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1,037 results for “large-scale”
Large-scale purification of HTT domain constructs 2019/04/01
<p><strong>Project: </strong>High resolution structural analysis of purified HTT samples</p> <p><strong>Experiment: </strong>Large-scale purification of HTT domain constructs</p> <p><strong>Date completed:­ </strong>2019/04/01</p> <p><strong>Rationale: </strong>Domain fragments of the huntingtin protein are useful reagents for examining protein-protein interaction characteristics of huntingtin and to map interaction interfaces. Stable, monodisperse and pure samples may also be amenable to high resolution structure solution by X-ray crystallography. Previously huntingtin fragments were cloned and screened for expression in small-scale (3 mL) culture experiments. Positive hits were scaled for production as detailed in the table on the next page. All previous work is described in this post:<a href="https://zenodo.org/record/2600051#.XKU89aeZPOQ">https://zenodo.org/record/2600051#.XKU89aeZPOQ</a>.</p>
Large-scale stringent purification of HTT-HAP40 using heparin affinity chromatography 2019/05/12
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale stringent purification of HTT-HAP40 using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/05/12</p> <p><strong>Rationale: </strong>Previous attempts to generate a much purer and homogenous HTT-HAP40 sample showed that the complex can bind heparin resin. In small-scale experiment, I also incorporated helpful suggestions from scientists at the CHDI Palm Springs meeting full-length HTT research breakout group i.e. ATP wash to remove HSP proteins. The experiment included 3 affinity chromatography steps with FLAG, heparin and NiNTA resin and finally a gel filtration step and yielded a highly pure HTT-HAP40 sample: <a href="https://zenodo.org/record/2628064">https://zenodo.org/record/2628064</a>. </p>
Large-scale stringent purification of Q23 HTT and HTT-HAP40 using heparin affinity chromatography 2019/05/22
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale stringent purification of Q23 HTT and HTT-HAP40 using heparin affinity chromatography</p> <p><strong>Date completed:­ </strong>2019/05/22</p> <p><strong>Rationale: </strong>Previous attempts to generate a much purer and homogenous HTT-HAP40 sample showed that the complex can bind heparin resin. In small-scale experiment, I also incorporated helpful suggestions from scientists at the CHDI Palm Springs meeting full-length HTT research breakout group i.e. ATP wash to remove HSP proteins. The experiment included 3 affinity chromatography steps with FLAG, heparin and NiNTA resin and finally a gel filtration step and yielded a highly pure HTT-HAP40 sample: https://zenodo.org/record/3234174.I now want to try this purification with apo HTT. </p>
Large-scale purification of Q23 HTT from Sf9 2019/09/30
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale purification of Q23 HTT from Sf9 </p> <p><strong>Date completed:­ </strong>2019/09/30</p> <p><strong>Rationale: </strong>HTT samples are to be purified from different systems for subsequent biophysical and structural studies. </p>
Large-scale purification of Q23 HTT-HAP40 from Sf9 expression system with contaminating nucleic acid material 2019/09/16
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale purification of Q23 HTT-HAP40 from Sf9 expression system with contaminating nucleic acid material</p> <p><strong>Date completed:­ </strong>2019/09/16</p> <p><strong>Rationale:</strong> To purify HTT-HAP40 + Sf9 derived nucleic acid material for cryoEM analysis</p>
Large-scale purification of Q23 and Q54 HTT-HAP40 from Sf9 expression system in PBS 2019/09/16
<p><strong>Project: </strong>Biophysical investigation of purified HTT protein samples</p> <p><strong>Experiment: </strong>Large-scale purification of Q23 and Q54 HTT-HAP40 from Sf9 expression system in PBS.</p> <p><strong>Date completed:­ </strong>2019/09/16</p> <p><strong>Rationale: </strong>To purify HTT-HAP40 Q23 and Q54 in PBS to see if this reduces nucleic acid contamination.</p>
Data for manuscript "Evidence for large-scale climate forcing of dense shelf water variability in the Ross Sea"
<p>Relevant data shown in figures of the manuscript "Evidence for large-scale climate forcing of dense shelf water variability in the Ross Sea"</p>
Script and data from: The best of two worlds: toward large-scale monitoring of biodiversity combining metabarcoding and optimised parataxonomic validation.
