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311 results for “function dataset”
Dataset of "Asparagine-Modified Magnetic Graphene Oxide: An Efficient and Green Nanocatalyst for Synthesis of 5-oxodihydropyrano[3,2-c]chromenes and dihydropyrano[2,3- c]pyrazole derivatives and the Density functional theory calculation".
<p>The primary focus of this study involved the fabrication of a novel nanocatalyst Fe3O4-supported asparagine functionalized graphene oxide (Fe3O4@GO-N-(Asparagine)). The catalyst was synthesized through a four-step procedure.</p>
DATASET: De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus
<p>The spiny lobster <em>Panulirus argus</em> is an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster<em> Panulirus argus</em> assembled from short Illumina 150 bp PE raw reads. A total 80,152,094 raw reads were assembled using the Oyster River Protocol pipeline that aspires to become the standard protocol for <em>de novo</em> transcriptome assembly. The assembly resulted in a total of 254,773 transcripts. Functional gene annotation was conducted using the software package 'dammit' that also aspires to become the standard protocol for <em>de novo</em> transcriptome annotation. Lastly, gene enrichment analyses were conducted using the Gene Ontology (GO), KEGG pathway analyses (Kaas), and KOG (WebMGA) databases. This resource will be of utmost importance in future research aiming at exploring the effect of local and regional anthropogenic disturbances as well as global climate change on the molecular physiology of this overexploited species.</p>
Divergent evolution of sleep functions - Joyce et al 2024 Dataset - Part 1 of 4
<p>This is the full experimental dataset associated to "Divergent evolution of sleep functions" by Joyce et al 2024, Nature Communications. See https://lab.gilest.ro/papers/divergent-evolution-of-sleep-functions/ for more information.</p> <p>The dataset contains 86 zip files for a total of about 170GB. Once uncompressed, they will explode 622 ethoscope db files for a total of 330Gb, covering behavioural analysis of more than 11.000 animals. These are the RAW data as collected from the ethoscopes. A separate zip archive with all the R/Python scripts and the metadata is also provided. This also contains confocal images for BRP analysis.</p> <ul> <li>Part 1 of 4: <a href="https://doi.org/10.5281/zenodo.10554851" target="_blank" rel="noopener">10.5281/zenodo.10554851 (this page) </a></li> <li>Part 2 of 4: <a href="https://doi.org/10.5281/zenodo.10557238" target="_blank" rel="noopener">10.5281/zenodo.10557238</a></li> <li>Part 3 of 4: <a href="https://doi.org/10.5281/zenodo.10557310" target="_blank" rel="noopener">10.5281/zenodo.10557310</a></li> <li>Part 4 of 4: <a href="https://doi.org/10.5281/zenodo.10966461" target="_blank" rel="noopener">10.5281/zenodo.10966461 </a></li> </ul>
Dataset Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T
<p>Scientific Reports - Nature - DOI : 10.1038/s41598-018-37825-8</p> <p>##################################<br> "Comparison of MRI-based automated segmentation methods and functional neurosurgery targeting with direct visualization of the Ventro-intermediate thalamic nucleus at 7T"<br> ##################################</p> <p>E. Najdenovska*, C. Tuleasca*, J. Jorge, P. Maeder, J.P. Marques, T. Roine, D. Gallichan, J.-P. Thiran, M. Levivier, and M. Bach Cuadra</p> <p>*Equally contributed authors</p> <p><br> Copyright (c) - All rights reserved. University of Lausanne. 2018.</p> <p><br> To reproduce the analyses presented in the referred study, in this repository you could find the MR images acquired from nine young healthy subjects (YS1-YS5), four elderly healthy subject (ES1-ES4) and two drug-resistant tremor patients treated treated with Vim radiosurgery by Gamma Knife (P1 and P2).</p> <p>The provided dataset includes the following NifTI files:</p> <p>- MPRRAGE @3T<br> - DWI @3T (together with the corresponding bvals and bvecs)<br> - MP2RAGE @7T<br> - SWI @7T<br> - binary masks of the manual delineation of both left and right Vim respectively that were done on the SWI (as NifTI files as well).</p> <p>Additionally, for the young cohort (YS1-YS5) we include as well the images used for building the quadrilateral of Guiot:<br> - T2-w @3T<br> - T2 CISS @3T</p> <p>For the patients (P1 and P2), a follow-up MPRAGE (acquired at 3T) with Gadolinium enhancement is also provided.</p> <p>——————————————<br> Notes:<br> 1. For YS3 MP2RAGE at 7T is missing, instead MPRAGE at 3T was used</p> <p>2. The code performing the thalamic nuclei clustering could be found in Zenodo (DOI: 10.5281/zenodo.123768)</p>
