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1,320 results for “degeneration”
Genetic association analysis of anti-VEGF treatment response in neovascular age-related macular degeneration
<p>Summary statisics of an association study of 6,908,005 genetic variants with anti-VEGF nAMD treatment response in 179 treatment-naïve nAMD probands. This dataset supplements the publication "Genetic Association Analysis of Anti-VEGF Treatment Response in Neovascular Age-Related Macular Degeneration" (DOI: 10.3390/ijms23116094). Details regarding the methods and version numbers can be found in the corresponding manuscript.</p>
ValRun: GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration
<p><strong>VaLRun: </strong></p> <p><strong>Raw data of "GMP-grade Manufacturing and Quality Control of a Non-Virally engineered Advanced Therapy Medicinal Product for Personalized Treatment of Age-Related Macular Degeneration"</strong></p> <p>(Excel-, pdf-, GraphPad-files, mp4 videos and a READ-ME text file)</p> <p>The introduction of new therapeutics requires validation of Good Manufacturing Practice (GMP)-grade manufacturing including suitable quality controls. This is challenging for Advanced Therapy Medicinal Products (ATMP) with personalized batches. We have developed a person-alized, cell-based gene therapy to treat age-related macular degeneration and established a vali-dation strategy of the GMP-grade manufacture for the ATMP; manufacturing and quality control were challenging due to a low cell number, batch-to-batch variability and short production duration. Instead of patient iris pigment epithelial cells, human donor tissue was used to produce the transfected cell product (“tIPE”). We implemented an extended validation of 104 tIPE productions. Procedure, operators and devices have been validated and qualified by determining cell number, viability, extracellular DNA, sterility, duration, temperature and volume. Transfected autologous cells were transplanted to rabbits verifying feasibility of the treatment. A container has been engineered to insure a safe transport from the production to the surgery site. Criteria for successful validation and qualification were based on tIPE’s Critical Quality Attributes and Process Parameters, its manufacture and release criteria. The validated process and qualified operators are essential to bring the ATMP into clinic and offer a general strategy for the transfer to other manufacture centers and personalized ATMPs.</p>
Bispectrum degenerate B8 data
<p>Dataset of 4000 pairs of bispectrum degenerate boron (B8) structures, along with scripts to generate the atom-centered (nu=7) and three-centered features that are complete. Also contains scripts to reconstruct the nu=7 single-centered features from the three center features using an encoder-decoder architecture, and to model the structural energies using these features</p>
Data to "Choroidal changes in intermediate age-related macular degeneration patients with drusen or pseudodrusen."
<p>This record contains experimental and analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p> <p>Rosa R., Corazza P., Musolino M., Mochi C., Maiello G., Traverso C. E., & Nicolò M. Choroidal changes in intermediate age-related macular degeneration patients with drusen or pseudodrusen. European Journal of Ophthalmology. (in press)</p> <p> </p>
Synthetic populations and trajectories for sdB stars ejected from the single degenerate helium donor channel for thermonuclear supernovae
<p>This repository is a supplement to a journal paper (Neunteufel+ 2022) and contains the synthetic populations of sdB stars and sdB remnants ejected from the single degenerate helium donor channel for thermonuclear supernovae. See Neunteufel+ 2021 and Neunteufel+ 2022 for simulation parameters. </p> <p>Synthetic populations, including initial and final positions, are contained in the MXX-out.tr (XX=10..15) files where XX is the mass of the WD companion divided by 0.1 solar masses. Each population is a snapshot of stars ejected at the end of a 300 Myr period. (Note that stellar lifetimes are not taken into account here. See Neunteufel+ 2022 on how stellar lifetimes should be truncated in order to produce realistic populations.)</p> <p>Columns:</p> <p>Zeroth column (ID) is the ID of the trajectory. These are assigned consecutively.</p> <p>First column (unnamed) indicates initial (0) and final (1) positions.</p> <p>Third column (time) is the time since ejection in Myrs. Note that stars further down in the list were ejected earlier.</p> <p>Fourth to Ninth columns (vx, y, vy etc..) are velocity (km/s) and position (kpc) in Gal. Carthesian coordinates (velocity first, position second)</p> <p>Tenth to Twelfth column are accelerations in Gal. carthesian coordinates </p> <p>Thirteenth column (v_space) is the total galactocentric space velocity (km/s) </p> <p>Fourteenth column (Phi) is the local Gal. potential according to Model 1 presented by Irrgang+2013</p> <p>Fifteenth column (E_kin/E_pot) is the local kinetic energy of the object divided by its potential energy with respect to the Gal. potential.</p> <p>Sixteenth column (rho) is the local Gal. baryon density according to Model 1 presented by Irrgang+2013</p> <p>Seventeenth column (label_c) is the mass of the ejected sdB star or sdB remnant in solar masses.</p>
