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7,195 results for “SET”
Training sets of complexes of fluorescent proteins chromophores in pi-stacking with substituted benzenes and imidazoles
<p>each zip archive containes a subset with the corresponding chromophore</p>
Role of the Cost Function for Material Parameter Estimation - Data Set
<p>##################################################################################################</p> <p><strong>Attention: We found an error in our optimisation template, related to the results that are provided in figure 2. We are working on fixing the issue and upload a corrected version in the upcoming days.</strong></p> <p> </p> <p> </p> <p> </p> <p>Dataset for the contribution "Role of the Cost Function for Material Parameter Determination" to the "<a href="https://www.femtc.com/events/2020/">Fire and Evacuation Modeling Technical Conference</a>" (FEMTC) 2020.</p> <p> </p> <p>It contains:</p> <ul> <li>the complete data of each IMP run,</li> <li>simulations of the best parameter sets of each IMP run,</li> <li>the IMP run for the reaction kinetics parameters,</li> <li>the validation simulations,</li> <li>the plots shown in the article and presentation, as well as</li> <li>the Jupyter Notebooks used for the data analysis.</li> </ul> <p>Note: The copper foil thickness is set to0.2 mm in all simulations, due to a typo in the FDS input file template and should have been 0.025 mm according to the <a href="https://www.sciencedirect.com/science/article/abs/pii/S0379711217300541">article describing CAPA II</a>. A simulation with the correct thickness showed very little divergence from the conducted simulations, thus the effect of the typo is regarded to be neglectable. Therefore, all files in this data repository are using the incorrect initial value. The mentioned simulations and a plot comparing both results are provided in this repository.</p> <p> </p> <p>Version 1.1:</p> <p>Added slides and article.</p>
Supplementary data (simulated metagenome set 1) to accompany "phyloFlash – Rapid SSU rRNA profiling and targeted assembly from metagenomes"
<p>Comparison of SSU rRNA read extraction and targeted assembly from simulated shotgun metagenome of divergent bacterial species.</p> <p>The phyloFlash software is available from https://github.com/HRGV/phyloFlash. Examples were generated with phyloFlash v3.3b.</p>
TSR-CRC-Training-Test-Evaluation-Sets
<p>The data used for training and testing of the deep learning model for TSR, including the training set part 1, the training set part 3, the test set 2, and the TSR evaluation set.</p> <p>For more information, please refer to the following article. <strong>Please cite this article when using the data set.</strong></p> <p>Zhao K, Li Z, Yao S, Wang Y, Wu X, Xu Z, et al. Artificial intelligence quantified tumour-stroma ratio is an independent predictor for overall survival in resectable colorectal cancer. EBioMedicine 2020;61:103054. https://doi.org/10.1016/j.ebiom.2020.103054.</p>
Test set of 140 complexes for AutoDock-GPU
<p>Set of 140 protein-ligand complexes<br> ===================================<br> <br> # Overview<br> <br> The ligands herein vary in the number of atoms and number of rotatable bonds.<br> This is the full data set used in the following study:<br> Accelerating AutoDock4 with GPUs and Gradient-Based Local Search<br> https://dx.doi.org/10.26434/chemrxiv.9702389.v1<br> <br> # Warning<br> <br> These structures, both proteins and ligands, were prepared in an automated way<br> without manual inspection. The following is a non-comprehensive list of<br> issues that may exist:<br> <br> * missing water molecules that bridge ligand-receptor interactions,<br> * missing atoms in the proteins,<br> * non-integer sum of partial charges,<br> * incorrect protonation state,<br> * incorrect protein conformations.<br> <br> This intended use of this data is to evaluate the performance of docking with<br> regard to computational and algorithmic efficiency, but not the accuracy of<br> the scoring function.<br> <br> # Details<br> <br> In ligand\_properties.csv<br> * `pdb` Protein Data Bank accession code<br> * `n_atom` number of atoms in the ligand<br> * `n_tors` number of bonds in the ligand that can rotate during docking.<br> * `score_of_probable_global_minimum` lowest (best) score (score is the sum of intra- and inter-mo<br> leculer energy components). The best score did not improve with an increase in the search effort<br> * `RMSD_of_probable_global_minimum` RMSD from X-ray pose for the solution with the lowst score <br> * `best_score_so_far` lowest score ever found but even lower scores are likely to exist<br> <br> </p>