Dataset: A database of near-field head-related transfer functions based on measurements with a laser spark source
<p>This is a database of near-field head-related transfer functions (HRTFs) of an artificial head, measured at four distances (0.2, 0.3, 0.4 and 0.5 m), with 49 positions recorded at each distance, for a total of 196 measurement points. The HRTFs were recorded using an acoustic pulse created by a laser-induced breakdown of air (LIB), which realizes a close to ideal, massless, monopole sound source. The repository contains the original measurement data (raw_data.zip), the derived HRTFs both with (NF_LIB_HRTF_LFE.sofa) and without (NF_LIB_HRTF_measured.sofa) a low-frequency extension (LFE) applied, as well as the MATLAB code used to process the measurement data and to apply the LFE (LIB_HRTF_DB.zip). The database is made publicly available to support future research into nearby sound localization, and virtual/augmented reality applications.</p> <p>Please see the accompanying paper for further details: Marschall et al. (2023), <a href="https://doi.org/10.1016/j.apacoust.2022.109173">A database of near-field head-related transfer functions based on measurements with a laser spark source</a>, Applied Acoustics. </p>
Dataset: Effects of high altitude reservoirs on the structure and function of lotic ecosystems: a case study in Italy
<p>Supporting data for "Effects of high altitude reservoirs on the structure and function of lotic ecosystems: a case study in Italy"</p> <p>Macroinvertebrate community composition</p> <p>Water chemical characteristics</p> <p>Daily mean water temperature and daily temperature variations</p> <p>Results of the leaf bags experiments</p>
Accompanying dataset; 'Agroforestry enhances biological activity, diversity and soil-based ecosystem functions in mountain agroecosystems of Latin America: A meta-analysis.'
<p>The database created as part of the meta-analysis is designed to facilitate the comparison of biological activity, diversity (BIAD), and ecosystem functions (EFs) between agroforestry systems (AFS) and other land-use types. It incorporates data extracted from selected studies, each record comprising a mean value, sample size, and a variance measure to compute standard deviation. The database also categorizes data according to 22 explanatory variables, including geographical coordinates, climate classification, soil type, AFS classification, and more, to characterize the sites and management systems involved. This detailed classification enables a nuanced analysis of how different factors might influence the BIAD and EFs in the context of AFS. The database supports the meta-analysis by allowing for the estimation of effect sizes using response ratios, which compare the relative difference in BIAD and EFs between AFS and other land uses. Data extraction from primary studies was meticulous, employing both direct and indirect methods such as graph digitizing software, and missing data were supplemented using reliable sources or direct communication with the original study authors. The comprehensive nature of this database ensures that the analysis can account for a wide range of variables that may affect the outcomes of interest in the meta-analysis. </p><p>For an in-depth exploration of the study's findings and methodology, refer to the comprehensive meta-analysis available in Global Change Biology (2024), entitled "<i>Agroforestry Enhances Biological Activity, Diversity, and Soil-Based Ecosystem Functions in Mountain Agroecosystems of Latin America: A Meta-Analysis</i>."</p>
qPCR raw datasets on the assessments of cover crop monocultures and mixtures improving the rhizosphere bacterial abundance and functionality through rerooting