Immune and genetic signature of HER2-driven breast carcinomas triggering anti-Yo paraneoplastic cerebellar degeneration
<ul> <li>Supplementary eTables from: Immune and genetic signature of HER2-driven breast carcinomas triggering anti-Yo paraneoplastic cerebellar degeneration: <ul> <li><strong>eTables 1</strong>: Results of DESeq2 on the differential gene expression analysis between Yo-PCD and control tumours for all genes and for differentially expressed genes.</li> <li><strong>eTables 2</strong>: Results of the Gene Ontology enrichment performed by clusterProfiler on genes over-expressed in Yo-PCD tumours</li> <li><strong>eTables 3</strong>: Results of the Gene Ontology enrichment performed by clusterProfiler on genes under-expressed in Yo-PCD tumours</li> </ul> </li> <li>Gene counts</li> <li>Gene TPMs</li> </ul>
Orthonectids are highly degenerate annelid worms
<p>These datasets hold the individual alignments and phylogenetic trees (including full PhyloBayes output) presented in our study showing that Mesozoa are polyphyletic and Orthonectida are annelids. A detailed description can be found in the manuscript.</p> <p>Briefly, there is a mitochondrial dataset, the full alignment and PhyloBayes data for the nuclear genes, and lastly several jackknife datasets subsampled from the full alignment and run under different evolutionary models and with different subset of genes.</p>
Histological validation of per-bundle water diffusion metrics within a region of fiber crossing following axonal degeneration
<p>Interactive plots showing the correlation between histological parameters of optic nerves and chiasm, and metrics derived from diffusion MRI in a rat model of unilateral retinal ischemia.</p> <p> </p> <p>There are two .html files, each containing an interactive figure, one for data pertaining to the optic nerve, the other for the chiasm. The left panel shows the correlation matrix. Click on any cell to see the corresponding scatter plot on the right panel. </p>
A comparative study of the effectivity of MSC-based, NP-based and combined therapies in an experimental model of NaIO3-induced retinal degeneration
<div><strong>Background</strong></div> <div>Mesenchymal stem cells (MSCs) are currently tested as one of the promising options for the therapy of retinal diseases, due to their immunomodulatory and neuroprotective abilities. However, there are several limitations associated with this type of treatment. Therefore, combinations of MSCs with other therapeutic agents are being considered. One of such approaches is represented by the application of MSCs with nanoparticles (NPs), which are widely used in medicine for their antimicrobial and immunomodulatory properties. Nevertheless, there is a possibility of negative effects of NPs on MSCs.</div> <div><strong>Methods</strong></div> <div>In this study, we tested the <em>in vitro</em> and <em>in vivo</em> effect of silver (Ag) NPs on the properties of MSCs in an experimental mouse model of chronic retinal degeneration induced by sodium iodate.</div> <div><strong>Results</strong></div> <div>The results showed that simultaneous intravitreal administration of MSCs with AgNPs had no effect on the survival of MSCs in the eye, but a less effective regulation of Iba-1 (activated microglia/macrophages) and interleukin-1β expression in the retinal tissue compared to MSCs or AgNP only treated groups was observed. However, all treated groups had decreased expression of the gene for galectin-3 compared to the untreated control. In addition, MSCs applied alone or in combination with AgNPs and sorted from the degenerated retina on day 7 after application had increased expression of genes for specific retinal markers, and for transforming growth factor-β and insulin-like growth factor-1 compared to untreated naïve MSCs. On the contrary, the increased expression of the gene for glial cell-derived growth factor was observed only in the MSCs combined with AgNPs. However, the application of MSCs with AgNPs triggered increased expression for the IL-6 gene in the CD45 cells separated from the retina.</div> <div><strong>Conclusion</strong></div> <div>Overall, the results show that the application of MSCs or AgNPs has an immunomodulatory effect in chronic retinal degeneration, but the combined application of MSCs and AgNPs could decrease the effects of a single therapy.</div>
Data set for "On the interplay between lipids and asymmetric dynamics of an NBS degenerate ABC transporter"
