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Fig. 1 in Biochemical analyses of Trichogramma dendrolimi (Hymenoptera: Trichogrammatidae) in vitro and in vivo rearing for 10 generations
Fig. 1. Protein concentration in Trichogramma dendrolimi reared in vitro and in vivo for 10 generations. Means (± SE) were calculated from 3 replicates. Data with an asterisk differ significantly according to paired-sample t-tests at P = 0.05.
Assessing amino acid solubility of black soldier fly larvae meal in Atlantic salmon (Salmo salar) in vivo and in vitro
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Quantitative susceptibility mapping of articular cartilage: ex vivo findings at multiple orientations and following different degradation treatments
<p>This dataset contains all the raw source data and MATLAB analysis functions that comprise the study:</p> <p><br> Quantitative susceptibility mapping of articular cartilage: Ex vivo findings at multiple orientations and following different degradation treatments</p> <p>Magnetic Resonance in Medicine | DOI: 10.1002/mrm.27216</p> <p>Nykänen Olli(1*), Rieppo Lassi(2,3), Töyräs Juha(1,4), Kolehmainen Ville(1), Saarakkala Simo(2,3,5), Shmueli Karin(6) and Nissi Mikko Johannes(1)</p> <p>(1) Department of Applied Physics, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland<br> (2) Research Unit of Medical Imaging, Physics and Technology, University of Oulu, POB 5000, FI-90014 Oulu, Finland<br> (3) Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland<br> (4) Diagnostic Imaging Center, Kuopio University Hospital, Kuopio, Finland<br> (5) Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland<br> (6) Department of Medical Physics & Biomedical Engineering, University College London(UCL), London, United Kingdom</p> <p><br> *Corresponding author:<br> Olli Nykänen<br> Department of Applied Physics,<br> University of Eastern Finland<br> POB 1627<br> FI-70211, Kuopio, Finland<br> olli.nykanen@uef.fi<br> +358-50-5556357</p> <p><br> Keywords: cartilage, collagen matrix, quantitative susceptibility mapping, MRI, osteoarthritis</p> <p><br> Included folders and files are:<br> - article_figures: all figures published in the manuscript<br> - data: all MRI, histological, and PLM data used in this article<br> - matlab_functions: matlab functions used in data analysis with subfolders:<br> - aedes_plugins: plugins for aedes (http://aedes.uef.fi) for calculation of QS- and T2* maps<br> - fitting_functions: functions for fitting relaxation times or TKD-method for QSM, used by the functions in above folder<br> - miscellaneous_functions: small helper functions for a number of small tasks utilized by the other scripts and functions<br> - ReadMe.txt: this file</p> <p><br> Notes for setting up Aedes correctly for this dataset:<br> Run Aedes -> Tools -> Edit VNMR Defaults:<br> - Return: FT + K-space<br> - DC: off<br> - Zeropadding: off<br> - Sorting & fastread: on<br> - Precision: single<br> - Read_fcn: readvnmr<br> - Orient: no</p> <p>See more info in separate readme files included in each folder.</p> <p><br> (Olli Nykänen, Apr 17, 2018)</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: In vitro data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG2_Histone_vs_free_GFP <ul> <li>data for Sparks et al Figure 2</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG3_in_vitro_dose_response <ul> <li>data for Sparks et al Figure 3#</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_SuppFIG2_endoscope_spectral_cross_talk <ul> <li>data for Sparks et al Supplementary Figure 2</li> <li>Supplementary information</li> </ul> </li> </ul> <p><strong>Cell lines</strong></p> <p>IGROV-1 cell lines were cultured in CO<sub>2</sub> dependent media with 10% fetal bovine serum and 1% Pen Strep at 37 ˚C. Before experiments, cells were grown to 80% confluence. For measuring doxorubicin uptake by fluorescence an IGROV-1 cell line stably expressing GFP fused to Histone-1 (H1) was made using the PiggyBac transposon system. As a control to show that effect of doxorubicin on GFP depends on whether it is fused to H1 or not, a stable whole cell expression of GFP by lentiviral transfection and selection by Geneticin was made. For bioluminescence imaging of xenograft tumors, all IGROV-1 cell lines were made to stably express firefly luciferase.