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FIGURE 2 in Redescription of soft tissue preservation in the holotype of Scaphognathus crassirostris (Goldfuss, 1831) using reflectance transformation imaging
FIGURE 2. Main slab (2A) and counter slab (2B) of the Scaphognathus crassirostris holotype, IGPB Goldfuss 1304a and b. Black rectangles and triangles illustrate the four different body regions in which soft part preservation is present: dorsal to the dorsal vertebral column until the base of the cervical vertebral column (1), ventral to the zeugopodial bones and next to the first and second phalanx of the fourth wing finger of the right wing (2), ventral to the cervical vertebral column (3), and the region enclosed by the zeugopodial and stylopodial bones of both wings (4). Images adapted from Jäger et al. (2018).
Data and code for: Dihydrothiazolo ring-fused 2-pyridone antimicrobial compounds effectively treat Streptococcus pyogenes skin and soft tissue infection
<p>We have developed GmPcides from a peptidomimetic dihydrothiazolo ring-fused 2-pyridone scaffold that have antimicrobial activities against a broad-spectrum of Gram-positive pathogens. Here we examine the treatment efficacy of GmPcides using skin and soft tissue infection (SSTI) and biofilm formation models by <em>Streptococcus pyogenes</em>. Screening our compound library for minimal inhibitory (MIC) and minimal bactericidal (MBC) concentrations identified GmPcide PS757 as highly active against <em>S. pyogenes</em> . Treatment of <em>S. pyogenes</em> biofilm with PS757 revealed robust efficacy against all phases of biofilm formation by preventing initial biofilm development, ceasing biofilm maturation and eradicating mature biofilm. In a murine model of <em>S. pyogenes</em> SSTI, subcutaneous delivery of PS757 resulted in reduced levels of tissue damage, decreased bacterial burdens and accelerated rates of wound-healing, which were associated with down-regulation of key virulence factors, including M protein and the SpeB cysteine protease. These data demonstrate that GmPcides show considerable promise for treating <em>S. pyogenes</em> infections.</p>
Survival-associated cellular response maintained in pancreatic ductal adenocarcinoma (PDAC) switched between soft and stiff 3D microgel culture
<div> <div> <div> <div> <p>Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection before metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path towards understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff," elastic modulus, E ≈ 10 kPa) microenvironment even whilst invading a healthy ("soft," E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the down-regulation of tumor suppressors (LATS1, BCAR3, CDKN2C ), as well as the up-regulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture, and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming.</p> </div> </div> </div> </div>
Рис. 3. Фотографии Laternula elliptica, сделанные около cтанции «Прогресс», ВосточнаЯ Антарктида. L. elliptica на морском дне с медкими камнЯми или гравием, глубина 27 м (А); несколько сифональных отверстий L. elliptica над поверхностью мЯгких осадков вокруг голотурии Staurocucumis turqueti, глубина 27 м (В); раковина L. elliptica (длина около 110 мм) на снегу около майны сраЗу после иЗвлечениЯ иЗ воды (С); пустые раковины L. elliptica на морском дне, глубина 56 м (D); раковина L. elliptica (вид с дорсального краЯ) на мЯгких осадках с камнЯми, покрытыми иЗвестковыми водорослЯми, глубина 30 м (Е); пара сифональных отверстий L. elliptica на поверхности мЯгких осадков, глубина 27 м (F). Фотографии О. Савинкина (A, B, D–F) и В. Потина (С). Fig. 3. Photographs of Laternula elliptica taken near «Progress» Research Station (East Antarctica). Softshelled clam L. elliptica on sea bottom with small stowns or gravel, depth 27 m (A); several open siphons of L. elliptica above soft bottom sediments around holothurian Staurocucumis turqueti, depth 27 m (B); a shell of L. elliptica (length about 110 mm) on snow near a dive hole just after dragging out of water (C); empty shells of L. elliptica on seafloor, depth 56 m (D); a shell of Laternula elliptica (dorsal view) on soft deposits among stones, covering by Lithothamnion, depth 30 m (E); pair of siphonal opening of L. elliptica on surface of soft sediments, depth 27 m (F). Photographs are taken by O. Savinkin (A, B, D–F) and V. Potin (C). in Species of warm-water origin Laternula elliptica (King, 1832) (Mollusca: Bivalvia: Laternulidae), a widespread mollusk in recent Antarctica
