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33,754 results for “Enhancers”
Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating CD8+ T cells_Supplemental_Data
<p>Processed Datasets for:</p> <p>EGA Study ID: EGAS00001006141</p> <p>EGA Dataset ID: EGAD00001008662</p> <p> </p> <p>Find processed files and arrow files</p> <p> </p> <p>Abstract:</p> <p>Despite extensive studies on the chromatin landscape of exhausted T cells, the transcriptional wiring underlying the heterogeneous functional and dysfunctional states of human tumor-infiltrating lymphocytes (TILs) is incompletely understood. Here, we identify gene-regulatory landscapes in a wide breadth of functional and dysfunctional CD8<sup>+</sup> TIL states covering four cancer entities using single-cell chromatin profiling. We map enhancer-promoter interactions in human TILs by integrating single-cell chromatin accessibility with single-cell RNA-seq data from tumor-entity-matching samples and prioritize cell-state-specific genes by super-enhancer analysis. Besides revealing entity-specific chromatin remodeling in exhausted TILs, our analyses identify a common chromatin trajectory to TIL dysfunction and determine key enhancers, transcriptional regulators, and deregulated genes involved in this process. Finally, we validate enhancer regulation at immunotherapeutically relevant loci by targeting non-coding regulatory elements with potent CRISPR activators and repressors. In summary, our study provides a framework for understanding and manipulating cell-state-specific gene-regulatory cues from human tumor-infiltrating lymphocytes.</p>
Data for 'Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis'
<p>Additional data for 'Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis'</p>
Professional Technology Enhanced Learning: Systematic Literature Review Dataset
<p>Professional Technology-Enhanced Learning is concerned with technology-enhanced learning for professionals, i.e. people in employed jobs. Other terms used instead of professional learning are sometimes workplace learning or work-related learning; and there is a large overlap with research that focusses on informal, situated, or lifelong learning. <br> In this spreadsheet, we publish data collected for a systematic mapping study. The goal of the study was to map existing literature on professional technology-enhanced learning. The data collection followed Kitchenham and Charter's (2007) method for systematic literature reviews. This spreadsheet shows 58 papers, for which we excerpted authors (one, two or three author surnames fully shown, for more authors, only the first author name is shown with the extension "et al."), title, DOI or permanent link, the citation as given by the source, and the abstract.</p> <p>We hope that others find this data useful, and if they do so reference this data collection, referring to it as follows: Cicchinelli and Pammer-Schindler (2023). Professional Technology Enhanced Learning: A Systematically Collected Dataset of Academic Publications in the Field. DOI: https://doi.org/10.5281/zenodo.7957206</p>
Analysis of the Ground Level Enhancement GLE 60 on April 15, 2001, and its Space Weather Effects: Comparison with Dosimetric Measurements - Data
<p>Computed data that was used within the "Analysis of the Ground Level Enhancement GLE 60 on April 15, 2001, and its Space Weather Effects: Comparison with Dosimetric Measurements" paper. Computations of cones were done by OTSO using TSY89 + IGRF13 magnetic field parameters. Contains the atmospheric yield functions used for radiation computation as well as the global radiation map at 35kft for GLE60. Data is provided in .csv format.</p>
Data from: Mitochondrial function is enhanced by thyroid hormones during zebra finch development
<p>An organism's response to its environment is largely underpinned by changes in the energy supplied by the aerobic mitochondrial metabolism via adenosine-tri-phosphate (ATP) production. ATP is especially important under energy-demanding conditions, such as during growth. The biological mechanisms through which environmental factors feed-back on mitochondrial function, and thus growth, are poorly understood, but recent studies suggest a role of hormones. In particular, thyroid hormones (THs) are key regulators of growth and metabolism in vertebrates, which react flexibly to environmental influences, such as temperature or nutrient availability. We manipulated TH levels within physiological ranges during the main growth phase in zebra finch (Taeniopygia guttata) nestlings, to test for causal relationships with mitochondrial function and growth. Our TH-treatment accelerated skeletal growth and maximal mitochondrial working capacity, ETS – a mitochondrial trait reflecting ATP production potential. Furthermore, TH marginally elevated cellular metabolic rate and oxidative phosphorylation, the final step of ATP production. To our knowledge, this is the first study to characterize the regulation of mitochondria by TH during development in a naturalistic context and to address the implications for fitness.</p>
Data for "Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea"
<p>Raw data linked to the publication "Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of <em>Cassiopea".</em> NanoSIMS data and data from the survival experiments are available as individual tabs in the excel file.</p>
Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management
