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15,733 results for “article”
Article: Modeling Mouse ICM - Complete Data Bank - Part II
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Article: Modeling Mouse ICM - Complete Data Bank - Part III
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Article: Modeling Mouse ICM - Complete Data Bank - Part I
<p>Our study presents a spatial-stochastic model for the gene regulatory network (GRN) and the signaling pathway governing cell-fate differentiation during early mouse embryogenesis, specifically at the blastocyst stage. Departing from biophysics-based models of gene regulation, we perform stochastic simulations of the biochemical processes driving early mouse embryogenesis both at the cell and tissue level. Combining these simulations with state-of-the-art AI-aided inference techniques, we successfully parameterize our model, replicating key experimental observations and providing mechanistic insights into the biochemical interactions giving rise to them. Thanks to the stochastic nature of our approach, we quantify the high robustness of ICM specification to various kinds of noise, and provide quantitative predictions for the effects of diverse experimentally testable perturbations. Altogether, we provide a deeper understanding of the intricate mechanisms driving early cell-fate decisions in mouse embryogenesis, highlighting the synergy of local cellular and broader tissue-scale interactions that shape development.</p>
Data analysis of article research tittle "Online GIS and Remote Sensing-Based Mapping of Flood Vulnerability in Samarinda Seberang Subdistrict"
<p>This dataset contains an explanation of data analysis for creating a flood vulnerability map of Samarinda Seberang District. The dataset contains sub-criteria for each flood parameter and its score value. In addition, this dataset contains the weight value of each parameter, flood vulnerability level and its coloring, and the results of calculating the area of each vulnerability level.</p>
Resulting videos from the article: A Novel Technique for the Extraction of Dynamic Events in Extreme Ultraviolet Solar Images
<p>Videos called 'MFM PCP DMD ...' correspond to Figure 5 in the mentioned article. They show comparison of MFM, PCP, and DMD algorithms. Upper images in each year correspond to the separated background matrix, the lower images correspond to matrix of dynamic component. The videos cover 1.7 hours of observations starting at 06:00:00 UTC on 2011 June 7, 16:50:00 UTC on 2012 April 16 and 18:30:11 UTC on 2014 October 2.<br><br>The other videos correspond to Figure 7 in the article. They compare the results from PCP algorithm applied to the 30.4 and 17.1 nm AIA bandpasses. The videos starting at 16:50:00 UTC on 2012 April 16 and 18:30:11 UTC on 2014 October 2, respectively, and cover 1.7 hours of observations.</p>
DataSet for article: TEAM BASED LEARNING AS A STRATEGY OF WORKING IN THE CLASSROOM
<p>Archive with the references of the RSL carried out in the article TEAM BASED LEARNING AS A STRATEGY OF WORKING IN THE CLASSROOM.</p>
Raw data for the article "In vitro culture of leukemic cells in collagen scaffolds and carboxymethylcellulose-polyethylene glycol gel"
<p>Uncropped original micrographs and raw numerical data of figures and tables from the article submitted to PeerJ. </p>
Data described in the article "Design and evaluation of composite films for in situ synthesis and antibacterial activity of allicin vapour"
Open the record for dataset details and reuse information.
Datasets and code used to generate the figures in the article "Influence of Forest Cover Loss on Land Surface Temperature Differs by Drivers in China"
<p>We have provided the data and code used to generate the figures in the article "Influence of Forest Cover Loss on Land Surface Temperature Differs by Drivers in China" for reference and further reading. These data can be used to replicate the analyses presented in the paper. If you wish to use the data for other purposes, please contact the authors for permission. Thank you.</p>
raw data for the article "Forging 1,1'-Bicyclopropenyls by Synergistic Au/Ag Dual-Catalyzed Cyclopropenyl Cross-Coupling"
<p>Raw NMR, IR and MS data for the article "Forging 1,1'-Bicyclopropenyls by Synergistic Au/Ag Dual-Catalyzed Cyclopropenyl Cross-Coupling" published in the Journal of the American Chemical Society DOI: </p> <p><a title="DOI URL" href="https://doi.org/10.1021/jacs.4c10996">https://doi.org/10.1021/jacs.4c10996</a></p> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Raw data and initial rudimentary coding for article on country music and alcohol
Open the record for dataset details and reuse information.
