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Datasets for chromatin hub prediction in six cell lines based on multiple genomic features
<p>Tables with features and classes for machine learning prediction of chromatin hubs. Genomic features include CTCF, EP300, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, RAD21, RNAPol2, and RNA.Seq, while the classes are Hubs and Non-Hubs.</p> <p>The cell lines featured here are A549, H1ESC, HeLa, IMR90, K562, and MCF7. They happen to be the 6 cell lines out of 8 existing in our integrative database, GREG (https://doi.org/10.1093/database/baz162). The normalized read-coverages from features (variables) are mapped through genomic intervals of 2 Kbs, genome-wide. Such genomic intervals (bins), are classified as Hubs or Non-Hubs. Hubs are those bins with multiple chromatin interactions, including at least one long-range interaction (larger than 1Mb) or an inter-chromosomal interaction (tagged as Inf).</p> <p>Columns per table:<br> chr start end CTCF EP300 H3K27me3 H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K9ac H3K9me3 RAD21 RNA.Seq RNAPol2 Class</p> <p>Note that features may be inconsistent across different cell types, due to the availability of data. The BAM files have been sourced from ENCODE and NCBI repositories.</p> <p>The analysis following this data can be found at https://github.com/mora-lab/GREG-Hubs.</p>
Proteomics data of mitochondrial fraction of CRL-2097 cancer cell line model
<p>The cancer cell line model developed using human dermal fibroblasts CRL-2097 was used in these experiments:</p> <p>Sample 1 - CRL2097 + hTERT</p> <p>Sample 2 - CRL2097 + hTERT + LT</p> <p>Sample 2 - CRL2097 + hTERT + LT + Ras</p> <p>The mitochondrial fraction was prepared from each of these cell lines and analysed via mass spec for their proteomics. The experiment was done in duplicates. </p>
Fig. 1 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 1. Photomicrographs of the olfactory epithelium of Pygocentrus nattereri by scanning electron microscopy (SEM) and histological architecture stained with Delafield's Haematoxylin-Eosin (HE) and Mallory's triple (MT) stain. A — oval shaped olfactory rosette showing olfactory lamellae (OL) radiating from median raphe (R). Note tongue shaped structure (arrow heads) on the apical end of the lamellae (SEM) ×50. B — sensory olfactory epithelium (OEP) lined with receptor cells. Note the presence of blood vessels (BV) in the central core (CC) which is distinguished from OEP by basement membrane (BM). Arrow heads indicate basal cells above BM (MT) ×400. C — higher magnification of OEP showing a large number of primary receptor cells (RC) with conspicuous nuclei (N), secondary recptor cells (broken arrows), microvillous cells (MV) intermingled with supporting cells (SC). Note the presence of BV in CC and BC (arrow heads) near CC. Solid arrow indicates the axons of secondary RC communicate to CC (MT) ×1000. D — OEP exhibiting cylindrical RC with knob like vesicles (black arrow heads), ciliated supporting cells (solid arrows), non-ciliated supporting cells (white arrow heads) and BC above CC. Broken arrows mark the cilia of supporting cells on the epithelial surface (HE) ×400. E — tuft of receptor cells (RC) in between supporting cells (SC) (SEM) ×4000. F — dendrite patches of RC (broken arrows) and microvillous cells (solid arrows) in between stratified epithelial cells (SEC). Note the opening of mucous cells (arrow heads) in between SEC (SEM) ×2500.
Fig. 2 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 2. Photomicrographs of the olfactory epithelium of P. nattereri by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and histological features stained with Mallory's triple (MT) stain. A — transitional zone between sensory epithelium (SE) with receptor cells (solid arrows) and non-sensory epithelium (NSE) having a series of mucous cells (MC) (Broken arrows), labyrinth cells (LC) and stratified epithelial cells (arrow heads). Olfactory epithelium separated from central core (CC) by a basement membrane (BM) (MT) ×400. B — surface of non-sensory epithelium showing densely arranged ciliated supporting cells (solid arrows) encircled the non-ciliated supporting cells (SC) with adhering mucin mass (arrow heads). Note the opening of MC (broken arrows) in between SC (SEM) ×4500. C — dendrite of receptor cell (RC) emerging out from basal body (broken arrow). Note microtubules of rod (solid arrow) parallel arranged (TEM) ×5000. D —nuclei of receptor cells (N) showing dispersed heterochromatin (arrow heads). Note the presence of mitochondria (solid arrows) adjacent to nucleus (TEM) ×500. (E) Showing cisterns of rough endoplasmic reticulum (rER) (arrow heads) encircling nucleus (solid arrow). Note Golgi apparatus (broken arrow) adjacent to rER (TEM) ×4000. F — OEP lined with microvillous cells (MV), mucous cell (MC) and supporting cell (broken arrow) (TEM) ×2100. G — microvillous cells exhibiting abundant ribosomes (broken arrows) and extended mitochondria (arrow heads). Solid arrow indicates nucleus (TEM) ×5000. H — axons (broken arrows) of receptor cells run parallel on both sides of basal cells (solid arrow) (TEM) ×5000.