<p><span>Extensive applications of fishery stock enhancement worldwide bring up broad concerns about its negative effects, creating a pivotal need for science-based assessment and planning of enhancement strategies. However, the lack of mechanistic understanding of enhanced population dynamics, particularly the density-dependent processes, leads to compromise in model development and limits the capacity in predicting enhancement effects. Here, we developed an individual-based model based on dynamic energy budget theory and full life history processes, to understand the mechanism of density dependence in population dynamics that emerge from individual-level processes. We demonstrated the utility of the model framework by applying it </span><span>to an extensively enhanced species, Chinese prawn (<em>Fenneropenaeus chinensis</em></span><span>, Penaeidae</span><span>). The model could yield projections reflecting the observed trajectory of population biomass and yields. The model also delineated the key effects of density dependence on the vital rates of growth, fecundity, and starvation mortality. Regarding the manifold effects of stock enhancement, we demonstrated a dampened shape in population biomass and yields with increasing magnitude of enhancement, and trade-offs between the ecological and economic objectives, i.e., pursuing high benefit might compromise the wild population without proper management. Furthermore, we illustrated the possibility of combining stock enhancement and harvest regulation in promoting population recovery while maintaining fisheries yields. We highlight the potential of the proposed model for understanding density dependence in enhancement program, and for designing integrated management strategies. The approach developed herein may serve as a general approach to assess the population dynamics in stock enhancement and inform enhancement management.</span><span> </span></p>
Imaging data from "Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD"
<p>3D 20ms, 3D 500ms and 2D dCas9 raw videos, localisation, tracking and trajectory analysis data</p> <p>From 'Live-cell 3D single-molecule tracking reveals modulation of enhancer dynamics by NuRD" (2021). Biorxiv. https://doi.org/10.1101/2020.04.03.003178</p>
Enhanced diffusion barrier layers for avoiding degradation in SOFCs aged for 14000 h during 2 years
<p>The dataset contains all the data used for the publication called Enhanced diffusion barrier layers for avoiding degradation in SOFCs aged for 14000 h during 2 years, Bernadet et al., Journal of Power Sources, 555, 2023, 232400 (10.1016/j.jpowsour.2022.232400) as well as for the supplementary information.</p> <p>Data is labeled with the figure number-letter and sample type.</p> <p>All the figures related to the nano-XRF data (Fig4, FigS1-4) were obtained from the same dataset, shared for Fig4 and FigS1.</p>
Improving nitrogen cycling in a land surface model (CLM5) to quantify soil N2O, NO and NH3 emissions from enhanced rock weathering with croplands
<p>This repository contains CLM5 model soil nitrogen (N2O, NO and NH3) output and metadata, and soil N<sub>2</sub>O fluxes from the Energy Farm ERW field trials used in the paper "Improving nitrogen cycling in a land surface model (CLM5) to quantify soil N2O, NO and NH3 emissions from enhanced rock weathering with croplands" (https://gmd.copernicus.org/preprints/gmd-2023-47/).</p>
Dataset and fitting methods for Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network
<p>This upload contains raw experimental data and the fitting methods used for the article "Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network".</p>
Root mutualistic fungi tailor the induction of direct and indirect antiherbivore defense strategies to enhance plant resistance
<p>GCMS raw data in netCDF format for the manuscript "Root mutualistic fungi tailor the induction of direct and indirect antiherbivore defense strategies to enhance plant resistance" </p> <p>Mutualistic microbes can trigger plant defenses against herbivores. Little is known about how microbes orchestrate multiple induced defense strategies that may trade-off against each other. We investigated how two root mutualistic fungi trigger simultaneously direct and indirect antiherbivore-defenses, and the regulatory mechanisms involved</p>
Expanding China's protected areas network to enhance resilience of climate connectivity
<p>The code used for analysis, mammalian species occurrence points, prediction accuracy(AUC), and prediction distribution.</p> <p>Specifically,</p> <p>The main nodes are named "network efficiency.R" and "network efficiency_random.R", which can be run in RStudio software (download at https://posit.co/), and the files "hfp_expanded.csv" and "EN_length_expanded.net" are example data.</p> <p>"Terrestrial mammalian species occurrence points.csv" is the latitude and longitude coordinates of occurrence records.</p> <p>"AUC_prediction accuracy of Maxent.xlsx" is the prediction accuracy of each species in the Maxent model.</p> <p>"all_species_maxent.zip" is the composite terrestrial mammalian species distribution of equal weight overlapping the spatial distribution of each species ("each_species_maxent.zip").</p> <p> </p> <p> </p>
GEOLAB Project CTP-ISSR: monotonic and cyclic Centrifuge Tests on Piles in sand proving Innovative Solutions to enhance Structural Resilience