Benchmark Data Set of "epiTracker - A framework for highly-reliable particle tracking for the quantitative analysis of fish movements in tanks"
<p>Data set containing five videos differing in fish species (zebrafish and medaka), number of individuals (3 to 10), lighting and type of tank for comparison of tracking algorithms. For each video a Matlab file (*.mat) exists, which contains the position data of the fish.</p> <p>Each of the five videos consists of ~10000 frames, which at a frame rate of 30FPS corresponds to a length of about 5.5min.</p>
Data Set of Focus Groups with Industry Representatives on Smart Dust and Micro Robots
<p>Data Set of Focus Groups with Industry Representatives on Smart Dust and Micro Robots</p> <p>This data set comprises the following documents:</p> <ul> <li>Coding scheme</li> <li>Focus group guidelines</li> <li>Focus group 01-03</li> </ul>
Data Set to: Effects of TNFα receptor TNF-Rp55- or TNF-Rp75- deficiency on corneal neovascularization and lymphangiogenesis in the mouse
<p>Data Set to: <strong>Effects of TNFα receptor TNF-Rp55- or TNF-Rp75- deficiency on corneal neovascularization and lymphangiogenesis in the mouse</strong></p> <p>Raw data and image files</p>
Data from: Proportion methylation at a set of CpGs from 4 amplicons
<p><span>The age structure of populations, or the ageing rate of individuals, impacts aspects of animal ecology, epidemiology and conservation. Yet for many wild organisms, age is an inaccessible trait. In many cases measuring age or ageing rates in the wild requires molecular biomarkers of age. Epigenetic clocks based on DNA methylation have been shown to accurately estimate the age of humans and laboratory mice, but they also show variable ticking rates that are associated with mortality risk above and beyond that predicted by chronological age. Thus, epigenetic clocks are proving to be useful markers of both chronological and biological age, and they are beginning to be applied to wild mammals and birds. We have acquired strong evidence that an accurate clock will be possible for the wood mouse <i>Apodemus sylvaticus </i>by adapting epigenetic information from the laboratory mouse. <i>Apodemus sylvaticus is</i> a well-studied field system that is amenable to experimental perturbations and longitudinal sampling of individuals across their lives, and these features of the wood mouse offer opportunities to disentangle causal relationships between ageing rates and environmental stress. Our wood mouse epigenetic clock is PCR-based, and so requires tiny amounts of tissue and non-destructive sampling. We quantified methylation using Oxford Nanopore sequencing technology and present a new bioinformatics pipeline for data analysis. We thus describe a new and generalizable system that should enable ecologists and other field biologists to go from tiny tissue samples to an epigenetic clock for their study animal. </span></p>
Anti Cancer Peptide and non-Anti Cancer Peptide data set.
<p>Anticancer and non-anticancer peptide data set. </p>
University of Denver Collections as Data - HTR Train and Validation Set JCRS_2020_5_27
<p><a href="https://zenodo.org/api/files/333ecb88-1f48-4ffd-b39e-5e70b800c276/HTR_Train_Set_JCRS_2020_5_27.zip">HTR_Train_Set_JCRS_2020_5_27.zip</a> <br> Description</p>
Figure 2 from: Koleva K, Todorova L, Marchev S, Vlaskovska M, Nikolov R (2020) Pharmacovigilance: procedures for uniform assessment of periodic safety update reports and their implementation in national settings. Focus on analgesics. Pharmacia 67(4): 283-288. https://doi.org/10.3897/pharmacia.67.e57134
Figure 2 A percentage of all active substances/products affected by the PSUR evaluation procedures. Legend: 1: The change is not implemented; 2: The change is implemented with an appropriate procedure; 3: The change is implemented outside the specified deadlines.
Figure 1 from: Koleva K, Todorova L, Marchev S, Vlaskovska M, Nikolov R (2020) Pharmacovigilance: procedures for uniform assessment of periodic safety update reports and their implementation in national settings. Focus on analgesics. Pharmacia 67(4): 283-288. https://doi.org/10.3897/pharmacia.67.e57134
Figure 1 Distribution of discrepancies by type of active substance for all active substances/products affected by the PSUR evaluation procedures. Legend: I: Total number of products by active substances; II: The change has not been implemented; III: The change is implemented by an appropriate procedure; IV: The change is implemented outside the specified deadlines.
