome 11 upon ectopic Xist expression. H3K9m2 (C) is not enhanced upon Xist expression. H3K4m2 (E) is reduced on Chromosome 11 upon Xist induction (green box) and absent from pericentric heterochromatin and the Y chromosome (orange arrow). (F) Histone H4 multiple-lysine acetylation is partially reduced (green box, left panel). Hypoacetylation (red) is restricted to chromosomal regions which show high levels of H3-K27 trimethylation (green, right panel). H3K9m3 (G) and H3K27m1 (H) are enriched at constitutive heterochromatin of pericentric regions and the Y (orange arrows).(I–K) Indirect immunofluorescence (upper panels) and subsequent Xist RNA FISH (red, Xist RNA; blue, DAPI) analysis of H3K27m3 (I), H4K20m1 (J), and Ezh2 (K) in interphase nuclei of undifferentiated clone 36 ES cells expressing Xist for 3 d.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449785-7-pbiop0020171pg001.jpg",
"summary": "The reduction of H3K4m2 on Chromosome 11 upon Xist induction is consistent with a state of transcriptional repression. This reduction is observed in metaphase spreads and is absent from pericentric heterochromatin and the Y chromosome. The heterochromatic Y chromosome completely lacks both H3K4m2 and H3K4m3, indicating that H3K4m2 reduction correlates with the inactive state of the chromosome in undifferentiated ES cells."
} | 000092 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "hairy Affects stg-lacZ Reporter Expression(A–F) β-galactosidase expression from the stg-lacZ reporter lines pstg β-E4.9 (A and B), pstg β-E6.4 (C and D), and pstg β-E6.7 (E and F) in wild-type (A, C, and E) and hairy mutant (B, D, and F) embryos. Note the expanded (de-repressed) lacZ expression in the hairy mutant background compared to wild-type for the E4.9 and E6.4 lines (compare [B] to [A] and [D] to [C], respectively).(G) β-galactosidase expression from the stg-lacZ reporter line pstg β-E4.9ΔHairy (same as the reporter construct shown in [A], but with a Hairy binding site mutation) in a wild-type background. Note the expanded (de-repressed) lacZ expression (compare with [A]). Anterior is to the left. Dorsal is up in (A–D) and (G), whereas the ventral surface is shown in (E–F).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449821-11-pbiop0020178pg003.jpg",
"summary": "For the stg-lacZ reporter genes, pstg β-E4.9 and pstg β-E6.4, which contain canonical Hairy binding sites, showed expanded lacZ expression in a hairy mutant background compared to wild-type. This indicates that Hairy represses these reporters, and the derepression in the mutant background is consistent with the presence of Hairy binding sites."
} | 000093 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Hairy Binds to Putative Target Loci on Polytene Chromosomes(A) Hairy binds to polytene region 1A, the location of the Hairy target, ac.\n(B) Hairy is not found at 84A, the cytological location for ftz.\n(C–F) Hairy also binds to polytene region 99A, the location of stg (C); polytene region 3A, the location of egh (D); polytene region 33C, the location of prd (E); and polytene region 82A, the location of hkb (F).(G–I) Hairy is recruited to the insertion site for the pstg βE-4.9 reporter construct (arrow in [H] and [I]). Compare to the equivalent region of wild-type X chromosomes marked by brackets in (A), (D), and (G).(J) In situ hybridization to polytene chromosomes from pstg βE-4.9 larvae showing that this line has two insertions on the X chromosome at 1F and 6C. The probe also recognizes sequences to the endogenous white locus (asterisk).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449821-3-pbiop0020178pg006.jpg",
"summary": "Hairy binding was detected at the cytological location for egh, which is polytene region 3A. This binding is consistent with the identification of egh as a Hairy target."
} | 000094 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Hairy Target Gene Expression Is Disrupted in the Mutant Background of the Cofactors Associated with a Particular TargetWhole mount in situ hybridization on wild-type (A, E, and I), groucho germline clone(B, F, and J), dCtBP germline clone (C, G, and K), and dSir2 mutant (D, H, and L) embryos with probes recognizing stg (A–D), kayak (E–H), or prd (I–L). Anterior is to the left. Dorsal is up.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449821-5-pbiop0020178pg008.jpg",
"summary": "Consistent with a requirement for Groucho, stg expression is derepressed in dCtBP and dSir2 mutant backgrounds, but not in groucho mutant backgrounds. Similarly, prd expression is altered in groucho and dCtBP mutant backgrounds, suggesting that prd may represent a minority of Hairy targets that could recruit both Groucho and dCtBP."
} | 000095 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Expression of Hairy Target Genes Is Disrupted in hairy Mutant EmbryosWhole mount in situ hybridization on wild-type (A, C, E, G, I, K, and M) or hairy7H mutant (B, D, F, H, J, L, and N) embryos with probes recognizing prd (A and B), stg (C and D), ImpL2 (E and F), mae (G and H), egh (I and J), kayak (K and L), or Idgf2 (M and N). Anterior is to the left. Dorsal is up, except in (M) and (N), which are dorsal views.",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Light microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449821-6-pbiop0020178pg002.jpg",
"summary": "Direct Hairy targets exhibit altered expression in a hairy mutant background compared to wild-type embryos. For example, segmental expression of stg is altered (expanded) in a hairy mutant background, and there is a failure of stripe sharpening for prd, consistent with a role for Hairy in prd repression and stripe maintenance."