</p> <p>To investigate the effect of doxorubicin on other histones, IGROV-1 cells were transiently transfected with a Histone-2B-GFP plasmid (gift from Kurt Anderson) using the Lipofectamine® 2000 reagent.</p> <p>IGROV-1 cells were obtained from Crick institute cell services and confirmed as IGROV-1 by Short Tandem Repeats (STR) profiling and no mycoplasma was detected.</p> <p><strong>In vitro experiments</strong></p> <p>IGROV-1 cells were grown to 80% confluence in 75 ml flasks before being re-plated in 12 or 24 well plates or 35 ml glass bottomed dishes and allowed to attach to the surface for 24 hours before experiments.</p> <p>To study how the fluorescence of GFP labelled H1 labelled IGROV-1 cells changes with doxorubicin treatment, fluorescence intensity and lifetime distributions were measured from cells after 3 hours of incubation with doxorubicin of varying concentrations (0, 0.18, 0.9, 1.8, 9, 18 µM) by serial dilutions of a stock solution with PBS. After 3 of hours, cells were washed in PBS then fixed for 20 minutes in 4% PFA. Cells were then imaged in PBS. Doxorubicin hydrochloride (Sigma-Aldrich, D1515-10 mg) was dissolved in PBS to a concentration of 9 mM and stored at -20˚C.</p>
Sparks et al, Heterogeneity in tumor chromatin-doxorubicin binding revealed by in vivo fluorescence lifetime imaging confocal endomicroscopy: in vivo data
<p>Data is divided into three folders:</p> <ul> <li>Sparks_et_al_FIG_6_IP_intranodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'FRET between chromatin-bound GFP and doxorubicin'</em></li> </ul> </li> <li>Sparks_et_al_FIG4_5_6_IP_IV_chemo_comparison <ul> <li>data for Sparks et al Figures 4,5 & 6</li> <li>main text section:<em> 'FLIM endomicroscope can monitor doxorubicin cellular uptake'</em></li> </ul> </li> <li>Sparks_et_al_FIG6_IP__internodule_heterogeneity <ul> <li>data for Sparks et al Figure 6</li> <li>main text section: <em>'Intra-tumor heterogeneity'</em></li> </ul> </li> </ul> <p><strong>In vivo experiments</strong></p> <p>Murine xenografts were prepared by intraperitoneal (IP) injection of IGROV-1 cancer cells. IGROV-1 cells were grown to 80% confluence before being trypsinized and re‑suspended in PBS at a concentration of cells per ml. cells were injected into ICRF nude mice. After 14 days post-injection, the presence of intraperitoneal tumors was confirmed by bioluminescence imaging. Briefly, an IVIS bioluminescence imaging system was used to image isoflurane anesthetized mice. 100 µl of D-luciferin (luciferase substrate) at 30mg ml<sup>-1</sup> was injected IP 10 minutes before recording of bioluminescence images. The presence of peritoneal tumors was confirmed if bioluminescence signals from the peritoneum were above background noise 10-30 minutes after D‑luciferin injections. Following confirmation of tumors, in vivo fluorescence imaging experiments were carried out after 21 days. To study differences in drug uptake between intravenous or intraperitoneal delivery, prior to imaging mice were subject to IP or IV doxorubicin-based chemotherapy for 1.5, 3 or 24 hours. Imaging involved terminal procedures, mice were anesthetized then peritoneal tumors were exposed by minor surgery and inspected with the CEM.</p> <p>All animal model procedures were approved by The Francis Crick Institute Biological Ethics Committee and UK Home Office authority provided by Project License 70/8380.</p> <p> </p> <p> </p>
Leaf wound induced ultraweak photon emission is suppressed under anoxic stress: observations of Spathiphyllum under aerobic and anaerobic conditions using novel in vivo methodology