<p>The existing structures are facing continuous changes in the loading conditions during their life span. These changes can be caused by weather and geo-hazards events and affect the structural response which is often already weakened by aging.</p> <p>A clear understanding of the interaction between the superstructure, the foundation and the surrounding soil is one of the crucial aspects to deal with to adapt the design and maintenance to enhance the resilience of new and existing Critical Infrastructures (CI) often used way beyond their life expectancy. Besides the loading components already considered in engineering practice, CI endure loads having cyclic nature acting continuously during service life (e.g., wind) which are often disregarded in foundation design and may trigger collapse mechanisms. Indeed, they are usually modelled as equivalent-static actions thus neglecting the accumulation of generalized permanent displacements of piled foundations in terms of settlement, sliding and rotation. This lack in design approach can be attributed to very limited research contributions dealing with cyclic loads. </p> <p>The CTP-ISSR (monotonic and cyclic Centrifuge Tests on Piles in sand proving Innovative Solutions to enhance Structural Resilience) project aims at investigating via centrifuge tests the behaviour of piled foundations under different loading types. Two series of centrifuge experiments on annular shaped pile groups and isolated piles embedded in Hostun sand were carried out at an increased gravity of 50 g in the Turner Beam Centrifuge at Schofield Centre, University of Cambridge. </p> <p>To simulate prototype reinforced concrete piles, model piles, made up of cement and metal wires, were manufactured in laboratory by means of an ad-hoc mould and manual mortar pouring. Such modelling is necessary to replicate the strong dependency of pile cross-sectional moment capacity on the axial force. Piles were installed in an 850 mm steel tub filled with manually poured Hostun sand prepared with a low-to-medium relative density. </p> <p>The first test included 2 single piles ad 2 groups of 8 piles connected by a circular rigid cap clear from the soil. The model foundations were subjected to monotonic vertical loads or vertical eccentric cyclic loads of different amplitudes and frequencies. In a similar fashion, the second test included 3 single piles ad 2 pile groups. In this case, the model foundations were subjected to monotonic vertical or horizontal loads or to cyclic horizontal loads of different amplitudes and frequencies. The response of the foundation system, in terms of loads and displacements, was monitored through loads cells, Linear Variable Differential Transformers (LVDTs) and Micro-Electro-Mechanical-Systems (MEMS). A miniaturized Cone Penetration Test (mini-CPT) was used to characterize the soil before the test execution. The experimental campaign was accomplished in 10 working days (including, among the others, model preparation, execution, data acquisition and dismantle). </p> <p>The results of the experiments will serve as benchmarks for the development of a non-linear macroelement for piled foundation. Adopting this innovative approach allows the strengthening of CI resilience by adapting the traditional design and maintenance to properly consider changing loading conditions in a simple yet reliable manner. </p> <p>Researchers and practitioners will be the beneficiaries of the outcome of this research, expecting the following advantages: <br> - Innovation in design, with the possibility to properly consider cyclic loading;<br> - Improvement in identifying possible failure mechanisms and the required maintenance to enhance reliability and resilience of existing CI.</p>
Not only hedgerows, but also flower fields can enhance bat activity in intensively used agricultural landscapes
<p>Agri-environment schemes (AES) have become important tools for farmland biodiversity conservation, providing suitable habitats, resources, and connectivity within agricultural landscapes. Bats are rarely studied in relation to AES effectiveness in contrast to birds, even though their presence and activity as biological control agents on insects, especially pest species, can be important for agricultural crops. While the role of hedgerows for bat occurrence and activity, as well as for their prey's diversity and abundance has been widely studied, the role of other AESs such as flower fields remains unclear. We monitored the activity of the main functional groups (edge, narrow and open space foragers) using ultrasound recorders, as well as potential prey abundances using light traps, across 35 study sites representing different AES in Central Germany from late July to September 2018. The sampled AES consisted of annual flower fields, mixed flower fields (with annual and biennial vegetation), perennial flower fields (sown every 5 years), hedgerows (surrounded by meadows and agricultural fields), and were compared to winter wheat (control) in a balanced design. Bat activity over hedgerows increased threefold for edge space foragers and sevenfold for narrow space foragers compared to wheat fields. Compared to wheat fields, narrow space forager activity increased fourfold over perennial flower fields, threefold over annual and twofold over mixed flower fields. This group's activity over hedgerows also increased almost threefold compared to mixed flower fields. However, the number of feeding buzzes and prey abundance did not differ significantly between AES. We detected foraging group-specific differences in bat activity between the studied AES. Thus, to promote bats in agricultural landscapes and to ensure their biological control services, it is important to establish more AES, such as hedgerows and flower fields, to increase their diversity and connectivity in intensively used agricultural landscapes.</p>