<p>Supplementary data from molecular dynamics simulations performed on different states of bMRP1 (IF apo, IF ATP- and/or LTX-bound, as well as OF ATP-bound states) and embedded in different lipid bilayer membranes (namely POPC, POPE, POPC:POPE (3:1), POPC-Chol (3:1) and POPC:POPE:Chol (2:1:1).</p> <p>Are included:</p> <p>- Initial and postMD data</p> <p>- MD inputs used</p> <p>- Raw source data used for plot (ABC structural parameters, H-bond and non-covalent analyses, lipid order parameters, and efficiencies from Allopath tool)</p> <p>- PCA supplementary movies (PC1)</p>
Degenerate four wave mixing measurements
<p>Transmission from a photonic molecule, measured with photodetector attached to a DAQ and OSA, as a function of detuning, for various input powers.</p>
e-MERLIN images in Kool et al. 2023 A radio-detected thermonuclear supernova from a single-degenerate progenitor with a helium star donor
<p>Fits images obtained with e-MERLIN on Nov 19 2021 and April 6-11 2022 on SN2020eyj. Results are published in Kool et al. 2023 "A radio-detected thermonuclear supernova from a single-degenerate progenitor with a helium star donor".</p> <p>Project RR12002<br> Target name: 1111+2923<br> Original observation correlation centre: 11:11:47.180000 +29.23.06.36000<br> Run code: RR12002_C_001_20211119</p> <p>Project RR13005<br> Target name: 1111+2923<br> Original observation correlation centre: 11:11:43.271400 +29.23.37.83200<br> Run codes (combined):<br> RR13005_C_001_20220406<br> RR13005_C_002_20220407<br> RR13005_C_003_20220408<br> RR13005_C_004_20220409<br> RR13005_C_005_20220410<br> RR13005_C_006_20220411</p> <p> </p>
Data for: Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence
<p><span>In cereal crops such as barley (<em>Hordeum vulgare</em> L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait was studied by microscopic dissection of immature inflorescence meristems under standardized growth conditions. We combined spatiotemporal metabolomic, transcriptomic, and genetic approaches to elucidate the mechanism of barley inflorescence PTD in two- and six-rowed barley cultivars 'Bowman' and 'Morex,' respectively. Metabolome profiling includes hormones and primary metabolites such as sugars, TCA intermediates, and amino acids by dividing spike meristems into dying apical and viable central and basal parts at four developmental stages during the spike growth phase. </span>Similarly, RNA sequencing was performed for three developmental stages in both genotypes. RNA sequencing data analyses were performed to identify differentially expressed and tissue-specific transcripts. Further, PTD-associated hub genes were identified by weighted gene coexpression network analysis. Based on transcriptome analyses, we identified an important modulator of inflorescence PTD and functionally validated it using Cas9-mediated mutagenesis and gene-based associated study using a diverse panel of barley accessions. </p>
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA gene
<p>mTAGs is a tool for the taxonomic profiling of metagenomes. It detects sequencing reads belonging to the small subunit of the ribosomal RNA (SSU-rRNA) gene and annotates them through the alignment to full-length degenerate consensus SSU-rRNA reference sequences. The tool is capable of processing single-end and pair-end metagenomic reads, takes advantage of the information contained in any region of the SSU-rRNA gene and provides relative abundance profiles at multiple taxonomic ranks (Domain, Phylum, Class, Order, Family, Genus and OTUs defined at a 97% sequence identity cutoff).</p>
Phase I/IIA Study of SAR422459 in Participants With Stargardt's Macular Degeneration
ClinicalTrials.gov study NCT01367444. IPD Sharing: YES. Countries: 2. Publications: 2.
A Study to Assess the Effects of Brolucizumab in Adult Patients With Neovascular Age Related Macular Degeneration
ClinicalTrials.gov study NCT04239027. IPD Sharing: YES. Countries: 1. Publications: 1.
Study to Evaluate the Safety and Effectiveness of Intravitreal Injections (IVI) of Brolucizumab in Patients With Neovascular Age-related Macular Degeneration (nAMD)
ClinicalTrials.gov study NCT05269966. IPD Sharing: YES. Countries: 1. Publications: 16.
Efficacy and Safety of Two Different Brolucizumab 6 mg Dosing Regimens in Neovascular Age-related Macular Degeneration
ClinicalTrials.gov study NCT04679935. IPD Sharing: YES. Countries: 2. Publications: 1.
Study of Brolucizumab in Adult Patients With Suboptimal Anatomically Controlled Neovascular Age-related Macular Degeneration
ClinicalTrials.gov study NCT04264819. IPD Sharing: YES. Countries: 1. Publications: 1.
Intravitreal LFG316 in Patients With Age-related Macular Degeneration (AMD)
ClinicalTrials.gov study NCT01527500. IPD Sharing: YES. Countries: 1. Publications: 1.
ScienceDex guides
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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.