<p>Quantitative PCR (qPCR) raw data includes the source data that corresponds to the the counts of 16S rRNA gene copies per gram of soil for different variations, as discussed in the research article - "Cover crop monocultures and mixtures improve the rhizosphere bacterial abundance and functionality through rerooting". The copy number of the 16S rRNA gene per gram of soil was quantified by SYBR® Green-based qPCR using a 7500 Fast Real-Time PCR System (Applied Biosystems™, Thermo Fisher Scientific, Waltham, MA, USA). Aliquots of the same DNA extract utilized in amplicon sequencing were used in qPCR. Dilutions of template DNA were used to compensate for the effect of PCR inhibitors in the samples. Each sample was analyzed in triplicate. A PCR amplicon of the <i>Escherichia coli</i> V3 region was used as standard. Each reaction of 20 µL contained 1 µL of template DNA, the forward primer 341F (Muyzer et al., 1993), the reverse primer 518R (Muyzer et al., 1993), and Luna® Universal qPCR Master Mix (NEB). Reaction conditions were an initial denaturation for 1 min at 95 °C, followed by 40 cycles of denaturation at 95 °C for 15 s and extension at 60 °C for 30 s. The melting curve was recorded in the temperature range of 60 °C to 95 °C. The 16S rRNA gene copy numbers per gram of soil were calculated using the standard curve method and then normalized against the standard (Adelowo et al., 2018). The average efficiency value was 100.77 ± 3.15 %. The absolute copy numbers for each bacterial phylum were calculated by multiplying the qPCR values by the relative abundance values in percent obtained from the 16S rRNA gene sequencing analyses.</p>
Dataset for "Olfactory system structure and function in newly hatched and adult locusts"
<p>This directory contains data for the article "Olfactory System Structure and Function in Newly Hatched and Adult Locusts" by Sun, Kui, Subhasis Ray, Nitin Gupta, Zane N. Aldworth, and Mark A. Stopfer. 2023.</p><p>- The folders with extension .zarr can be read with xarray package as Datasets.</p><p>- The files with extension .mat are matlab data files.</p>
Artificial fingerprints engraved through block-copolymers as nanoscale physical unclonable functions for authentication and identification - Dataset
<p>This is the dataset of "Artificial fingerprints engraved through block-copolymers as nanoscale physical unclonable functions for authentication and identification" by Irdi Murataj, Chiara Magosso, Stefano Carignano, Matteo Fretto, Federico Ferrarese Lupi, and Gianluca Milano, Nature Communications (2024), DOI: 10.1038/s41467-024-54492-8</p> <p>Part of this was funded by the project MEMQuD, code 20FUN06. The project has received funding from the EMPIR program co-financed by the Participating States and from the European Union's Horizon 2020 research and innovation program.</p> <p>Part of this work was supported by the European project OpMetBat, code 21GRD01. The project has received funding from the European Partnership on Metrology, cofinanced from the the European Union's Horizon Europe Research and Innovation Programme, and by Participating States.</p> <p>Part of this work was supported by the European Union - Next Generation EU under the National Recovery and Resilience Plan (NRRP), Mission 04 Component 2 Investment 3.1 | Project Code: IR0000027 - CUP: B33C22000710006 - iENTRANCE@ENL: Infrastructure for Energy TRAnsition aNd Circular Economy @EuroNanoLab.</p>
Dataset of "Introduction to neuromorphic functions of memristors: The inductive nature of synapse potentiation"
<p>This dataset supports the article "Introduction to Neuromorphic Functions of Memristors: The Inductive Nature of Synapse Potentiation," published in the Journal of Applied Physics.</p> <p>Raw data for the article "Introduction to neuromorphic functions of memristors: The inductive nature of synapse potentiation". For further details see the Readme.txt file.</p>
Dataset and R code: Above and belowground functional trait coordination in the Neotropical understory genus Costus
<p>Dataset and R code accompanying the paper "Above and belowground functional trait coordination in the Neotropical understory genus <em>Costus</em>" published by AoB Plants. </p>
Dataset for Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity
<p>Per-trial dataset accompanying the publication Stauch, Peter, Schuler, and Fries (2020): Stimulus-specific plasticity in human visual gamma-band activity and functional connectivity.<br> Additionaly, preprocessing code is provided as Codebase.zip.</p>
Dataset: Environment effects on X-ray absorption spectra with quantum embedded real-time Time-dependent density functional theory approaches