Рис. 3. Фотографии Laternula elliptica, сделанные около cтанции «Прогресс», ВосточнаЯ Антарктида. L. elliptica на морском дне с медкими камнЯми или гравием, глубина 27 м (А); несколько сифональных отверстий L. elliptica над поверхностью мЯгких осадков вокруг голотурии Staurocucumis turqueti, глубина 27 м (В); раковина L. elliptica (длина около 110 мм) на снегу около майны сраЗу после иЗвлечениЯ иЗ воды (С); пустые раковины L. elliptica на морском дне, глубина 56 м (D); раковина L. elliptica (вид с дорсального краЯ) на мЯгких осадках с камнЯми, покрытыми иЗвестковыми водорослЯми, глубина 30 м (Е); пара сифональных отверстий L. elliptica на поверхности мЯгких осадков, глубина 27 м (F). Фотографии О. Савинкина (A, B, D–F) и В. Потина (С). Fig. 3. Photographs of Laternula elliptica taken near «Progress» Research Station (East Antarctica). Softshelled clam L. elliptica on sea bottom with small stowns or gravel, depth 27 m (A); several open siphons of L. elliptica above soft bottom sediments around holothurian Staurocucumis turqueti, depth 27 m (B); a shell of L. elliptica (length about 110 mm) on snow near a dive hole just after dragging out of water (C); empty shells of L. elliptica on seafloor, depth 56 m (D); a shell of Laternula elliptica (dorsal view) on soft deposits among stones, covering by Lithothamnion, depth 30 m (E); pair of siphonal opening of L. elliptica on surface of soft sediments, depth 27 m (F). Photographs are taken by O. Savinkin (A, B, D–F) and V. Potin (C).
Fig. 17. Soft X in A New Species with Two New Subspecies of Rhinogobius (Teleostei: Gobiidae) from Yaeyama Group, the Ryukyu Islands, Japan
Fig. 17. Soft X-ray nagatives of holotypes of two subspecies of Rhinogobius aonumai. A: Rhinogobius aonumai aonumai, B: Rhinogobius aonumai ishigakiensis. Red and yellow spots indicate abdominal and caudal vertebrae, respectively; white arrows show anteriormost two pterygiophores (proximal radials) of second dorsal fin. Photographed and annotated by T. Suzuki.
FIGURE 5 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 5. Simplified overview of factors that influence the preservation and destruction of the cellular, soft tissue, and mineral content of bone. Diagenesis of these materials is more complex than is shown here. Additional factors also have influence, and multiple levels and modes of preservation and destruction may occur in different regions of a single bone (see text for details).
FIGURE 4 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 4. The geologic column according to science vs. YEC ideology. Time periods are not shown to scale. The dates according to science are from radiometric dating (Schmitz, 2020). The dates according to YEC ideology are based on biblical genealogies (Jones, 2016). YEC identifications of Paleozoic, Mesozoic, and pre-Quaternary Cenozoic strata as Flood deposits (e.g., Clarey, 2020; Oard and Carter, 2021) are based on misinterpretations of geologic data (Senter, 2011; Willoughby, 2016; Prothero, 2017; Senter, 2019).
FIGURE 2 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 2. Microstructure of bone matrix. A. Part of a collagen molecule, showing its triple helical structure (based on figure 2 of Bella (2016), with modifications), with each of the three helices shown in a different color: black, dark gray, and light gray. B. A collagen microfibril and associated bone mineral crystallites, showing that the microfibril consists of five staggered collagen molecules and that the crystallites form between the tips of the collagen molecules in the microfibrils (based on figure 1d of Alexander et al. (2012), with modifications). C. Part of a collagen fibril, showing that bone mineral crystallites form both within microfibrils (unshaded crystallites) and between microfibrils (shaded crystallites).
