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4,004 results for “In vivo”
Data for: Evaluation of a full-scale wastewater treatment plant with ozonation and different post-treatments using a broad range of in vitro and in vivo bioassays
<p>This repository contains research data linked to the following publication: Kienle, C., Werner, I., Fischer, S., Lüthi, C., Schifferli, A., Besselink, H., Langer, M., McArdell, C.S. and Vermeirssen, E.L.M. 2022. Evaluation of a full-scale wastewater treatment plant with ozonation and different post-treatments using a broad range of <em>in vitro</em> and <em>in vivo</em> bioassays. Water Research, 118084. https://doi.org/10.1016/j.watres.2022.118084</p> <p>Abstract: Micropollutants present in the effluent of wastewater treatment plants (WWTPs) after biological treatment are largely eliminated by effective advanced technologies such as ozonation. Discharge of contaminants into freshwater ecosystems can thus be minimized, while simultaneously protecting drinking water resources. However, ozonation can lead to reactive and potentially toxic transformation products. To remove these, the Swiss Federal Office for the Environment recommends additional "post-treatment" of ozonated WWTP effluent using sand filtration, but other treatments may be similarly effective. In this study, 48 h composite wastewater samples were collected before and after full-scale ozonation, and after post-treatments (full-scale sand filtration, pilot-scale fresh and pre-loaded granular activated carbon, and fixed and moving beds). Ecotoxicological tests were performed to quantify the changes in water quality following different treatment steps. These included standard <em>in vitro</em> bioassays for the detection of endocrine, genotoxic and mutagenic effects, as well as toxicity to green algae and bacteria, and flow-through <em>in vivo</em> bioassays using oligochaetes and early life stages of rainbow trout.</p> <p>Results show that ozonation reduced a number of ecotoxicological effects of biologically treated wastewater by 66 - 93 %: It improved growth and photosynthesis of green algae, decreased toxicity to luminescent bacteria, reduced concentrations of hormonally active contaminants and significantly changed expression of biomarker genes in rainbow trout liver. Bioassay results showed that ozonation did not produce problematic levels of reaction products overall. Small increases in toxicity observed in a few samples were reduced or eliminated by post-treatments. However, only relatively fresh granular activated carbon (analyzed at 13,000 - 20,000 bed volumes) significantly reduced effects additionally (by up to 66 %) compared to ozonation alone. Inhibition of algal photosynthesis, rainbow trout liver histopathology and biomarker gene expression proved to be sufficiently sensitive endpoints to detect the change in water quality achieved by post-treatment.</p>
In vivo screening for functional HIF2A enhancers in renal carcinoma.
<p>High throughput sequencing data and analysis from a CRISPRi-based in vivo functional screen for oncogenic HIF2A-bound transcriptional enhancers in renal cancer. </p>
Preliminary In Vivo Pulse-Acquire MRI with Concentric Ring Trajectories at 7 Tesla
<p>Pulse-Acquire MRI with Concentric Ring Trajectories, 305 Hz Readout Bandwidth, 350x350x99 Matrix,<br> voxel size 0.63x0.63x1.34 mm3, TR 60 ms, 5° FA, Acquisition Delay 5 ms, TA 13 min</p>
MRI data for "Stress-inducible phosphoprotein 1 (HOP/STI1/STIP1) regulates the spreading, aggregation, and toxicity of α-synuclein in vivo"
<p>Repository for magnetic resonance imaging data from the project titled "Stress-inducible phosphoprotein 1 (HOP/STI1/STIP1) regulates the spreading, aggregation, and toxicity of α-synuclein in vivo"</p> <p>Contains the pre-processed ex vivo T1-weighted images (Bruker 7T; 70 micron isotropic voxel resolution) for WT mice, M83 homozygous, and M83 homozygous mice with one copy of the TPR transgene. Full subject list can be viewed with the prado_MRI_M83dTPR_subjectlist_final.csv file.</p> <p>Whole brain region segmentations are available for these mice. These labels were generated using the MAGeT-Brain segementation pipleine (https://github.com/CobraLab/MAGeTbrain) and using a modified/merged version of the Allen brain atlas. The full list of regions included can be found in the file named Allen_brain_mapping_final.csv.</p> <p>See readme.txt file for more information</p>
Data: Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography.
