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opencc-by-4.0Aug 2022View details →

Additional Sponge Rheology Data for "Rheology of Marine Sponge Tissue Reveals Anisotropic Mechanics and Tuned Dynamics"

These plots further support the general conclusions of the manuscript "Rheology of Marine Sponge Tissue Reveals Anisotropic Mechanics and Tuned Dynamics". These data were collected on a Kinexus rheometer and the sponges were from a distinct shipment of sponges than those presented in the main manuscript.

opencc-by-4.0Jun 2024View details →

Data for the paper: The Role of Glycerol in Manufacturing Freeze-Dried Chitosan and Cellulose Foams for Mechanically Stable Scaffolds in Skin Tissue Engineering

The Dataset contains all the data, described in the article "The Role of Glycerol in Manufacturing Freeze-Dried Chitosan  and Cellulose Foams for Mechanically Stable Scaffolds in Skin Tissue Engineering." Abstract Various strategies have extensively explored enhancing the physical and biological properties of chitosan and cellulose scaffolds for skin tissue engineering. This study presents a straightforward method involving the addition of glycerol into highly porous structures of two polysaccharide complexes: chitosan/carboxymethyl cellulose (Chit/CMC) and chitosan/oxidized cellulose (Chit/OC); during a one-step freeze-drying process. Adding glycerol, especially to Chit/CMC, significantly increased stability, prevented degradation, and improved mechanical strength by nearly 50%. Importantly, after 21 days of incubation in enzymatic medium Chit/CMC scaffold has almost completely decomposed, while foams reinforced with glycerol exhibited only 40% mass loss. It is possible due to differences in multivalent cations and polymer chain contraction, resulting in varied hydrogen bonding  and, consequently, distinct physicochemical outcomes. Additionally, the scaffolds with glycerol improved the cellular activities resulting in over 40% higher proliferation of fibroblast after 21 days of incubation. It was achieved by imparting water resistance to the highly absorbent material and aiding in achieving a balance between hydrophilic and hydrophobic properties. This study clearly indicates the possible elimination of additional crosslinkers and multiple fabrication steps that can reduce the cost of scaffold production for skin tissue engineering applications while tailoring mechanical strength and degradation. Figure 2. Morphology. SEM micrographs of the internal structure of the freeze-dried scaffolds. Results of porosity analysis. The methodology and data are described in the README file in the folder. Figure 3. Mechanical test results. Representative stress-strain curves from the tensile test of all freeze-dried scaffolds, where (A) – measurement performed in dry conditions, (B) – measurement performed in wet conditions. All are described in the README file in the folder. Figure 4. Swelling behavior of all scaffolds. B – Two representative vials with a visual demonstration of swelling, samples marked with circles: Chit/CMC sample submerged in the PBS (blue circle) and Chit/CMC/Glyc sample floating on the surface (green circle). The arrows lead to photos of scaffolds taken from vials directly after swelling. C – Gel fraction analysis in aqueous solution after 24  6 h. D – Time after which the water droplet is absorbed into the scaffold. E – Photographs of water droplet shape changes on Chit/CMC and Chit/CMC/Glyc scaffolds over time. All are described in the README file in the folder. Figure 5. Fourier Transform Infrared Spectroscopy (ATR-FTIR) analysis results. Details are in the README file in the folder. Figure 6. The FTIR spectra of eluates from degraded scaffolds collected on a microscopic glass slide. Details are in the README file in the folder. Figure 7.  The degradation studies of all scaffolds over 21 days of experiments in A – enzymatic medium. B – cell culture medium. Details are in the README file in the folder. Figure 9. Cell experiments and toxicity analysis. Cytotoxicity of eluates taken from degraded scaffolds. B – Direct fibroblast seeding on scaffolds during 14 days of culture period. C – Direct fibroblast seeding on scaffolds during 14 days of culture period without control to better see the effect of glycerol. Details are in the README file in the folder.