} | 000096 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Hairy Binds to Specific Loci on Polytene Chromosomes(A and B) Hairy staining (green) on third instar larval salivary gland polytene chromosome sets counterstained with DAPI (blue) to visualize the chromosomes.(C and D) Higher magnification of chromosome arms X, 3R (C) and 2L, 2R (D).",
"domain": null,
"primary_modality": null,
"secondary_modality": null,
"source_license": null,
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449821-7-pbiop0020178pg005.jpg",
"summary": null
} | 000097 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "Polytene chromosomes (blue) stained for Hairy (green) and Groucho (red) binding",
"domain": "Other",
"primary_modality": "Other",
"secondary_modality": "Other",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449864-0-pbiop0020204pg001.jpg",
"summary": "Proteins coded by special genes called transcription factors bind to DNA to block or encourage expression of specific genes, which is crucial for the development of segments in the growing embryo. In the context of the figure, Hairy and Groucho are such transcription factors that bind to polytene chromosomes, influencing gene expression."
} | 000098 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar | |
{
"caption": "FISH Confirmation of a Human-Specific Duplication of a Gene Cluster on Chromosome 5q13.3 Detected by Interspecies cDNA aCGH(A) Human duplication of a cluster of genes at Chromosome 5q13.3. is shown by two separate, and sometimes multiple, red BAC probe (CTD-2288G5) signals in interphase cells, with only one green BAC probe signal (RP11-1077O1) for a flanking region. Metaphase FISH shows both probes at band 5q13. The third nucleus in (A) shows four signals of the control probe (green) and eight copies of the BAC probe duplicated in the aCGH assay, consistent with the pattern expected in an S/G2 nucleus.(B–E) Bonobo (B), chimpanzee (C), gorilla (D), and orangutan (E) interphase FISH studies all show no increased signal for the human duplicated gene cluster, with signals of comparable size for the CTD-2288G5 (red) and the flanking RP11-107701 (green) probes. Metaphase FISH analyses show the gene cluster to be in the p arm of Chromosomes 4 (corresponding to the human Chromosome 5) in both the bonobo and chimpanzee, in the q arm of Chromosome 4 (corresponding to the human Chromosome 5) in the orangutan, and in the p arm of the gorilla Chromosome 19 (syntenic regions to human Chromosomes 5 and 17).",
"domain": "Medical",
"primary_modality": "Microscopy",
"secondary_modality": "Fluorescence microscopy",
"source_license": "other",
"subfigure_path": "/datasets/PMC-15M/filtered_biomedica/filtered_v4/subfigures_final/subfig_0_filelist_commercial_batch_0_1-PMC449870-5-pbiop0020207pg003.jpg",
"summary": "The FISH studies in the four great ape species (bonobo, chimpanzee, gorilla, and orangutan) showed no duplication of the gene region, with a single signal for the test probe (CTD-2288G5, red) and a single signal of comparable size for the flanking probe (RP11-107701, green). Metaphase FISH analyses revealed that the gene cluster is located in the p arm of Chromosome 4 in bonobo and chimpanzee, in the q arm of Chromosome 4 in orangutan, and in the p arm of Chromosome 19 in gorilla."
} | 000099 | hf://datasets/vector-institute/open-pmc-18m@b0869356d8648269d85183f2d5161f550cea2c30/data_00000.tar |
End of preview.
OPEN-PMC
Arxiv: Arxiv | Code: Open-PMC Github | Model Checkpoint: Hugging Face
Dataset Summary
This dataset consists of image-text pairs extracted from medical papers available on PubMed Central. It has been curated to support research in medical image understanding, particularly in natural language processing (NLP) and computer vision tasks related to medical imagery. The dataset includes:
- Extracted images from research articles.
- Associated captions and sub-captions with each image.
- All pairs are filtered medical image-text pairs.
- All images are decomposed compound figures with their respective sub-captions.
- Summarized in-text references to corresponding images for better model training.
Supported Tasks and Benchmarks
This dataset is designed for research in:
- Medical Image Captioning: Training and evaluating models that generate descriptions for medical images.
- Multimodal Learning: Studying the relationship between medical images and their textual descriptions.
- Image-Text Retrieval: Enabling models to retrieve relevant images based on textual queries and vice versa.
- Medical Language Understanding: Assisting in understanding complex medical terminology in images.
Languages
The dataset primarily contains text in English.
Dataset Structure
Data Fields
Each record in the dataset contains:
- Image: Filename of each extracted and decomposed image.
- Full caption: Original figure caption from the research paper.
Data Splits
The dataset does not contain predefined splits. Users can split the data as needed for training, validation, and testing.
Dataset Creation
Source Data
Initial Data Collection and Processing
- Data Collection: We used the raw data provided in BIOMEDICA.
- Filtering: Non-medical image-text pairs were removed to ensure a focused dataset.
- Compound Figure Decomposition: Multi-panel figures were split into individual sub-figures.
Annotations
The dataset does not contain additional manual annotations.
Uses
This dataset is designed for research purposes only and should not be used for:
- Clinical diagnosis.
- Medical decision-making.
- Any real-world patient care applications.
Ethical Considerations
- This dataset is derived from open-access publications available on PubMed Central.
- Researchers should comply with ethical guidelines and ensure that their work does not imply clinical utility.
- The dataset is intended strictly for academic and research purposes.
Citation
If you find the code useful for your research, please consider citing
@article{baghbanzadeh2025open,
title={Open-PMC-18M: A High-Fidelity Large Scale Medical Dataset for Multimodal Representation Learning},
author={Baghbanzadeh, Negin and Ashkezari, Sajad and Dolatabadi, Elham and Afkanpour, Arash},
journal={arXiv preprint arXiv:2506.02738},
year={2025}
}
License
This dataset is licensed under CC-BY-4.0, meaning it can be used for research purposes with appropriate attribution.
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