<p>This dataset collects the outputs from real-time TDDFT simulation of X-ray absorption of halides in model systems, using the frozen density embedding (FDE) and block-orthogonalized Manby-Miller embedding (BOMME), as well as processing tools and scripts used to carry out the calculations.</p>
Dataset for the manuscript "ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the central canal"
<p>Description: Dataset that supports the expansion-STED and light sheet microscopy methods in spinal cord and support the findings in the manuscript: ExSTED microscopy reveals contrasting functions of dopamine and somatostatin CSF-c neurons along the central canal (Elham Jalalvand, Jonatan Alvelid, Giovanna Coceano, Steven Edwards, Brita Robertson, Sten Grillner, Ilaria Testa).</p> <p>The software used to open the files and perform the analysis: Imspector v0.10_rev8575 and ImageJ 1.52i.</p> <p>The preprint of the manuscript can be found here: https://doi.org/10.1101/2021.08.17.456595</p>
Survey on Open Science Practices in Functional Neuroimaging. Dataset and Materials
<p>Preregistration of the hypotheses and methods of an empirical study before analysis, the sharing of primary research data, and compliance with data standards such as the Brain Imaging Data Structure (BIDS), are considered effective practices to secure progress and to substantiate quality of research. We investigated the current level of adoption of open science practices in neuroimaging and the difficulties that prevent researchers from using them. A PubMed search with the search terms ("fMRI" OR "functional magnetic resonance imaging" OR "functional Magnetic Resonance Imaging") was done to collect email addresses from corresponding authors of scientific articles published between 2010/01/01 and 2020/08/28. An email was sent to 14,690 addresses on 2020/01/12 with an invitation to participate, including a personalized link to the survey. If the recipients did not click the link or did not complete the survey after 14 days, they received a single reminder email. The questionnaire was composed of five building blocks. The Blocks 1-3 focused on three areas of open science practices: data structure, preregistration and data sharing. The fourth block asked about technical expertise with software and the fifth part assessed sociodemographic data.</p>
Dataset of "Chronic TCR-MHC (self)-interactions limit the functional potential of TCR affinityincreased CD8 T lymphocytes"
<p><strong>Background</strong>: Affinity-optimized T cell receptor (TCR)-engineered lymphocytes targeting tumor antigens can mediate potent antitumor responses in cancer patients, but also bear substantial risks for off-target toxicities. Most preclinical studies have focused on T cell responses to antigen-specific stimulation. In contrast, little is known on the regulation of T cell responsiveness through continuous TCR triggering and consequent tonic signaling. Here, we addressed the question whether increasing the TCR affinity can lead to chronic interactions occurring directly between TCRs and MHC-(self) molecules, which may modulate the overall functional potency of tumor-redirected CD8 T cells. For this purpose, we developed two complementary human CD8 T cell models (i.e. HLA-A2 knock-in and knock-out) engineered with incremental-affinity TCRs to the HLA-A2/NY-ESO-1 tumor antigen.<br> <strong>Methods</strong>: The impact of HLA-A2 recognition, depending on TCR affinity, was assessed at the levels of the TCR/CD3 complex, regulatory receptors, and signaling, under steady-state conditions and in kinetic studies. The quality of<br> CD8 T cell responses was further evaluated by gene expression and multiplex cytokine profiling, as well as real-time quantitative cell killing, combined with co-culture assays.<br> <strong>Results</strong>: We found that HLA-A2 per se (in absence of cognate peptide) can trigger chronic activation followed by a tolerance-like state of tumor-redirected CD8 T cells with increased-affinity TCRs. HLA-A2pos but not HLA-A2neg T cells displayed an activation phenotype, associated with enhanced upregulation of c-CBL and multiple inhibitory receptors. T cell activation preceded TCR/CD3 downmodulation, impaired TCR signaling and functional<br> hyporesponsiveness. This stepwise activation-to-hyporesponsive state was dependent on TCR affinity and already detectable at the upper end of the physiological affinity range (KD ≤ 1 μM). Similar findings were made when<br> affinity-increased HLA-A2neg CD8 T cells were chronically exposed to HLA-A2pos-expressing target cells.<br> <strong>Conclusions</strong>: Our observations indicate that sustained interactions between affinity-increased TCR and self-MHC can directly adjust the functional potential of T cells, even in the absence of antigen-specific stimulation. The<br> observed tolerance-like state depends on TCR affinity and has therefore potential implications for the design of affinity-improved TCRs for adoptive T cell therapy, as several engineered TCRs currently used in clinical trials share<br> similar affinity properties.</p>