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).

opencc-by-4.0Sep 2024View details →

Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient

The Matlab code and dataset for the manuscript "Physiological mechanisms and life history trade-offs shape in-tissue correlations of an essential micronutrient". The dataset is packed in the ZIP archive 'Dataset_EjsmondTodisco_etal.zip' with variable description in the Matlab code file EjsmondTodisco_etal.m. To run the program, place the files EjsmondTodisco_etal.m and Fun_PlotResults.m in a catalog. The results are stored in two catalogs: 'ThReabsorptionAndSecretion' - modeling the rate of thiamine loss with processes of active reabsorption and secretion; and 'ThReabsorptionOnly' - modeling the rate of thiamine loss with the process of active reabsorption only. The ThReabsorptionAndSecretion catalog contains data for three life history types: iteroparity (baseline model), semelparity, and determinate growth (constant mass of somatic tissues in adults). For details see the manuscript by Ejsmond, Todisco et al.

dryad36/100

Data from: A pioneering experimental investigation of a novel in-situ dynamic characterization of the tensile/compression stress-strain mechanism on human plantar soft tissue

We have conducted the first in-situ and in-vivo dynamic mechanical test on human plantar soft tissue. A dynamic mechanical analysis (DMA)-like device has been invented to perform the in-situ and in-vivo stress-strain tests on living plantar in order to characterize the material mechanism of biological soft tissue, whereas it is nearly impossible to prepare a sample from a living body for classical tests. A series of pioneering tests of tensile/compression on the heel of ten volunteers are reported, with the reference of tests on mimic foot model made by silicon rubber, standard silicon rubber brick sample, and finite elementary analysis. In addition to demonstrating the effectiveness of the device and approach, interesting correlations between the results and clinic data were found, suggesting considerable potential for the invention in future research.

opencc-zeroNov 2023View details →

zenodo36/100

A 3D multi-cellular tissue model of the human omentum to study mechanisms of ovarian cancer metastasis

Here, the design of 3D multi-cellular tissue model of the human omentum is presented to study mechanisms of ovarian cancer metastasis.

opencc-by-4.0Dec 2020View details →

dryad36/100

Universality in the mechanical behavior of vertex models for biological tissues

Open the record for dataset details and reuse information.

publicJul 2025View details →

dryad36/100

Data from: A pioneering experimental investigation of a novel in-situ dynamic characterization of the tensile/compression stress-strain mechanism on human plantar soft tissue

Open the record for dataset details and reuse information.

publicNov 2023View details →

opennotspecifiedOct 2019View details →

Figure 3 in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

Figure 3. SR-FTIR full spectra of isolated T. rex vascular tissue and chicken type I collagen (no treatment). All key bands for the identification of protein (Amide I, Amide II, Amide III) are present in the dinosaur tissue spectrum. The T. rex spectrum also presents a strong non-peptide carbonyl (C=O) band at 1739 cm−1 and a carbohydrate band at ~1010 cm−1.

opennotspecifiedOct 2019View details →

Figure 5 in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

Figure 5. SR-FTIR analysis of T. rex vascular tissue, NaBH4 reduced T. rex vascular tissue, chicken type I collagen without treatment, and chicken type I collagen treated with Fenton reagent and iron-catalysed glycation. (a,b) Average FTIR spectra in the non-peptide carbonyl and protein amide I regions for all five samples. (a) Significant reduction in the non-peptide carbonyl band follows treatment of T. rex vascular tissue with NaBH4, which reduces (immature) peptide crosslinks. The blue-shifted Amide I band of the dinosaur tissue, Fenton reagent-treated chicken type I collagen, and Fe-catalysed glycation-treated chicken type I collagen indicate increasing α-helix structure (~1660 cm−1) as the higher-energy triple-helix and intermolecular sub-bands (see Fig. 1 for method of identification) increasingly predominate the spectra. The development of aldehydic carbonyl, ketoaldehyde, and/or immature ketoimine bands in both treated chicken tissues is consistent with the strong carbonyl band in the dinosaur tissue.

opennotspecifiedOct 2019View details →

Figure 1. Amide I in Mechanisms of soft tissue and protein preservation in Tyrannosaurus rex

Figure 1. Amide I sub-band localisation of untreated and treated chicken type I collagen in SR-FTIR spectra. Sub-bands (β-sheet, ~1633 cm−1; triple-helix, ~1658–1660 cm−1; intermolecular, ~1683–1690 cm−1) are indicated in the figures. Red traces denote second derivatives of experimental curves. Although the intermolecular sub-band typically presents at lower wavenumber, the identified value was the nearest local minimum in each of the second derivative traces and consistently appears across all samples; therefore, in this sample, the intermolecular sub-band was indexed at 1697–1699 cm−1.

openMay 2023View details →

TRACE Dataset: Predicting molecular mechanisms of hereditary diseases by using their tissue-selective manifestation

Features dataset, as described in Simonovsky, Eyal, et al. "Predicting molecular mechanisms of hereditary diseases by using their tissue‐selective manifestation." Molecular Systems Biology (2023): e11407.Article: https://doi.org/10.15252/msb.202211407Code: https://github.com/eyalsim/trace