Fig. 3 in Histological, Topographical And Ultrastructural Organization Of Different Cells Lining The Olfactory Epithelium Of Red Piranha, Pygocentrus Nattereri (Characiformes, Serrasalmidae)
Fig. 3. Photomicrographs of the olfactory epithelium of P. nattereri by transmission electron microscopy (TEM) and scanning electron microscopy (SEM). A — olfactory epithelium (OEP showing mucous cell (MC) having granules, microvillous cell (arrow head), labyrinth cell (broken arrow) and vesicular cytoplasm of supporting cell (solid arrow) (TEM) ×2100. B — flat surface ciliated supporting cell (solid arrow) provided with plenty of kinocilia (arrow heads) showing microtubular pattern (broken arrows). Note large number of mitochondria within the cytoplasm of supporting cells (TEM) ×5000. C — non-sensory olfactory epithelium (OEP) comprised of MC filled with large granules and supporting cells (solid arrows) (TEM) ×2100. D — basal cells provided with conspicuous lobular nuclei (N) having dense nucleolus (solid arrow). Note the presence of small vesicles (arrow head) adjacent the nucleus and rough endoplasmic reticulum (rER) (broken arrows) (TEM) ×2500. E — showing nuclear division of basal cells provided with dense nucleus (solid arrows). Broken arrows indicate mature nucleus of basal cells (TEM) ×2500. F — showing labyrinth cells (solid arrow) with conspicuous folding encircled by compactly arranged stratified epithelial cells (SEC). Note the presence of MC (broken arrows) in between SEC and mucin droplets (arrow heads) over SEC (SEM) ×4500. G — surface epithelium of raphe provided with packed SEC having labyrinth pattern microridges. Note the presence of opening of MC (solid arrows) and mucin droplets (arrow heads) over SEC (SEM) ×4500. H — raphe showing oval and elongated nuclei (N) of Stratified epithelial cells. Note the presence of rER (solid arrows) and vesicles (broken arrows) adjacent to nucleus (TEM) × 2500.
Establishment of a Spermatogonial Stem Cell Line with Potential of Meiosis in a Hermaphroditic Fish, Epinephelus coioides
<p>Figure S1. Cell localization of ly75, thy1, and dmc1 in adult testis of orange-spotted grouper. (A-C) Antisense probe signals of ly75, thy1, and dmc1. (D-F) Sense probe signals of ly75, thy1, and dmc1. Sg, Spermatogonium; Sc, Spermatocyte; St, spermatid. Scale Bars: 20 μm.</p> <p>Figure S2. Fluorescent immunostaining of antibodies in adult testis of orange-spotted grouper. (A-D and M-O) Fluorescence signals of Piwi, Dazl, Ssea1, Nanog, PCNA, Sycp3, and Dmc1. (E-H and P-R) Nuclei are counterstained with PI. (I-L and S-U) Merge images. Sg, Spermatogonium; Sc, Spermatocyte; St, spermatid; Sz, spermatozoa. Scale Bars: 20 μm.</p> <p>Figure S3. Derivation of a single colony from a single cell of GPT line. (A) A small colony after five days of culture. (B) A distinct colony after 10 days of culture. (C) A large colony containing hundreds of cells after 20 days of culture. Scale Bars: 20 μm in A; 50 μm in B; 200 μm in C.</p> <p>Figure S4. Prolonged cultivation of GPT cells under the lack of bFGF. (A-D) All GPT cells would differentiate into large epithelial-like cells and gradually die out during 25 days of culture under the lack of bFGF, LIF, and SCF (-/-). (E-H, J-M, and O-R) GPT cells consisted of some polygonal-like cells and many epithelial-like cells during 25 days of culture in the ESM media containing SCF and/or LIF. (I, N and S) All GPT cells transformed into very large epithelial-like cells and gradually died after 35 days of culture in the ESM media containing SCF and/or LIF. Scale Bars: 50 μm.</p> <p>Figure S5. Morphology of GPT cells under a condition of high cell confluence. (A) GPT cells were cultured for 14 days without subculture and (B) generated a few spherical cells (Arrows). Scale Bars: 50 μm in A; 20 μm in B.</p> <p>Figure S6. Establishment of a GPT cell line stably expressing green fluorescence protein. (A-C) Bright-field image, fluorescent image, and merged image of GPT cells after 48 hours of culture following electrotransfection with pEGFP-N3 plasmid. (D-F) Bright-field image, fluorescent image, and merged image of GPT cells after G418 resistance screening. Scale Bars: 200 μm in A-C; 100 μm in D-F.</p>