<h2>Description</h2> <div> <p>Zenodo linked to : Penel, B., Meynard, C.N., Benoit, L., Bourdonné, A., Clamens, A., Soldati, L., Migeon, A., Chapuis, M.-P., Piry, S., Kergoat, G. and Haran, J. (2025), The best of two worlds: toward large-scale monitoring of biodiversity combining COI metabarcoding and optimized parataxonomic validation. Ecography, 2025: e07699. <a href="https://doi.org/10.1111/ecog.07699">https://doi.org/10.1111/ecog.07699</a></p> <div> <div> <div> <div> <p><strong>Publication abstract </strong></p> </div> </div> </div> <p>In a context of unprecedented insect decline, it is critical to have reliable monitoring tools to measure species diversity and their dynamic at large-scales. High-throughput DNA-based identification methods, and particularly metabarcoding, were proposed as an effective way to reach this aim. However, these identification methods are subject to multiple technical limitations, resulting in unavoidable false-positive and false-negative species detection. Moreover, metabarcoding does not allow a reliable estimation of species abundance in a given sample, which is key to document and detect population declines or range shifts at large scales. To overcome these obstacles, we propose here a Human-Assisted Molecular Identification (HAMI) approach, a framework based on a combination of metabarcoding and image-based parataxonomic validation of outputs and recording of abundance. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 492 mixed beetle samples from a biodiversity monitoring initiative conducted throughout France. On average, 23% of the species are missed when relying exclusively on metabarcoding, this percent being consistently higher in species-rich samples. Importantly, on average, 20% of the species identified by molecular-only approaches correspond to false positives linked to cross-sample contaminations or mis-identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces the intrinsic biases of metabarcoding and recovers reliable abundance data. This approach also enables users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing or incorrectly assigned barcodes. As such, HAMI fills an important gap in the toolbox available for fast and reliable biodiversity monitoring at large scales.</p> <div> <h4><strong>File description: </strong></h4> <h4>MiSeq raw sequences of the COI barcode from 492 Coleoptera field samples :</h4> <div>The Raw_sequencage_data ZIP directory contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each Coleoptera field samples in duplicate using the MiSeq platform GenSeq (ISEM - University of Montpellier)</div> <div> </div> <div>The HAMI_data_script_results_R zip directory contains Rmarkdown script files (.Rmd and .html) and associated data used to analyse the systemic errors of the metabarcoding approach (N= 492 Coleoptera field samples).</div> <div> </div> <div>The HAMI_pipeline zip directory contains all the codes associated with the HAMI pipeline, as well as a ReadMe file and a test data set.</div> <div> </div> <div>The Residual_chimera.zip directory contains lists of MOTUs associated to residual chimeric sequences that were not filtered using FROGS pipeline but secondarily detected with the <em>de novo</em> approach implemented in HAMI pipeline with ‘isBimeraDenovo’ R function from DADA2 v1.28.0. It contains two distinct files according to the two sequencing runs.</div> <div> </div> <div>The NUMTS_filtered.zip directory contains lists of MOTUs that were excluded of the final dataset according to the NUMTS filtering. File xxx_pseudogene_f1_deteled.csv corresponds to MOTUs that were excluded according to the first filtrering step based on DNA sequencing. File xxx_pseudogene_f2_deteled.csv corresponds to merged MOTUs that were excluded according to the second filter based on occurrence and percentage of identity. This folder contains files for the two sequencing runs.</div> </div> </div> </div>
Ab initio design of microbial communities from large-scale seed pools using deep learning and rapid ptimization
<h4>This repository contains the full results of our paper: <strong><em>Ab initio</em> design of microbial communities from large-scale seed pools using deep learning and rapid ptimization.</strong></h4> <p>Authors: Xiaoqing Jiang#, Jiaheng Hou#, Haoyu Zhang#, Jinyuan Guo, Shaohua Gu, Yulin Liao, Xinrun Yang, Peter X. Geng, Yiyan Zhou, Qian Guo, Chunhui Wang, Mo Li, Alexandre Jousset, Zhong Wei*, and Huaiqiu Zhu*</p> <p>The results including:</p> <p><strong>(1)</strong> <strong>GEM.tar.gz</strong>: The eBiota-GEM dataset, containing 21,514 Genome-Scale Metabolic Models (GEMs) constructed using CarveMe based on RefSeq complete genomes.</p> <p><strong>(2) Baterial_evaluation.tar.gz</strong>: The evaluation of the ability to uptake substrates and secret productions for all 21,514 GEMs.</p> <p><strong>(3) Community_results.tar.gz</strong>: The results calculated from eBiota-GEM includes various combinations for two-bacterial consortia, covering strain IDs, substrates, products, yields, dual-bacterial growth, single-bacterial growth, co-occurrence predictions, interactions and total production.</p> <p><strong>(4) DeepCooc_files.tar.gz</strong>: The parameter files of DeepCooc, required by eBiota platform.</p>
Systematic creation and phenotyping of Mendelian disease models in C. elegans: towards large-scale drug repurposing