<p>Dataset for paper: ABSTRACT: </p> <p>Plants have evolved a variety of means to energetically sense and respond to abiotic and biotic environmental stress. Two typical photochemical signaling responses involve the emission of volatile organic compounds and light. The emission of certain leaf wound volatiles and light are mutually dependent upon oxygen which is subsequently required for the wound-induced lipoxygenase reactions that trigger the formation of fatty acids and hydroperoxides; ultimately leading to photon emission by chlorophyll molecules. A low noise photomultiplier with sensitivity in the visible spectrum (300 – 720 nm) is used to continuously measure long duration ultraweak photon emission of dark-adapting whole <em>Spathiphyllum</em>leaves (<em>in vivo</em>). Leaves were mechanically wounded after two hours of dark adaptation in aerobic and anaerobic conditions. It was found that (1) nitrogen incubation did not affect the pre-wound basal photocounts; (2) wound induced leaf biophoton emission was significantly suppressed when under anoxic stress; and (3) the aerobic wound induced emission spectra observed was > 650 nm, implicating chlorophyll as the likely emitter. Limitations of the PMT photocathode’s radiant sensitivity, however, prevented accurate analysis from 700 – 720 nm. Further examination of leaf wounding profile photon counts revealed that the pre-wounding basal state (aerobic and anoxic), the anoxic wounding state, and the post-wounding aerobic state statistics all approximate a Poisson distribution. It is additionally observed that aerobic wounding induces two distinct exponential decay events. These observations contribute to the body of plant wound-induced luminescence research and provide a novel methodology to measure this phenomenon <em>in vivo</em>.</p>
Data: In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells
<p>This data set is composed of magnetic resonance images (MRI) that are supporting the article entitled <em>In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells </em>by the same authors. Nanoparticle contrast agents are used to label stem cells and monitor their bio-distribution in pre-clinical models of disease. Due to the impact on the interpretation of imaging results, understanding the <em>in vivo</em> fate of the particles is important. The bio-distribution after intra-cardiac injection of labelled cells with superparamagnetic iron oxide nanoparticles was monitored longitudinally by MRI. </p>
Time-averaged simulation results and in vivo measurements to show the impact of red blood cells on the flow field in the cortical microvasculature
<p>The dataset contains 5 files. 4 of them are time-averaged results of blood flow simulations with discrete red blood cell (RBC) tracking in realistic microvascular networks. The 5th file contains median values of RBC velocity measurements at capillary bifurcations in the somatosensory cortex of the mouse.</p> <p>Further notes on the simulation results:<br> - The realistic microvascular networks are from the mouse parietal cortex and have first been published in Blinder et al., 2013, Nature Neuroscience (<a href="https://doi.org/10.1038/nn.3426">https://doi.org/10.1038/nn.3426</a>).<br> - The numerical model to simulate blood flow in realistic microvascular networks has been described in Schmid et al., 2017, PLOS Computational Biology (<a href="https://doi.org/10.1371/journal.pcbi.1005392">https://doi.org/10.1371/journal.pcbi.1005392</a>).<br> - MVN1 and MVN2 stands for microvascular network 1 and 2, respectively.<br> - wRBCs and wpPs stands for 'with red blood cells' and 'with passive particles'. These terms describe two different numerical models: The wRBC-model accounts for all RBC related flow phenomena. The wpP neglects the phase-separation and the Fahraeus-Lindqvist effect, i.e. RBCs and flow are decoupled. Further details are available from Schmid et al. (2019, <a href="https://doi.org/10.1371/journal.pcbi.1007231">https://doi.org/10.1371/journal.pcbi.1007231</a>)</p> <p><strong>File format: </strong>pickle (Python)</p> <p><strong>Files 1 - 4 </strong>(Time-averaged simulation results):<br> Filenames: MVN1_wpPs.tar.bz2, MVN2_wpPs.tar.bz2, MVN1_wRBCs.tar.bz2, MVN2_wRBCs.tar.bz2</p> <p>Each compressed folder contains two files:<br> <br> edgesDict.pkl: dictionary with edge/vessel related data: </p> <ul> <li>flow: Flow