FIGURE 1 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 1. Cells and soft tissues from bones of the hadrosaurid dinosaur Edmontosaurus annectens, from the Standing Rock Hadrosaur Site (SHRS) in South Dakota (Upper Cretaceous: Maastrichtian). The images are reprinted from figure 2 of Cretaceous Research vol. 99, Ullmann et al., "Patterns of soft tissue and cellular preservation in relation to fossil bone tissue structure and overburden depth at the Standing Rock Hadrosaur Site, Maastrichtian Hell Creek Formation, South Dakota, USA" (2019), with permission from Elsevier. A. Osteocyte from fragment of ossified tendon. B. Osteocyte from caudal vertebra SRHS-DU-220. C. Blood vessels with spherical structures in the lumen, from metatarsal SHRS-DU-274. D. Blood vessel (right) and sheets of CBM (lower left) from fragment of ossified tendon. E. Sheet of CBM with embedded osteocytes, from metatarsal SHRS-DU-274.
FIGURE 3 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 3. Histology of bone. A. Macroscopic view of compact and spongy bone in a cross-section of the humerus of a domestic cow (Bos taurus). B. Arrangement of microstructures in compact and spongy bone. C. Human compact bone viewed through a compound microscope, with cells boiled away and voids filled with black ink, to make lacunae and canaliculi stand out.
FIGURE 6 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 6. Recrystallization of bone mineral. Note that through geologic time, the crystallite has become enlarged, and many of its original ions have been replaced by other ions from groundwater. Here, ions are not shown to scale with respect to each other or to the size of the crystallite. For details on relative abundances of the various ions in fossil bone, see Hubert et al. (1996); Kiseleva et al. (2019); Ullman et al. (2021); Schroeter et al. (2022); and Ullmann et al. (2022). REE = rare earth elements.
FIGURE 7 in Cells and soft tissues in fossil bone: A review of preservation mechanisms, with corrections of misconceptions
FIGURE 7. Spherical objects in a blood vessel from fossil bone, and items with which such structures have been hypothetically identified. The scale bar applies to A, C, and the smaller version of the image in B. The correct identity of the spherical objects in blood vessels of fossil bone remains unknown. A. Spherical objects in a blood vessel from fossil bone of the theropod dinosaur Beipiaosaurus inexpectus, from the Yixian Formation of Liaoning, China (Lower Cretaceous: Barremian–Aptian). This image is used with the permission of the journal PeerJ. It is from figure 2C of "Putative fossil blood cells reinterpreted as diagenetic structures," PeerJ, vol. 9: e12651, Korneisel et al. (2019). B. Pyrite framboids, shown to scale with A and C (left) and enlarged (right). This image is used with the permission of the journal PALAIOS. It is from figure 1 of "Rapid formation of framboidal sulfides on bone surfaces from a simulated marine carcass fall," PALAIOS, vol. 30: 327-334, Vietti et al. (2015). C. Red blood cells of the crocodilian species Caiman yacare (spectacled caiman). This image is reprinted by permission from Springer, from figure 1A of "Hepatozoon caimani Carini, 1909 (Adeleina: Hepatozoidae) in wild population of Caiman yacare Daudin, 1801 (Crocodylia: Alligatoridae), Pantanal, Brazil," Parasitology Research, vol. 116: 1907-1916 (2017).
FIGURE 4 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE 4. MicroCT (µCT) scan results of the crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota. The external surface of the crab is translucent to show the position of the preserved internal structures that the scan detected. Blue: cardiac stomach; yellow: esophagus; red: apodemes and mandibles. A, dorsal view. B, frontal view. C, right lateral view. D, closeup of dorsal view. E, closeup of frontal view. F, closeup of right lateral view. G, closeup of left lateral view.
FIGURE 3 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE 3. Exposed gills of the crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota and an interpretative drawing. 1-4: inferred number of gills;?af: possible afferent vessel.