Dataset for the article "Transforming ceria into 2-dimensional clusters enhances catalytic activity"
<p>CONTCAR files of the structures discussed in the article "Transforming ceria into 2-dimensional clusters enhances catalytic activity"</p>
Data for Article "Climate change activity in small and medium-sized Polish towns"
<p>Research Data for Article "Climate change activity in small and medium-sized Polish towns"<br>ZIP file contains:<br>- spreadsheet with anonymised survey data<br>- 10 text files with anonymised interviews with research subjects.<br>The interviews have been edited for clarity (technical parts with no connection to the research have been omitted). The interviews and surveys have been uploaded in the original language.</p>
Dataset for the article 'Selective electroreduction of acetylene to 1,3-butadiene on iodide-induced Cuδ+-Cu0 sites'
<p>Data sets for the article 'Selective electroreduction of acetylene to 1,3-butadiene on iodide-induced Cuδ+-Cu0 sites', published in Nature catalysis (DOI : 10.1038/s41929-024-01250-0)</p>
Data for journal article "Dancing Sprites Above a Lightning Mapping Array - an analysis of the storm and flash/sprite developments"
<p>Data used for the analysis presented in the paper: "Dancing Sprites Above a Lightning Mapping Array - an analysis of the storm and flash/sprite developments" published in JGR Atmospheres.</p>
Supplementary data for article: Central insulin modulates dopamine signaling in the human striatum
<p><b>Objective:</b> Activity in the dopaminergic pathways of the brain is highly sensitive to body weight and metabolic states. Animal studies show that dopamine neurons are important targets for the metabolic hormone insulin with abolished effects in the insulin resistant state, leading to increases in body weight and food intake. In humans, the influence of central acting insulin on dopamine and effects of their interplay are still elusive.</p> <p><b>Research Design and Methods:</b> We investigated whether central administered insulin influences dopaminergic activity in striatal regions and whole-brain neural activity. Using a PET/MRI hybrid scanner, we simultaneously performed [<sup>11</sup>C]-raclopride-PET and resting state fMRI in 10 healthy normal weight men after application of intranasal insulin or placebo on two separate days in a randomized, placebo-controlled, blinded, crossover trial.</p> <p><b>Results:</b> In response to central insulin compared to placebo administration, we observed greater [<sup>11</sup>C]-raclopride binding potential (BP<sub>nd</sub>) in the bilateral ventral and dorsal striatum. This suggests an insulin-induced reduction in synaptic dopamine levels. Resting-state striatal activity was lower 15 and 30 min after nasal insulin compared to placebo. Functional connectivity of the mesocorticolimbic circuitry associated with differences in dopamine levels: individuals with a stronger insulin-induced effect on dopamine levels showed a stronger increase in functional connectivity 45 min after intranasal insulin.</p> <p><b>Conclusions</b>: This study indicates that central insulin modulates dopaminergic tone in the striatum, which may affect regional brain activity and connectivity. Our results deepen the understanding of the insulin-dopamine interaction and the complex network that underlies the regulation of whole-body metabolism.</p>
Data for manuscript: "Using Word Embeddings to Probe Sentiment Associations of Politically Loaded Terms in News and Opinion Articles from News Media Outlets"
<p>This data set contains material for the purpose of scientific reproducibility of the accompanying manuscript "Using Word Embeddings to Probe Sentiment Associations of Politically Loaded Terms in News and Opinion Articles from News Media Outlets".</p> <p>Note that this data set is distributed with an Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) License. NonCommercial means you may not use the material for commercial purposes. NoDerivatives means if you remix, transform, or build upon the material, you may not distribute the modified material. Attribution means you must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. See attached license terms for details.</p> <p>The work "Using Word Embeddings to Probe Sentiment Associations of Politically Loaded Terms in News and Opinion Articles from News Media Outlets" describes an analysis of political associations in 27 million diachronic (1975-2019) news and opinion articles from 47 news media outlets popular in the United States. We use embedding models trained on individual outlets content to quantify outlet-specific latent associations between positive/negative sentiment words and terms loaded with political connotations such as those describing political orientation, party affiliation, names of influential politicians and ideologically aligned public figures. </p> <p>News and opinion articles from the outlets listed in Figure 3 are available in the outlet's online domains and/or public cache repositories such as Google cache, The Internet Wayback Machine [31] and Common Crawl [32]. This work has not analyzed video or audio content of news media organizations, except when the outlet explicitly provides a transcript of such content in article form.