<p>This data set includes all the raw data collected for the following article: "Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography."</p>
Micro-CT Imaging Dataset on ex-vivo Ovine Functional Spinal Segments as Healthy, Injured and Treated with Cement Discoplasty
<p>General information:</p> <p>- This dataset contains micro-CT images and mechanical test data from ovine functional spinal units (FSU). <br> - The micro-CT data was produced using a Bruker SkyScan 1172. The settings for the scans are given in the '.log' files in each folder. <br> - The compression testing was conducted on an MTS 858 Mini Bionix T/II. The settings for each test can be found in test '.txt' files.<br> - In short, every FSU was mechanically tested in compression under different conditions. Before and after every test, the FSUs were scanned to ensure there was no damage<br> to the sample. More information can be found in the related publication: <br> - The mechanical testing data is arranged in folders with consecutive cycles. It is highly recommended to use the last three cycles for analysis. </p> <p>Data set notation:</p> <p>- All the datasets are noted by Sheep number. Sh7 = Sheep 7; Sh8 = Sheep 8; Sh9 = Sheep 9. In the publication, the numbers were switched to 1,2,3 respectively.<br> - files denoted with '_rec' contain the reconstruction of the projection images. <br> - 'Tested' or 'After test' files refers to the scan after mechanical testing. </p>
In vivo metallophilic self-assembly of a light-activated anticancer drug
<p>This data set contains all data of our submitted manuscript with the same title.</p> <p> </p>
CT Dataset associated with the paper: (PLOSONE) Modular robotic platform for precision neurosurgery with a bio-inspired needle: system overview and first in-vivo deployment
<p>Imaging dataset associated with the work entitled "Modular robotic platform for precision neurosurgery with a bio-inspired needle: system overview and first in-vivo deployment.", published in the journal PLOS ONE</p>
Pre-processed ex vivo MRI data for manuscript titled "Neuroanatomical and cognitive biomarkers of alpha-synuclein propagation in a mouse model of synucleinopathy prior to onset of motor symptoms""
<p>Repository for <em>ex vivo</em> magnetic resonance imaging data from the project titled "Presymptomatic neuroanatomical and cognitive biomarkers of alpha-synuclein propagation in a mouse model of synucleinopathy"</p> <p>Contains the pre-processed <em>ex vivo</em> T1-weighted images (Bruker 7T; 70 micron isotropic voxel resolution) for M83 alpha-synuclein A53T hemizygous mice that received either a phosphate buffered saline (PBS) or alpha-synuclein pre-formed fibrils (PFF) injection in the right dorsal striatum. Full subject list can be viewed with the "subject_list.csv" file. More details are available in the manuscript. </p>
In vivo polymer mechanochemistry with polynucleotides
<p>Original data underpinning Figures, Schemes, Videos, and Tables of the manuscript and supplementary information.</p>
Data from: Residues neighboring an SH3-binding motif participate in determining affinity and specificity in vivo
<p>In signaling networks, many protein-protein interactions are mediated by modular domains that bind short linear motifs. The motifs' sequences modulate many factors, among them affinity and specificity, or the ability to bind strongly and to bind the appropriate partners. Previous studies have proposed a trade-off between affinity and specificity, suggesting that motifs with high affinity are less capable of differentiating between domains with similar sequences and structures. Using Deep Mutational Scanning to create a mutant library of a well characterized binding motif, and protein complementation assays to measure protein-protein interactions, we tested this trade-off in vivo for the first time. We measured the binding strength and specificity of a library of mutants of a binding motif on the MAP kinase kinase Pbs2, which binds the SH3 domain of the osmosensor protein Sho1 in Saccharomyces cerevisiae. We find that many mutations in the region surrounding the binding motif modify binding strength, but that few mutations have a strong impact on specificity. Moreover, we find no systematic relationship between affinity and specificity as measured in vivo. Interestingly, all Pbs2 mutations which increase affinity or specificity are situated outside of the Pbs2 residues that interact with the canonical SH3-binding pocket, suggesting that other surfaces on Sho1 contribute to binding. We use predicted structures to propose a model of binding which involves residues neighboring the core Pbs2 motif binding outside of the canonical SH3-binding pocket, allowing affinity and specificity to be determined by a broader range of sequences than what has previously been considered.</p>