FIGURE 1 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE 1. Location of study area in South Dakota. A, paleobiogeographic map of most of North America during the Late Cretaceous (late Campanian) with the locality indicated by a red dot (modified from Sampson et al., 2010, figure 1). B, photo of the locality in Pennington County, South Dakota, USA, where the studied crab specimen was discovered. A massive limestone from the upper Campanian Didymoceras cheyennense ammonite Zone is located at the top of the hill on the right and many limestone pieces are found downslope.
FIGURE 2 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE 2. The crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota. A, carapace in dorsal view. B, closeups of the preserved gills in left branchial chamber. C, carapace in ventral view. D, carapace in frontal view.
FIGURE S3 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE S3. Rotating illustration of the microCT (µCT) scan results of the crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota. Blue: cardiac stomach; yellow: esophagus; red: apodemes and mandibles; purple-pink: possible anterior gastric muscles. See online version for rotation (https://palaeo-electronica.org/content/2023/3973- soft-tissues-in-fossil-crab).
FIGURE 5 in Internal anatomy of a brachyuran crab from a Late Cretaceous methane seep and an overview of internal soft tissues in fossil decapod crustaceans
FIGURE 5. Rotating illustration (spin around the dorsal and ventral sides) of the microCT (µCT) scan results of the crab Secretanella sp. (ALMNH:Paleo:6522) from an upper Campanian methane seep limestone in Pennington County, South Dakota. Blue: cardiac stomach; yellow: esophagus; red: apodemes and mandibles. See online version for rotation (https://palaeo-electronica.org/content/2023/3973-soft-tissues-in-fossil-crab).
Dataset for the article: Robotic Feet Modeled After Ungulates Improve Locomotion on Soft Wet Grounds
<div> <div>This repository contains data for three different experiments presented in the paper:</div> <br> <div>(1) moose_feet (40 files): The moose leg experiments are labeled as ax_y.nc,</div> <div>where 'a' indicates attached digits and 'f' indicates free digits. The</div> <div>number 'x' is either 1 (front leg) or 2 (hind leg), and the number 'y'</div> <div>is an increment from 0 to 9 representing the 10 samples of each set.</div> <br> <div>(2) synthetic_feet (120 files): The synthetic feet experiments are labeled</div> <div>as lw_a_y.nc, where 'lw' (Low Water content) can be replaced by 'mw'</div> <div>(Medium Water content) or 'vw' (Vast Water content). The 'a' can be 'o'</div> <div>(Original Go1 foot), 'r' (Rigid extended foot), 'f' (Free digits anisotropic</div> <div>foot), or 'a' (Attached digits). Similar to (1), the last number is an increment from 0 to 9.</div> <br> <div>(3) Go1 (15 files): The locomotion experiments of the quadruped robot on the</div> <div>track are labeled as condition_y.nc, where 'condition' is either 'hard_ground'</div> <div>for experiments on hard ground, 'bioinspired_feet' for the locomotion of the</div> <div>quadruped on mud using bio-inspired anisotropic feet, or 'original_feet' for</div> <div>experiments where the robot used the original Go1 feet. The 'y' is an increment from 0 to 4.</div> <br> <div>The files for moose_feet and synthetic_feet contain timestamp (s), position (m), and force (N) data.</div> <div>The files for Go1 contain timestamp (s), position (rad), velocity (rad/s), torque (Nm) data for all 12 motors, and the distance traveled by the robot (m).</div> <br> <div>All files can be read using xarray datasets (https://docs.xarray.dev/en/stable/generated/xarray.Dataset.html).</div> </div>
FIG. 1 Early pygostylian Sapeornis STM 15-15 shows faint soft-tissue details that A in Pennaraptoran Theropod Dinosaurs Past Progress And New Frontiers
FIG. 1 Early pygostylian Sapeornis STM 15-15 shows faint soft-tissue details that A, under white light are vivid and B, under LSF, extensive.
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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.