<br> The temporal coverage of articles from different news outlets is not uniform. For most media organizations, news articles availability in their online domains or Internet cache backups becomes sparse as a function of articles’ age. This is not the case for some news outlets, where availability of news articles goes back to the 1970s. The Supplementary Material (SM) illustrates the time ranges of article data analyzed based on news outlets articles online availability.</p> <p>Textual content included in our analysis is circumscribed to the articles’ headlines and main text and does not include other article elements such as figure captions. Targeted textual content was located in HTML raw data using outlet specific XPath expressions. Tokens were lowercased prior to estimating embedding models. Markup language tags, URLs, nonalphanumeric characters, punctuation, digits, 330 common stop words and multiple spaces were removed prior to estimating word embeddings models.<br> All the analysis scripts and the diachronic word embedding models built from each of the 47 news media outlets analyzed in this work are available in this repository.</p> <p>For the purpose of reproducibility, we also provide in the above repository the articles’ text used to train the news outlets embedding models with the caveat that outlets articles not accessible without a subscription have been excluded. Also, for the included articles, stop words have been removed and the remaining words have been randomly scrambled within a sliding window of size 10 to render the articles incomprehensible to a human reader. These steps have been taken to not infringe articles copyright. These preprocessing steps have only minor impact on Continuous Bag of Words (CBOW) word2vec and the results reported in this work are similar when using the scrambled articles text to train outlet-specific embedding models.</p> <p>We derived outlet-specific word embedding models at every five-year time intervals within the 1975-2019 time range. The gensim [33] implementation of word2vec was used to train the embedding models. The continuous bag of words (CBOW) architecture performed slightly better than the Skip-Gram architecture in commonly used validation metrics so it was used for all subsequent analysis. </p> <p>For training the word embedding models, the following parameters were used: vector dimensions=300, window size=10, negative sampling=10, down sampling frequent words = 0.0001, minimum frequency count of 5 (only terms that appear more than 5 times in the corpus were included into the word embedding model vocabulary), number of training iterations (epochs) through the corpus=5. The exponent used to shape the negative sampling distribution was the default 0.75. </p> <p>Outlet-specific embedding models performance across a range of commonly used semantic, syntactic and analogy tasks was similar to popular pre-trained embedding models trained on corpora such as Twitter or Google books on similarity, association and word analogy tasks, see Supplemeentary Material of the manuscript for detailed validation tests results.</p> <p> </p>
Data Sharing - Article GIScience e Remote Sensing
<p>Confidence Interval: Comparative of the Delta Models.</p>
Velocity, density and energy budget statistics from the article: Validation and application of the lattice Boltzmann algorithm for a turbulent immiscible Rayleigh-Taylor system
<p>We develop a multicomponent lattice Boltzmann (LB) model for the 2D Rayleigh--Taylor turbulence with a Shan-Chen pseudopotential implemented on GPUs. Accuracy of the LB model is tested both for early and late stages of instability. For the developed turbulent motion we analyze the balance between different terms describing variations of the kinetic and potential energies. Then, we analyze the role of interface in the energy balance, and also the effects of the vorticity induced by the interface in the energy dissipation. Statistical properties are compared for miscible and immiscible flows.</p> <p>In this Dataset, we have included the files for the statistics of the energy budget for the miscible and immiscible Rayleigh-Taylor flows studied in the referred article.</p> <p>We also included the examples of the density and velocity fields showed in the Figures 1 and 2 of the article.</p>
Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"
<p>Data set of the article "Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation"</p>
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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.