<p>Data collected for the eLife OpenAccess paper: Systematic creation and phenotyping of Mendelian disease models in <em>C. elegans</em>: towards large-scale drug repurposing. (doi: 10.7554/eLife.92491.1)</p> <p>Contains: extracted features, calculated stats, normalised z-scores and timerseries data of all the disease model mutants generated. In addition, there is a static .html file that allows for mousing over the clustermaps to easily view differences in strains compared to the N2 wild-type. Dataset also contains, metadata and feature summary/file name information of FDA-library drug screen and the confirmation screen of the hit from this (i.e., all data collected in published in the associated paper). </p>
Replication package for: Acceptance of inequality between children: Large-scale experimental evidence from China and Norway
<p>CAppelen, Alexander W., Falch, Ranveig, Huang, Zhongjing, and Tungodden, Bertil, "Acceptance of inequality between children: Large-scale experimental evidence from China and Norway," October 2024</p>
Reduced atomic models for large-scale computations: Fe XIII near-infrared lines
<p>The tar file contains two directories. One contains the CHIANTI v.8-11 format main files<br>produced relative to a 33 merged states Fe XIII model.</p> <p>The other contains CHIANTI and P-CORONA format files for a 55-states Fe XIII model.</p> <p>In both cases the models were built to obtain accurate emissivities of the Fe XIII near-infrared lines withtin the ground configuration. </p> <p><br>The models are described in Del Zanna and Hebbur Dayananda, 2024, submitted to MNRAS.</p> <p>Information on the CHIANTI programs can be found in chianti-vip.com</p> <p>Information on P-CORONA can be found on https://research.iac.es/proyecto/polmag/pages/codes/p-corona.php</p>
Large-Scale Atmospheric Drivers of Snowfall over Thwaites Glacier, Antarctica
<p>Monthly RACMO2 snowfall rates (1979-2015, in mm w.e. per month), as described in Lenaerts et al., 2018 (https://www.cambridge.org/core/journals/annals-of-glaciology/article/climate-and-surface-mass-balance-of-coastal-west-antarctica-resolved-by-regional-climate-modelling/E3DD6D0DA914C6031F96A548AF53603A), and used in this paper. </p>
Rapid adaptive evolution to drought in a subset of plant traits in a large-scale climate change experiment
<p>Rapid evolution of traits and of plasticity may enable adaptation to climate change, yet solid experimental evidence under natural conditions is scarce. Here, we imposed rainfall manipulations (+30%, control, -30%) for ten years on entire natural plant communities in two Eastern Mediterranean sites. Additional sites along a natural rainfall gradient and selection analyses in a greenhouse assessed whether potential responses were adaptive. In both sites, our annual target species <i>Biscutella didyma</i> consistently evolved earlier phenology and higher reproductive allocation under drought. Multiple arguments suggest that this response was adaptive: it aligned with theory, corresponding trait shifts along the natural rainfall gradient, and selection analyses under differential watering in the greenhouse. However, another seven candidate traits did not evolve, and there was little support for evolution of plasticity. Our results provide compelling evidence for rapid adaptive evolution under climate change. Yet, several non-evolving traits may indicate potential constraints to full adaptation.</p>
Replication package for: The real effects of monetary expansions: evidence from a large-scale historical experiment
<p>The replication materials contain a README file, STATA datasets and do-files. This replication package for Palma (2021) constructs the entire analysis from the data sources described in the published paper, using STATA. The replicator should expect the code to run for less than 10 minutes.</p> <p>Palma, N. (2021). The real effects of monetary expansions: evidence from a large-scale historical experiment. Review of Economic Studies, forthcoming</p> <p> </p>
Supplemental data for "Large-scale quantum machine learning"
<p>This data supports "Large-scale quantum machine learning" by Tobias Haug, Chris N. Self, M. S. Kim (arxiv:2108.01039) https://arxiv.org/abs/2108.01039</p> <p>Related code can be found in the GitHub repository: (https://github.com/chris-n-self/large-scale-qml). The 'studies' folder here can be dropped inside the code repository in order to run the analysis scripts.</p> <p>Both 'processed' and 'unprocessed' data is provided. Unprocessed data is the qiskit measurement results for each case study, executed on the IBM Quantum device <em>ibmq_guadalupe</em> and <em>ibmq_toronto</em>. Processed is the Gram matrix evaluated from the measurements and the data vectors needed to fit support vector machine classifiers.</p>
Large-scale drivers of relationships between soil microbial properties and organic carbon across Europe