Text-fig. 8. Pterocaryoxylon sp., a–c, e: UF 279-85024; d, f: UF 279-24551. a, b: Wood semi-ring-porous, vessels solitary and in short radial multiples, axial parenchyma scanty vasicentric, marginal, and in narrow lines, TS. c: Crowded alternate intervessel pitting, simple perforation plate (PP), TLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e: Rays mostly 1–3 cells wide, occasionally 4 cells, uniseriate rays probably mostly square to upright cells, TLS. f: Rays heterocellular, body cells procumbent. Scale bars: 200 µm in a, b; 100 µm in e, f; 50 µm in c; 20 µm in d. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa
Text-fig. 8. Pterocaryoxylon sp., a–c, e: UF 279-85024; d, f: UF 279-24551. a, b: Wood semi-ring-porous, vessels solitary and in short radial multiples, axial parenchyma scanty vasicentric, marginal, and in narrow lines, TS. c: Crowded alternate intervessel pitting, simple perforation plate (PP), TLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e: Rays mostly 1–3 cells wide, occasionally 4 cells, uniseriate rays probably mostly square to upright cells, TLS. f: Rays heterocellular, body cells procumbent. Scale bars: 200 µm in a, b; 100 µm in e, f; 50 µm in c; 20 µm in d.
Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 7. Exbeckettia mastixioides (E.REID et M.CHANDLER) comb. nov. Details of anatomy in transverse section on cut surfaces from bilocular fruit shown in Text-fig. 6i, V. 23013(3). a: Details of seed (S), locule (L), distinct endocarp planes of separation (arrows). b: Detail of endocarp adjacent to the locule, and surrounding mesocarp. Blue lines indicate thickness of sclerenchyma lining the locule. Note layer of horizontally oriented periclinal fibres a few cells thick, lining the locule (arrow). c: Enlargement showing parenchyma cells of the mesocarp decreasing in diameter toward the periphery. d: Enlargement showing fibres and sclereids of the endocarp. e: Sharp contact between endocarp and mesocarp. f, g: Detailed anatomy of endocarp including locule lining, and contact with mesocarp. Scale bars 2 mm in (a), (b), 1 mm in (c–g).
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k). in Mastixioid Fruits (Cornales) From The Early Eocene London Clay Flora: Morphology, Anatomy And Nomenclatural Revision
Text-fig. 5. Mastixiopsis nyssoides KIRCHH. a, b, g–n: Organic preservation. a, b: Lignitic, unpermineralized, early Eocene Dorset Pipe clays at Arne, V. 40762. a: Ventral view (original illustration from pl. 18, fig. 1 of Chandler 1962). b: Transverse fracture, somewhat distorted by compression. c–f: Pyrite permineralization. c: Ventral view, V. 22963(1) from Sheppey, originally listed as Mastixia cantiensis. d: Lateral view, V. 22969 from Sheppey (identified as Mastixia grandis by Reid and Chandler 1933: pl. 25, fig. 8). e: Equatorial transverse physical section from (c). f: Equatorial transverse physical section from (d). g: Detail of pericarp from (e), showing endocarp formed of dense fibrous tissue, surrounded by mesocarp of anticlinally oriented larger cells. h: Detail of pericarp from (f). i–n: Type material from Eocene of Riestadt, Germany, MNB. i: Ventral view. j, k: Ventral and apical views of holotype. l: View of the transversely fractured surface from (j) showing horseshoe shaped locule. m: Equatorial transverse physical cut of the specimen in (i); note yellow resin cavity (arrow). n: Scanning electron microscopy of pericarp from (l) with locule lining at lower edge of image. Note dense endocarp tissue composed of small cells (fibres and sclereids), extending about 3/5 of distance to periphery, surrounded by mesocarp of larger, anticlinally oriented cells. Scale bars 1 cm in (a–f), (i–k), 1 mm in (g), 2 mm in (h), 3 mm in (l), m, 250 Μm in (n). Bar in (d) applies also to (c). Bar in (l) also applies to (m). Bar in (i) also applies to (j) and (k).
Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer
<p>Raw and processed cell lines (melanomaC818/melanomaMUM-2B/SK-MEL-28) data for detecting DMKN's mutations in melanoma cancer. This research was concluded that DMKN is a trigger of epithelial-mesenchymal transition-driven melanoma.</p>
Cancer cell line CNV samples
<p>This tab separated file includes all cancer cell line samples used for cell line heterogeneity analysis.</p> <p>Columns: sample ID, original NCIT code, cellosaurus ID, bins.</p> <p>All bins, duplications (1) and deletions (2), are merged while keeping their original order. Bin size: 5 Mb.</p> <p>This dataset belongs to the publication: https://doi.org/10.1101/2024.05.15.594310</p> <p> </p>
SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed. in External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment
SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed.
◂Fig. 1 Morphology of thecate and coccoid cells, with labelled thecal plates. a–c, i, m Light microscopy, d–h, k–l scanning electron microscopy. a Ventral view of strain GeoM*788; b dorsal view of strain GeoM*793; c apical view of strain GeoK*044; d ventral view of strain GeoK*037; e dorsal view of strain GeoM*788; f apical view of strain GeoK*024, with the dehiscence of epithecal opening indicated by a blue line; g antapical view of strain GeoK*044; h leftlateral view of strain GeoM*866; i motile cell of strain GeoK*037; k–m coccoid cells showing variability in shape and size of strains k GeoM*866, l GeoM*793 and m GeoK*024. Abbreviations: n′: apical plate, n′′: precingular plate, n′′′: postcingular plate, n′′′′: antapical plate, na: anterior intercalary plate, nC: cingular plate, Sa: anterior sulcal plate, Sd: right sulcal plate, Sp: posterior sulcal plate. Ss: left sulcal plate. Scale bar: 10 µm. UA: 15 kV in Morphological and molecular variability of Peridinium volzii Lemmerm. (Peridiniaceae, Dinophyceae) and its relevance for infraspecific taxonomy
◂Fig. 1 Morphology of thecate and coccoid cells, with labelled thecal plates. a–c, i, m Light microscopy, d–h, k–l scanning electron microscopy. a Ventral view of strain GeoM*788; b dorsal view of strain GeoM*793; c apical view of strain GeoK*044; d ventral view of strain GeoK*037; e dorsal view of strain GeoM*788; f apical view of strain GeoK*024, with the dehiscence of epithecal opening indicated by a blue line; g antapical view of strain GeoK*044; h leftlateral view of strain GeoM*866; i motile cell of strain GeoK*037; k–m coccoid cells showing variability in shape and size of strains k GeoM*866, l GeoM*793 and m GeoK*024. Abbreviations: n′: apical plate, n′′: precingular plate, n′′′: postcingular plate, n′′′′: antapical plate, na: anterior intercalary plate, nC: cingular plate, Sa: anterior sulcal plate, Sd: right sulcal plate, Sp: posterior sulcal plate. Ss: left sulcal plate. Scale bar: 10 µm. UA: 15 kV
Individual allotype responses to HEK-293T-based cell lines ex-pressing single MHC class I chain-related gene B alleles
<p><span>Figure S1.</span><span> Individual allotype responses between 64 sera collected from kidney transplant patients and 5 single </span><span>MICB</span><span> allele-expressing cell lines established in </span><span>HLA</span><span> class I, </span><span>MICA,</span><span> and </span><span>MICB</span><span>-null HEK-293T cells. </span><span>HLA</span><span> class I, </span><span>MICA,</span><span> and </span><span>MICB</span><span> genes were removed using CRISPR/Cas9 in previous studies [20, 21]. Some of the 64 sera showed responses to single </span><span>MICA</span><span> allele-expressing cell lines [21]. However, none of the 64 sera showed individual allotype responses in this study.</span></p>
MinION 1D² Reads From Mus musculus GL261 Cell Lines