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data
<p><span>This repository provides datasets for the study: https://broad.io/DILIPredictor</span></p> <p><span>Full Paper: https://www.biorxiv.org/content/10.1101/2024.01.10.575128v1</span></p> <p><span>This work is on enhancing the early detection of Drug-Induced Liver Injury (DILI) through the integration of predicted in vivo and in vitro data. This project utilizes advanced machine learning models and chemical informatics to predict the likelihood of DILI for various compounds. </span></p> <p><span>For code see: <a href="https://github.com/srijitseal/DILI">https://github.com/srijitseal/DILI</a><br><br>Drug-induced liver injury (DILI) has been significant challenge in drug discovery, often leading to clinical trial failures and necessitating drug withdrawals. The existing suite of in vitro proxy-DILI assays is generally effective at identifying compounds with hepatotoxicity. However, there is considerable interest in enhancing in silico prediction of DILI because it allows for the evaluation of large sets of compounds more quickly and cost-effectively, particularly in the early stages of projects. In this study, we aim to study ML models for DILI prediction that first predicts nine proxy-DILI labels and then uses them as features in addition to chemical structural features to predict DILI. The features include <em>in vitro</em> (e.g., mitochondrial toxicity, bile salt export pump inhibition) data, <em>in vivo</em> (e.g., preclinical rat hepatotoxicity studies) data, pharmacokinetic parameters of maximum concentration, structural fingerprints, and physicochemical parameters. We trained DILI-prediction models on 888 compounds from the DILIst dataset and tested on a held-out external test set of 223 compounds from DILIst dataset. The best model, DILIPredictor, attained an AUC-ROC of 0.79. This model enabled the detection of top 25 toxic compounds compared to models using only structural features (2.68 LR+ score). Using feature interpretation from DILIPredictor, we were able to identify the chemical substructures causing DILI as well as differentiate cases DILI is caused by compounds in animals but not in humans. For example, DILIPredictor correctly recognized 2-butoxyethanol as non-toxic in humans despite its hepatotoxicity in mice models. Overall, the DILIPredictor model improves the detection of compounds causing DILI with an improved differentiation between animal and human sensitivity as well as the potential for mechanism evaluation. DILIPredictor is publicly available at </span><a href="https://broad.io/DILIPredictor">https://broad.io/DILIPredictor</a> <span>for use <em>via</em> web interface and with all code available for download and local implementation via </span><a href="https://pypi.org/project/dilipred/"><span>https://pypi.org/project/dilipred/</span></a><span>.</span></p>
Figure 3 in Analysis of the toxicological and pharmacokinetic profile of Kaempferol-3-O-β-D-(6"-E-p-coumaryl) glucopyranoside - Tiliroside: in silico, in vitro and ex vivo assay
Figure 3. Photomicrography of exfoliated oral mucosa cells with: (A) karyorrhexis; (B) karyolysis; (C) micronucleus; (D) binucleation; and (E) macronucleus. Magnification X1000.
Figure 2 in Analysis of the toxicological and pharmacokinetic profile of Kaempferol-3-O-β-D-(6"-E-p-coumaryl) glucopyranoside - Tiliroside: in silico, in vitro and ex vivo assay
Figure 2. Cytotoxic effect of tiliroside (H. velutina) against RBC; (C-) Negative control (erythrocytes 0.5%), (C+) Positive control (1% Triton X-100). P <0.05 (*), P <0.01(**) and P <0.001 (***) versus positive control.