dataset: Responses of the structure and function of the understory plant communities to precipitation reduction across forest ecosystems in Germany
<p><strong>Context</strong>: Understory plant communities play a central role in forest biogeochemistry and the recruitment of trees making up the future forest. It is so far poorly understood how climate change will affect understory structure and functions in forest of different management intensity.</p> <p> </p><p><strong>Aims</strong>: We monitored understory functional traits including transpiration and carbon isotope discrimination, community structure and diversity during two growing seasons as affected by drought in forests subjected to different management intensities. We hypothesized that drought would affect ecophysiological traits such as transpiration but not species richness and diversity. Moreover, we assumed that stand-specific characteristics and forest management intensity modify the drought-resistance of the understory community.</p> <p></p> <p><strong>Methods</strong>: We set up roofs in beech and conifer stands with different management intensity in three different regions across Germany and a drought event close to the 2003 drought was imposed in two consecutive years.</p> <p><strong>Results</strong>: Precipitation reduction decreased soil water content by 2 to 8%, depending on stand and region, in comparison to the control subplots. In the first year, leaf level transpiration was reduced for different functional groups, which scaled to community transpiration modified by additional effects of drought on functional group specific leaf area. Acclimation effects in most functional groups were observed in the second year. We did not observe a significant reduction of plant diversity or a consistent management effect upon drought.</p> <p><strong>Conclusion</strong>: Our results indicate high plasticity and acclimation responses of the forest understory vegetation to changing climate conditions and recurrent drought events.</p> <p><strong>Abbreviations:</strong></p> <p>sp12 - campaign spring 2012; ls12 - campaign late summer 2012; es13 - campaign early summer 2013; ls13-campaign late summer 2013</p> <p>SEW16 - Schorfheide plot 16; SEW49 - Schorfheide plot 49; SEW48 - Schorfheide plot 48;HEW03 - Hainich plot 03; HEW12 - Hainich plot 12; HEW47- Hainich plot 47; AEW13 - Alb plot 13; AEW29 - Alb plot 29; AEW08 - Alb plot 08<br> explo - exploratory<br> SEW - Schorfheide; HEW - Hainich; AEW - Schwäbische Alb<br> in - conifer intensive managed; ma - beech managed; un - beech unmanaged<br> c- control; r - roof<br> LAIs - community leaf area index m<sup>2</sup>/m<sup>2</sup>; H - Shannon´s diversity index; Ts - community transpiration rate (weighted by LAI) mmol H<sub>2</sub>O m-<sup>2</sup> leaf area s-<sup>1</sup>; Ets - Evapotranspiration (mmol/m2/sec); E - Evaporation (mmol/m2/sec); C - leaf photosynthetic carbon isotope discrimination (∆<sup>13</sup>C) according to Farquhar et al. (1982); Cs - community photosynthetic carbon isotope discrimination (∆<sup>13</sup>C) according to Farquhar et al. (1982) (weighted by LAI)</p> <p> </p>
RNA-seq dataset for Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism
<p>Data to be used along with <a href="https://github.com/neelroop/asd-development-coexpression-2013">code</a> from 2013 paper that was originally on a site hosted at UCLA, but may no longer be accessible.</p>
Neural force functional: dataset and model
<p>Dataset and trained model used in the publication:</p> <p>Neural force functional for non-equilibrium many-body colloidal systems, T. Zimmermann, F. Sammüller, S. Hermann, M. Schmidt, and D. de las Heras<br>arXiv 2406.03606 (2024).</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.