rate in vessel [um^3/ms]</li> <li>length: Vessel length [um] (Tortuosity is considered)</li> <li>htt: Tube hematocrit in vessel [-]</li> <li>diameter: Effective vessel diameter [um]</li> <li>connectivity: Vertex indices, e.g. start and end vertex of the corresponding vessel</li> </ul> <p>verticesDict.pkl: dictionary with vertex/bifurcation related data:</p> <ul> <li>index: Index of the current vertex </li> <li>coords: Coordinates to describe the position of the vertex [um]</li> <li>pressure: Pressure at the vertex [mmHg]</li> </ul> <p> </p> <p><strong>File 5</strong> (in vivo RBC velocity measurements):<br> Filename: measurementDict.pkl</p> <p>keys:</p> <ul> <li>divergent_d1: divergent bifurcation, RBC velocity measurement in daughter vessel 1</li> <li>divergent_d2: divergent bifurcation, RBC velocity measurement in daughter vessel 2</li> <li>convergent_m1: convergent bifurcation, RBC velocity measurement in mother vessel 1</li> <li>convergent_m2: convergent bifurcation, RBC velocity measurement in mother vessel 2</li> </ul> <p><br> Data structure: list of list,<br> e.g. daughter vessel 1:<br> [[bif.1 - measure.1, bif.1 - measure.2, bif.1 - measure.3], [bif.2 - measure.1, bif.2 - measure.2, bif.2 - measure.3],...]<br> bif.: bifurcation, measure.: measurement.<br> The order of bifurcations is the same for 'divergent_d1' and 'divergent_d2' (and for 'convergent_m1' and 'convergent_m2'). </p> <p> </p>
Allocation of rhodamine-loaded nanocapsules from blood circulatory system to adjacent tissues assessed in vivo by fluorescence spectroscopy
<p>Modern fluorescent modalities play an important role in the functional diagnostic of various physiological processes in living tissues. Utilizing the fluorescence spectroscopy approach we observe the circulation of fluorescent-labelled nanocapsules with rhodamine tetramethylrhodamine in a microcirculatory blood system. The measurements were conducted transcutaneously on the surface of healthy Wistar rat thighs in vivo. The administration of the preparation capsule suspension with a rhodamine concentration of 5 mg kg−1 of the animal weight resulted in a two-fold increase of fluorescence intensity relative to the baseline level. The dissemination of nanocapsules in the adjacent tissues via the circulatory system was observed and assessed quantitatively. The approach can be used for the transdermal assessment of rhodamine-loaded capsules in vivo.</p>
Source data belonging to "Visualisation of dCas9 target search in vivo using an open-microscopy framework"
<p>Source data corresponding to "Visualisation of dCas9 target search <em>in vivo</em> using an open-microscopy framework". Contains pTarget and pNonTarget raw datasets, as well as all localization data, cell UV intensity data, cell outline data, and analysed diffusion coefficient lists.</p>
Figure 1 in Embryonic development of the olive fruit fly, Bactrocera oleae Rossi (Diptera: Tephritidae), in vivo
Figure 1. In vivo photographic illustration of Bactrocera oleae eggs. A) Anterior and posterior ends of the egg (1 h old); B) the chorion; C), D), and E) sequence of pole cell formation in a living embryo. The arrow indicates the posterior tip of the egg.
Figure 3 in Earthworm, a novel in vivo system to validate antimitotic compounds
Figure 3. Microscopy analysis of blastema development. Worms treated with water showed development of blastema 3 days after amputation (A), whereas wound healing alone was observed in worms treated with colchicine (B) or aqueous extract of A. calamus (C). Healed wounds are indicated by arrows. Histological studies show the regenerating budding tissue in water-treated worms (D), healed wounds alone in colchicine-treated worms (E), or aqueous extract of A. calamus (F). All tissues (D, E, and F) were stained with hematoxylin and eosin and were photographed with 4× magnification using a light microscope. The arrows in panels D, E, and F indicate the borders of the lesion. rb - regenerating blastema, wh - wound healing, ECL - epithelial cell layer, CML - circular muscle layer, LCL - longitudinal cell layer. Scale bar equals 50 µm.