In vivo and in vitro electrochemical impedance spectroscopy analysis of acute and chronic intracranial electrodes
<p>Invasive intracranial electrodes are used in both clinical and research applications for recording and stimulation of brain tissue, providing essential data in acute and chronic contexts. The impedance characteristics of the electrode–tissue interface (ETI) evolve over time and can change dramatically relative to pre-implantation baseline. Understanding how ETI properties contribute to the recording and stimulation characteristics of an electrode can provide valuable insights for users who often do not have access to complex impedance characterizations of their devices. In contrast to the typical method of characterizing electrical impedance at a single frequency, we demonstrate a method for using electrochemical impedance spectroscopy (EIS) to investigate complex characteristics of the ETI of several commonly used acute and chronic electrodes. We also describe precise modeling strategies for verifying the accuracy of our instrumentation and understanding device–solution interactions, both in vivo and in vitro. Included with this publication is a dataset containing both in vitro and in vivo device characterizations, as well as some examples of modeling and error structure analysis results. These data can be used for more detailed interpretation of neural recordings performed on common electrode types, providing a more complete picture of their properties than is often available to users.</p>
A photo-switchable gold nanoformulation based on the dCas9 protein for spatiotemporal controlled gene editing activation in vivo
Open the record for dataset details and reuse information.
Source Data for Supplementary Information of "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo"
<p>The attached excel file contains the source data for LC-MS traces shown in the Supplementary Information of the paper "Expanding the substrate scope of PylRS enzymes to include non-⍺-amino acids in vitro and in vivo." Each graph is contained in a tab and labeled with the Supplementary Figure number and panel with which it is associated.</p>
Data from: In vitro to in vivo extrapolation from three-dimensional hiPSC-derived cardiac microtissues and physiologically based pharmacokinetic modeling to inform next-generation arrythmia risk assessment
<p>Proarrhythmic cardiotoxicity remains a substantial barrier to drug development as well as a major global health challenge. <em>In vitro</em> human pluripotent stem cell-based new approach methodologies have been increasingly proposed and employed as alternatives to existing <em>in vitro</em> and <em>in vivo</em> models that do not accurately recapitulate human cardiac electrophysiology or cardiotoxicity risk. In this study, we expanded the capacity of our previously established three-dimensional human cardiac microtissue model to perform quantitative risk assessment by combining it with a physiologically based pharmacokinetic model, allowing a direct comparison of potentially harmful concentrations predicted <em>in vitro</em> to <em>in vivo</em> therapeutic levels. This approach enabled the measurement of concentration responses and margins of exposure for two physiologically relevant metrics of proarrhythmic risk (<em>i.e.</em>, action potential duration and triangulation assessed by optical mapping) across concentrations spanning three orders of magnitude. The combination of both metrics enabled accurate proarrhythmic risk assessment of four compounds with a range of known proarrhythmic risk profiles (<em>i.e., </em>quinidine, cisapride, ranolazine, and verapamil) and demonstrated close agreement with their known clinical effects. Action potential triangulation was found to be a more sensitive metric for predicting proarrhythmic risk associated with the primary mechanism of concern for pharmaceutical-induced fatal ventricular arrhythmias, delayed cardiac repolarization due to inhibition of the rapid delayed rectifier potassium channel, or hERG channel. This study advances human induced pluripotent stem cell-based three-dimensional cardiac tissue models as new approach methodologies that enable <em>in vitro</em> proarrhythmic risk assessment with high precision of quantitative metrics for understanding clinically relevant cardiotoxicity.</p>
Fig. 14 in In vivo and post-mortem bioerosion traces in solitary corals from the upper Pliocene deposits of Tunisia
Fig. 14. Talpina cf. hackberryensis (Thomas, 1911), a domichnion produced by phoronids in the skeleton of caryophylliid coral Ceratotrochus (Edwardsotrochus) duodecimcostatus (Goldfuss, 1826), from the El Melah stream section, the upper part of the Argiles de Sidi Barka Formation (upper Pliocene) of Tunisia. A. INGUJ265P168. B. INGUJ265P164.
Fig. 13 in In vivo and post-mortem bioerosion traces in solitary corals from the upper Pliocene deposits of Tunisia
Fig. 13. Sulcichnus sigillum Martinell and Domènech, 2009, a fixichnion produced by commensal polychaetes in the skeleton of caryophylliid coral Ceratotrochus (Edwardsotrochus) duodecimcostatus (Goldfuss, 1826), from the El Melah stream section, the upper part of the Argiles de Sidi Barka Formation (upper Pliocene) of Tunisia. A. INGUJ265P173. B. INGUJ265P170 in different side views (B1, B2). C. INGUJ265P175 in different side views (C1, C2). Abbreviation: Me, Maeandropolydora elegans.
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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.