Data set for "Logic-in-Memory Based on an Atomically Thin Semiconductor"
<p>Curves related to device characteristics from the paper "Logic-in-Memory Based on an Atomically Thin Semiconductor", Nature 2020, doi:10.1038/s41586-020-2861-0</p>
Intermedia agenda-setting networks
<p>We investigate the impact of noise and topology on opinion diversity in social networks. We do so by extending well-established models of opinion dynamics to a stochastic setting where agents are subject both to assimilative forces by their local social interactions, as well as to idiosyncratic factors preventing their population from reaching consensus. We model the latter to account for both scenarios where noise is entirely exogenous to peer influence and cases where it is instead endogenous, arising from the agents' desire to maintain some uniqueness in their opinions. We derive a general analytical expression for opinion diversity, which holds for any network and depends on the network's topology through its spectral properties alone. Using this expression, we find that opinion diversity decreases as communities and clusters are broken down. We test our predictions against data describing empirical influence networks between major news outlets and find that incorporating our measure in linear models for the sentiment expressed by such sources on a variety of topics yields a notable improvement in terms of explanatory power.</p>
Dataset from Article "INGe: Intensity-ground motion data set for Italy"
<p><strong>There is a newer version of this record available at <a href="https://zenodo.org/record/4623732#.YMN8ofkzY2w">https://zenodo.org/record/4623732#.YMN8ofkzY2w</a>.</strong></p> <p>An updated and homogeneous earthquake data set for Italy compiled by joining the Italian Macroseismic Database DBMI15 and the Engineering Strong-Motion (ESM) accelerometric data bank. The database has been compiled through an extensive procedure of selection and revision based on two main steps: 1) the removal of several earthquakes in DBMI15 because the data source has been considered to be largely unreliable and 2) the extraction of all the localities reporting intensity data which are located within 3 km from the accelerograph stations that recorded the data.</p> <p><br> The final data set includes 323 recordings from 65 earthquakes and 227 stations in the time span 1972-2016. The events are characterized by magnitudes in the range 4.0-6.9 and depths in the range 0.3-45.0 km.</p> <p><br> Here, we illustrate the data collection and the properties of the database in terms of recording, event and station distributions as well as Mercalli-Cancani-Sieberg (MCS) macroseismic intensity points. Furthermore, we list the most relevant features of engineering interest showing several statistics with reference to the most significant metadata (such as moment magnitude, several distance metrics, style of faulting etc).</p> <p> </p>
Data sets for compound promiscuity analysis and predictions
<p>Deposited are three data sets containing compounds with multi- or single-target activity, which were assembled from the PubChem BioAssay database for promiscuity predictions [1]. The design and composition of these data sets are described in the original publication [1] and a forthcoming data note detailing the deposition. A brief summary of the data structure is provided in the readme.txt file accompanying the data sets.</p>
Data Set "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"
<p>Data set accompanying the publication "Systematic partitioning of proteins for quantum-chemical fragmentation methods using graph algorithms"</p> <p>The data set contains:</p> <p>- Input script for PyADF (v0.97) for calculating (a) all two body terms to use as graph weights and (b) fragmentation error for all k and nmax (aspf)</p> <p>- PDB files of proteins and the "regions of interest" (RoI) used in this work.</p> <p>- Raw data: protein graph representations, resulting partitions, data underlying all figures shown in our article.</p> <p>- Jupiter notebook to create all figures shown in the article and in the supporting information from data in the results folder.</p> <p>- Images of protein structures and graph representations of ubiquitin.</p>
HSV-2/HIV-1 primer sets, extended data, and their associated raw data
<p>Herpes simplex viruses (HSVs) are highly pervasive and show a strong synergistic interaction with human immunodeficiency virus (HIV). 44 convenience samples were screened for HSV and HIV-1 using the highly sensitive enzyme-linked immunosorbent assay (ELISA). Of 44 samples, 81.8% were positive for HIV-1, while 79.5% were positive for HSV when screened with ELISA kits. The results of PCR with type specific primers showed that 11.4% samples were specific for HSV-1 while 85.7% were specific for HSV-2. Pearson's chi-squared test established that there is a significant relationship between HSV-2 and HIV-1 transmission specific for HSV-1 while 85.7% were specific for HSV-2. Pearson's chi-squared test established that there is a significant relationship between HSV-2 and HIV-1 transmission.</p>
From refugia to contact: pine processionary moth hybrid zone in a complex biogeographic setting
<p class="MsoCommentText">Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyse their co-occurrence and hybridisation patterns in this biogeographical context.</p> <p class="MsoCommentText">We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals.</p> <p class="MsoCommentText">We confirmed the parapatric distribution of <i>Thaumetopoea</i><i> pityocampa </i>(Lepidoptera: Notodontidae) in the west and <i>T. wilkinsoni </i>in the east and identified a narrow contact zone. We identified several glacial refugia of <i>T. wilkinsoni</i> in southern Turkey with a strong east-west differentiation in this species. Unexpectedly, <i>T. pityocampa</i> crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in north-western Turkey, but we did not identify any F<sub>1</sub> individuals. The identified hybrid zone was mostly bimodal.</p> <p>The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. <i>Thaumetopoea pityocampa</i> and <i>T. wilkinsoni</i> survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of<i> T. wilkinsoni</i> constrained <i>T. pityocampa</i> to the western Turkish shore. Additionally, we found evidence of recurrent introgression by <i>T. wilkinsoni</i> males in several <i>T. pityocampa</i> populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.</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.