<p>Called FASTQ and raw FAST5 MinION cDNA reads (1D²) from a murine GL261 neuroblastoma cell line, cultured at the Malaghan Institute of Medical Research, sequenced on a R9.5 flow cell in August 2017 using the LSK309 1D² kit for ligating ONT adapters to cDNA generated using strand-switching primers.</p> <p>The called reads for the entire sequencing run are available:</p> <ul> <li>called_reads_1Dsq_Olivier_GL261_cDNA_2017-Aug-04.tar.gz -- called reads from both/all runs (1D²-corrected fastq files only).</li> <li>called_reads_uncorrected_Olivier_GL261_cDNA_2017-Aug-04.tar.gz -- uncorrected reads from both/all runs.</li> <li>metadata_called_reads_Olivier_GL261_cDNA_2017-Aug-04.tar.gz -- metadata associated with all called sequences (e.g. sequencing_summary.txt)</li> </ul> <p>This dataset only includes a subset of the total reads as raw signal / FAST5 files:</p> <ul> <li>Actb_GL261_cDNA_2017-Aug-04_1D2.tar -- reads from one run that mapped (in whole or in part) to a mouse beta-actin transcript [<a href="http://asia.ensembl.org/Mus_musculus/Transcript/Summary?db=core;g=ENSMUSG00000029580;r=5:142903234-142903654;t=ENSMUST00000100497">ENSMUST00000100497.10</a>].</li> <li>Ubb_GL261_cDNA_2017-Aug-04_1D2.tar -- reads from one run that mapped (in whole or in part) to a mouse ubiquitin transcript [<a href="http://asia.ensembl.org/Mus_musculus/Transcript/Summary?db=core;g=ENSMUSG00000019505;r=11:62551171-62553213;t=ENSMUST00000019649">ENSMUST00000019649.3</a>].</li> </ul>
Steady states using PARADIGM for 8 cell lines from CCLE
<p>This dataset has the input data + result dataset (steady states per cell line) that was the product of using the CLSS rbbt workflow (that uses the PARADIGM tool) for 8 cell lines from CCLE. A CASCADE-derived pathway file was used as input for PARADIGM.</p>
In vitro antiproliferative data of metallodrugs in skin cancer cell lines
<p>Compiled <em>in vitro</em> antitumoral potency (IC<sub>50</sub>, GI<sub>50</sub> and/or TGI values) of metallodrugs in skin cancer cell lines. This information is complemented by structural parameters of each compound testted, such as molecular weight with and without the counter-ion, charge, oxidation state of the metal center and ligand type. Information on the antiproliferative assay is also given, such as type of cell line and incubation time. Additional details are provided when the compounds have been assayed upon light activation (PDT), as part of the NCI-60 panel and if <em>in vivo</em> data is also available.</p>
Text-fig. 54. Scanning electron microscope (SEM; a–e, g, h) and synchrotron x-ray microscopy (SRXTM; f, i) images of unnamed angiosperm fruits and seeds; Torres Vedras locality, Portugal. a) Follicle sp. 1, narrow elongate follicle with sessile and decurrent stigma; b) Follicle sp. 2, broad, dehisced follicle with elongate and transverse fibers lining the locule; c) Angiosperm seed sp. 1 with thin, smooth seed coat; d) Angiosperm seed sp. 2 with verrucate seed coat; e) Angiosperm seed sp. 3 with exotestal and foveolate seed coat; f) Angiosperm seed sp. 4 with smooth seed coat; g, h) Angiosperm seed sp. 5 with raised epidermal cells forming a reticulate pattern; i) Wedge-shaped angiosperm fruit with remains of floral parts near apex. Specimens, TV43-S136726 (a), TV44-S148144 (b), TV43-S170074 (c), TV43-S136747 (d), TV43-S170073 (e), TV38-S174615 (f), TV44-S148003 (g), TV44-S148004 (h), TV43-S174685 (i). Scale bars 300 Μm (a–i). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 54. Scanning electron microscope (SEM; a–e, g, h) and synchrotron x-ray microscopy (SRXTM; f, i) images of unnamed angiosperm fruits and seeds; Torres Vedras locality, Portugal. a) Follicle sp. 1, narrow elongate follicle with sessile and decurrent stigma; b) Follicle sp. 2, broad, dehisced follicle with elongate and transverse fibers lining the locule; c) Angiosperm seed sp. 1 with thin, smooth seed coat; d) Angiosperm seed sp. 2 with verrucate seed coat; e) Angiosperm seed sp. 3 with exotestal and foveolate seed coat; f) Angiosperm seed sp. 4 with smooth seed coat; g, h) Angiosperm seed sp. 5 with raised epidermal cells forming a reticulate pattern; i) Wedge-shaped angiosperm fruit with remains of floral parts near apex. Specimens, TV43-S136726 (a), TV44-S148144 (b), TV43-S170074 (c), TV43-S136747 (d), TV43-S170073 (e), TV38-S174615 (f), TV44-S148003 (g), TV44-S148004 (h), TV43-S174685 (i). Scale bars 300 Μm (a–i).