Over-coupled resonator for broadband surface enhanced infrared absorption (SEIRA)
<p>This repository contains all datasets and MATLAB codes used in the paper "Over-coupled resonator for broadband surface enhanced infrared absorption (SEIRA)"</p> <p>3 folders can be found</p> <ul> <li>BMM contains a main python script that reproduces the electromagnetic computations of the article</li> <li>CMT : contains 3 scripts <ul> <li><strong>Absorption2D.m</strong> computes a 2D map of the absorption from the resonator from eq.1 of the main text as a function of f and (ω − ωr )/γnr .</li> <li><strong>DeltaRm.m</strong> plots the analytical expression of Delta Rm computed in the SI as a function of f.</li> <li><strong>DRanalytics.m</strong> plots the reflexion with the absorber as a function of omega. The expression is derived from the coupled mode formalism as described in the supplemental information.</li> </ul> </li> <li>Data_exp: contains raw experimental datasets of the figures.</li> <li>over_coupling_package : contains scripts to reproduce the electromagnetic simulations presented in the paper</li> </ul> <p>===============================</p> <p>PAPER ABSTRACT:</p> <p>Detection of molecules is a key issue for many applications. Surface enhanced infrared absorption (SEIRA) uses arrays of resonant nanoantennas with good quality factors which can be used to locally enhance the illumination of molecules. The technique has proved to be an effective tool to detect small amount of material. However nanoresonators can detect molecules on a narrow bandwidth so that a set of resonators is necessary to identify a molecule fingerprint. Here, we introduce an alternative paradigm and use low quality factor resonators with large radiative losses (over-coupled resonators). The bandwidth enables to detect all absorption lines between 5 and 10 µm, reproducing the molecular absorption spectrum. Counterintuitively, despite a lower quality factor, the system sensitivity is improved and we report a reflectivity variation as large as one percent per nanometer of molecular layer of PMMA. This paves the way to specific identification of molecules. We illustrate the potential of the technique with the detection of the explosive precursor 2,4-dinitrotoluene (DNT). There is a fair agreement with electromagnetic simulations and we also introduce an analytic model of the SEIRA signal obtained in the over-coupling regime.</p>
Manganese Enhanced Magnetic Resonance Imaging reveals light-induced brain asymmetry in embryo
<p>The idea that sensory stimulation to the embryo (in utero or in ovo) may be crucial for brain development is widespread. Unfortunately, up to now evidence was only indirect because mapping of embryonic brain activity in vivo is challenging. Here we applied for the first time Manganese Enhanced Magnetic Resonance Imaging (MEMRI), a functional imaging method, to the eggs of domestic chicks. We revealed both spontaneous and light-induced brain asymmetry by comparing embryonic brain activity in vivo of eggs that were stimulated by light or maintained in the darkness. Our protocol paves the way to investigation of the effects of a variety of sensory stimulations on brain activity in embryo.</p>
Capturing Pertinent Symbolic Features for Enhanced Content Based Misinformation Detection
<p>Datasets for the paper <em>Capturing Pertinent Symbolic Features for Enhanced Content-Based Misinformation Detection</em>. The compressed folder contains <strong><em>annotated</em></strong> data carried out using the symbolic models presented in the paper.</p>
Direct evidence for atmospheric carbon dioxide removal via enhanced weathering in cropland soil: Supporting data
<p>Datasets (climate, alkalinity, moisture sensors) associated with the manuscript "Direct evidence for atmospheric carbon dioxide removal via enhanced weathering in cropland soil."</p>
CyTOF and Flow Cytometry dataset assocaited with "Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females"
<p>This dataset contains all the raw mass cytometry (CyTOF) and flow cytometry fcs files associated with Capelle <i>et al</i>. '<i>Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females',</i> <i><strong>Nature Communications</strong>, <strong>2023</strong>,</i> In Press.</p><p>The dataset contains the following information:</p><p>1, The folder " CoPImmunoPD Flow Zenodo V2.zip " contains all the raw fcs files of flow cytometry analysis and the excel table with marker information of five staining panels in the initial discovery analysis using fresh blood samples. The folder also includes the fcs files of analyzing cytotoxicity potential within CD8 T cells and of validation analyses using cryopreserved samples. Single-color/fluorochrome staining files have also been provided for the relevant experiments in the given subfolders for compensation.</p><p>2, The folder "<a href="https://zenodo.org/api/files/75c910aa-3615-4eff-a201-9d2d46e33ea0/CoPImmunoPD_CyTOF_Zenodo.zip">CoPImmunoPD_CyTOF_Zenodo.zip</a>" contains all the raw fcs files generated from the CyTOF measurements in the initial discovery analysis.</p><p><strong>To reproduce our published Figures, please be assure to first read all the accompanied readme/excel information annotation files deposited in the corresponding folders within the zip files, all the Source Data files of different main and supplementary Figure subpanels, Methods and/or any other relevant sections in our manuscript.</strong></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.