<p>The aim of this study was to quantify direct and indirect relationships between soil microbial community properties (potential basal respiration, microbial biomass) and abiotic factors (soil, climate) in three major land-cover types.</p> <p>Location: Europe</p> <p>Time period: 2018</p> <p>Major taxa studied: Microbial community (fungi and bacteria)</p> <p>We collected 881 soil samples from across Europe in the framework of the Land Use/Land Cover Area Frame Survey (LUCAS). We measured potential soil basal respiration at 20ºC and microbial biomass (substrate-induced respiration) using an O2-microcompensation apparatus. Climate and soil data were obtained from previous LUCAS surveys and online databases. Structural equation modeling (SEM) was used to quantify relationships between variables, and equations extracted from SEMs were used to create predictive maps. Fatty acid methyl esters were measured in a subset of samples to distinguish fungal from bacterial biomass. Soil microbial properties in croplands were more heavily affected by climate variables than those in forests. Potential soil basal respiration and microbial biomass were correlated in forests but decoupled in grasslands and croplands, where microbial biomass depended on soil carbon. Forests had a higher ratio of fungi to bacteria than grasslands or croplands. Soil microbial communities in grasslands and croplands are likely carbon-limited in comparison with those in forests, and forests have a higher dominance of fungi indicating differences in microbial community composition. Notably, the often already-degraded soils of croplands could be more vulnerable to climate change than more natural soils. The provided maps show potentially vulnerable areas that should be explicitly accounted for in coming management plans to protect soil carbon and slow the increasing vulnerability of European soils to climate change.</p>
A novel big data mining framework for reconstructing large-scale daily MAIAC AOD across China from 2000 to 2020
<p>This dataset contains the mean reconstructed MAIAC AOD and mean percentage of coverage of reconstructed MAIAC AOD across China from 2000 to 2020. </p>
Large-scale supplemental feeding alters lay date and nest survival in Eastern Bluebirds but not in two species of chickadees
<p>Wild bird feeding is a popular and growing activity, with approximately half of households participating in nations including the United States, Canada, the United Kingdom, New Zealand, and Australia. Supplemental feeding can increase survival and reproductive success of birds (which is often a goal of supplemental feeding efforts), but it raises concerns about phenological mismatch, reduced clutch size, or increased risk of nest predation. Our objectives were to test whether access to supplemental food during the breeding season was correlated with (1) advanced egg-laying phenology, (2) increased clutch size, or (3) improved nest survival of 3 cavity-nesting species (Carolina Chickadee, <i>Poecile carolinensis</i>; Black-capped Chickadee, <i>P. atricapillus</i>; and<i> </i>Eastern Bluebird, <i>Sialia</i> <i>sialis</i>) at a large spatial scale (United States and Canada; 22 degrees latitude difference and 55 degrees longitude difference). We examined data from 24,528 nest attempts submitted to NestWatch from 2014–2019. For Eastern Bluebirds, birds with access to supplemental insects initiated clutches 5.83 (± 0.89 SE) days earlier than birds without access to food subsidies, while predicted nest survival was 5% greater for birds with access to supplemental insects (probability of nest success = 0.79, 95% CI = 0.77–0.81) when compared to birds without (0.74, 95% CI = 0.72–0.75). Clutch size of Eastern Bluebirds did not differ between birds with and without access to supplemental insects. For chickadees, supplemental feeding (of seeds, suet, insects, or fruit) was not correlated with phenology, clutch size, or nest survival. <span>Our results suggest that supplemental feeding of insects can be an effective tool for increasing nest survival in Eastern Bluebirds and potentially other food-limited insectivores. However, the efficacy of supplemental feeding for improving reproductive success varies across <a>taxa</a></span><span>. </span>Our results can help elucidate how wild bird feeding contributes to global phenomena such as earlier nesting, nest survival, and population <a>change</a>.</p>
High-Throughput-Methyl-Reading (HTMR) assay: A solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases
<p>Epigenetic therapy has significant potential for cancer treatment. However, few small potent molecules have been identified against DNA or RNA modification regulatory proteins. Current approaches for activity detection of DNA/RNA methyltransferases and demethylases are time-consuming and labor-intensive, making it difficult to subject them to high-throughput screening. Here, we developed a fluorescence polarization-based "High-Throughput Methyl Reading" (HTMR) assay to implement large-scale compound screening for DNA/RNA methyltransferases and demethylases-DNMTs, TETs, ALKBH5, and METTL3/METTL14. This assay is simple to perform in a mix-and-read manner by adding the methyl-binding proteins MBD1 or YTHDF1. The proteins can be used to distinguish FAM-labelled substrates or product oligonucleotides with different methylation statuses catalyzed by enzymes. Therefore, the extent of the enzymatic reactions can be coupled with the variation of FP binding signals. Furthermore, this assay can be effectively used to conduct a cofactor competition study. Based on the assay, we identified two natural products as candidate compounds for DNMT1 and ALKBH5. In summary, this study outlines a powerful homogeneous approach for high-throughput screening and evaluating enzymatic activity for DNA/RNA methyltransferases and demethylases that is cheap, easy, quick, and highly sensitive.</p>
ScienceDex guides
Understand access before you commit
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.