Text-fig. 11. Silutanispermum kvacekiorum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a, b) Holotype (S170238), seed in oblique (a) and lateral (b) view showing large triangular hilar scar (hi) and transverse micropylar slit (mi). c) Oblique view of seed showing slightly raised raphal area (S174352); remains of mounting media (¤). d) Details of holotype showing triangular hilum (hi) and transverse micropylar slit in the exotesta (mi). e) Cut volume rendering of holotype (cut at yz1170) through the median plane showing hilum (hi) and micropylar slit (mi) lined by radially expanded exotestal cells. Scale bars = 500 µm (a–c); 250 µm (d, e). in Extinct Taxa Of Exotestal Seeds Close To Austrobaileyales And Nymphaeales From The Early Cretaceous Of Portugal
Text-fig. 11. Silutanispermum kvacekiorum gen. et sp. nov. seeds from the Early Cretaceous Famalicão locality (sample 025), Portugal; Synchrotron radiation X-ray tomographic microscopy (SRXTM, volume renderings). a, b) Holotype (S170238), seed in oblique (a) and lateral (b) view showing large triangular hilar scar (hi) and transverse micropylar slit (mi). c) Oblique view of seed showing slightly raised raphal area (S174352); remains of mounting media (¤). d) Details of holotype showing triangular hilum (hi) and transverse micropylar slit in the exotesta (mi). e) Cut volume rendering of holotype (cut at yz1170) through the median plane showing hilum (hi) and micropylar slit (mi) lined by radially expanded exotestal cells. Scale bars = 500 µm (a–c); 250 µm (d, e).
Assessing the Cytotoxicity of Phenolic and Terpene Fractions Extracted from Iraqi Prunus arabica on AMJ-13 and SK-GT-4 Human Cancer Cell Lines
<p>Breast and esophagus cancer are the most aggressive and prominent causes of death worldwide. In addition, these cancers showed resistance to current chemotherapy regimens with limited success rates and fatal outcomes. Recently many studies reported the significant cytotoxic effects of phenolic and terpene fractions extracted from various <em>Prunus</em> species against different cancer cell lines. This suggests the probability to be a candidate as an alternative or adjuvant to the current chemotherapeutic regimens. The study aimed to evaluate the cytotoxicity of phenolic and terpene fractions extracted from Iraqi <em>Prunus arabica</em> on breast (AMJ-13) and esophagus (SK-GT-4) cancer cell lines by using the MTT assay. Analysis using Chou-Talalay method performed to assess the synergistic effect between the extracted fractions and chemotherapeutic agent (docetaxel). Moreover, HPLC analysis has been conducted for the quantitative determination of different bioactive molecule of both phenolic and terpene fractions in the extract. According to the findings, the treatment modalities significantly decreased cancer cell viability of AMJ-13 and SK-GT-4 and had insignificant cytotoxicity on the normal cells (normal human fibroblast cell line) (all less than 50% cytotoxicity). Analyzing with Chou-Talalay showed a strong synergism with docetaxel on both cancer cell lines (higher cytotoxicity even in low concentrations) and failed to induce a cytotoxicity on the normal cells. Important flavonoid glycosides and terpenoids were detected by HPLC in the particularly ferulic acid, catechin, chlorogenic acid, B sitosterol, and campesterol. In conclusion, the extracted fractions selectively inhibited the proliferation of both cancer cell and showed minimal cytotoxicity on normal cells. Thus, the study suggested the possible natural source of selected fractions as breast and esophagus cancer drugs</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.