Figure 2 in Earthworm, a novel in vivo system to validate antimitotic compounds
Figure 2. Inhibition of blastema development in Eudrilus eugeniae by colchicine and aqueous extract of Acorus calamus. A) The adult earthworm, E. eugeniae, is marked to show anterior (ar), clitellum (cl), and posterior (pr) regions. The control worms were injected with distilled water every 24 h for a period of 7 days, and the development of the blastema was observed after day 3 (B), day 5 (C), or day 7 (D). Colchicine was injected similarly for 7 consecutive days and the development of blastema was not observed after day 3 (E), day 5 (F). or day 7 (G). Aqueous extract of A. calamus rhizomes was injected every 24 h for a period of 7 days and the development of blastema was not observed after day 3 (H), day 5 (I), or day 7 (J). rb - regenerating blastema, wh - wound healing.
Figure 1 in Earthworm, a novel in vivo system to validate antimitotic compounds
Figure 1. Inhibition of cell division in AllIum cepa root tips by colchicine and water extract of Acorus calamus. All root tips were incubated with respective samples for 16 h before the processing. A) Different stages of mitosis of roots treated with distilled water, observed with a 40× objective lens; B) the arrest of cell division predominantly in metaphase by colchicine (100 µg/mL); C) more prophases compared to the stages of metaphase and anaphase in samples treated with Acorus calamus (1 mg/mL); D) magnified images of all 4 phases of mitosis (prophase, metaphase, anaphase, and telophase) in water-treated samples; E) the magnified images of 6 metaphases and 1 anaphase in colchicine-treated samples; F) the magnified images of metaphase, anaphase, and prophase. The graph (G) shows the % of cells observed in different phases of mitotic cell division with mean ± SEM bar and P-value (***: P <0.05). Marked circles indicate the different phases of cell division.
Figure 6 in Effects of in vivo exposures to nanoparticles (Al O , CuO, TiO ) on the activities of ATPases in the gill and muscle of freshwater mussel (Unio tigridis)
Figure 6. Effects of NPs on Ca-ATPase activity in the muscle of mussels after 14 days. * indicates significant (p <0.05) differences compared to control.
Figure 4 in Effects of in vivo exposures to nanoparticles (Al O , CuO, TiO ) on the activities of ATPases in the gill and muscle of freshwater mussel (Unio tigridis)
Figure 4. Effects of NPs on Ca-ATPase activity in the gill of mussels after 14 days. * indicates significant (p <0.05) differences compared to control.
Figure 3 in Effects of in vivo exposures to nanoparticles (Al O , CuO, TiO ) on the activities of ATPases in the gill and muscle of freshwater mussel (Unio tigridis)
Figure 3. Effects of NPs on Mg-ATPase activity in the gill of mussels after 14 days. * indicates significant (p <0.05) differences compared to control.
Figure 5 in Effects of in vivo exposures to nanoparticles (Al O , CuO, TiO ) on the activities of ATPases in the gill and muscle of freshwater mussel (Unio tigridis)
Figure 5. Effects of NPs on Mg-ATPase activity in the muscle of mussels after 14 days. * indicates significant (p <0.05) differences compared to control.
Figure 1 in Effects of in vivo exposures to nanoparticles (Al O , CuO, TiO ) on the activities of ATPases in the gill and muscle of freshwater mussel (Unio tigridis)
Figure 1. TEM images of Al O (a), CuO (b), and TiO (c) nanoparticles in stock solutions (Canli and Canli, 2020).
Figure 2. – A in Transmission of Induced Chromosomal Aberrations through Successive Mitotic Divisions in Human Lymphocytes after In Vitro and In Vivo Radiation
Figure 2. – A: Transverse section of the brown meagre otolith. B: Focus on annual marks (red points).
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.