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11,177 results for “identify”
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Laurence Livermore, <a href="https://orcid.org/0000-0002-7341-1842">https://orcid.org/0000-0002-7341-1842</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Stomach as the target organ of Rickettsia heilongjiangensis infected C57BL/6 mice identified by click chemistry
<p>Code used for analyses and generate figures in the manuscript *Stomach as the target organ of Rickettsia heilongjiangensis infected C57BL/6 mice identified by click chemistry*.</p> <p>Input and scripts are included in corresponding files.</p> <p> </p>
Identifying priority survey sites for early-season milkweed conservation
<p>Monarch butterfly (<em>Danaus plexippus</em>) populations are experiencing decline due to habitat degradation and climate threats. In 2024, this iconic species became protected under the Endangered Species Act. Critical to the persistence of this species of cultural and ecological importance is milkweed (<em>Asclepias spp.</em>), which monarchs rely on as an essential resource for food and reproduction. Motivated by concerns over the loss of monarch habitat, the Santa Barbara Botanic Garden (SBBG) and local collaborators are working to identify potential restoration areas in the Los Padres National Forest (LPNF). However, the vast size and complex terrain of the LPNF pose a logistical challenge to surveying. Therefore, there is a need for a tool to aid in selecting sites to prioritize. Our team created a priority index for surveying milkweed within the LPNF by predicting the habitat suitability for four early-season milkweed species using Maximum Entropy (MaxEnt) species distribution modeling and creating a novel survey site accessibility index. We identified high priority sites for the team to survey based on high predicted suitability for each species of early-season milkweed and high physical accessibility. To communicate these results, we created an interactive web dashboard, which the SBBG team will use for field planning to support the ongoing monitoring of milkweed populations for monarch habitat restoration efforts within the LPNF.</p>
Data for "Identifying and Fitting Eclipse Maps of Exoplanets with Cross-Validation" (Hammond et al. 2024)
<p>This archive contains the data and scripts needed to reproduce the analysis in "Identifying and Fitting Eclipse Maps of Exoplanets with Cross-Validation" (Hammond et al. 2024).</p> <p>Contents</p> <p>data/: Input data and posterior distributions of different model fits</p> <p>datasets/: Observational datasets</p> <p>figures/: Folder to save figures in</p> <p>fluxes/: Saved lightcurves for auxiliary plotting purposes</p> <p>archive_paper_plotter.ipynb: Example script to plot fitted eclipse maps</p> <p>eclipse_pixel_sampling.py: Script to fit eclipse map and test k-fold CV score</p> <p>paper_eclipse_suite.py: Script to use simulated or observational data to fit an eclipse map</p>
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution
<p>In this repository we provide the datasets for the results of the Cellstates method as shown in the article: “Identifying cell states in single-cell RNA-seq data at statistically maximal resolution” by Pascal Grobecker, Thomas Sakoparnig, and Erik van Nimwegen.</p> <p>A preprint is available under the following DOI: https://doi.org/10.1101/2023.10.31.564980</p> <p>There is a README file that describes the contents and formats of each of the tab-separated values files. There is one subdirectory containing files with Cellstates' results on the dataset of Zeisel et al. (DOI: 10.1016/j.cell.2018.06.021) which is accompanied by another README file describing the formats and contents of these files. </p>
Novel Activation Modulating Sites in a GPCR Identified with a Large-Scale Alchemical Mutation Scan
<p>This dataset contains the starting configurations and mdp files for the alchemical free energy calculations using pmx.<br>The MD parameter files (*.mdp) for the forward reaction (lambda 0 to 1, wt to mutant) and reverse reaction (lambda 1 to 0, mutant to wt) start with f (forward) and r (reverse). Mdp files are available for the energy minimization (em), npt (npt), equilibrium run (equilibrium) and non equilibrium alchemical transition (nonequilibrium). <br>The starting configurations for mutants of the DRD2 receptor can be found in WT7jvr and WT6cm4 for the active and inactive state respectively. Mutant folders are labeled with the residue number and the amino acid it is mutated to.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Alexa DiNicola, <a href="https://orcid.org/0000-0001-7763-4376">https://orcid.org/0000-0001-7763-4376</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Carlos Alonso Maya-Lastra, <a href="https://orcid.org/0000-0002-0550-3331">https://orcid.org/0000-0002-0550-3331</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Data from: Transcriptional profiling of lung macrophages following ozone exposure in mice identifies signaling pathways regulating immunometabolic activation
<p>Macrophages play a key role in ozone-induced lung injury by regulating both the initiation and resolution of inflammation. These distinct activities are mediated by pro-inflammatory and anti-inflammatory/pro-resolution macrophages which sequentially accumulate in injured tissues. Macrophage activation is dependent, in part, on intracellular metabolism. Herein, we used RNA-sequencing (seq) to identify signaling pathways regulating macrophage immunometabolic activity following exposure of mice to ozone (0.8 ppm, 3 hr) or air control. Analysis of lung macrophages using an Agilent Seahorse showed that inhalation of ozone increased macrophage glycolytic activity and oxidative phosphorylation at 24 and 72 hr post exposure. An increase in the percentage of macrophages in the S phase of the cell cycle was observed 24 hr post ozone. RNA-seq revealed significant enrichment of pathways involved in innate immune signaling and cytokine production among differentially expressed genes at both 24 and 72 hr after ozone, while pathways involved in cell cycle regulation were upregulated at 24 hr and intracellular metabolism at 72 hr. An interaction network analysis identified tumor suppressor 53 (TP53), E2F family of transcription factors (E2Fs), Cyclin Dependent Kinase Inhibitor 1A (CDKN1a/p21), and Cyclin D1 (CCND1) as upstream regulators of cell cycle pathways at 24 hr and TP53, nuclear receptor subfamily 4 group a member 1 (NR4A1/Nur77), and estrogen receptor alpha (ESR1/ERα) as central upstream regulators of mitochondrial respiration pathways at 72 hr. These results highlight the complex interaction between cell cycle, intracellular metabolism, and macrophage activation which may be important in the initiation and resolution of inflammation following ozone exposure.</p>
Identifying Mediterranean Hotspots: The MED-HOT Index
<p>This folder contains the data and the scripts for producing the results of the manuscript entitled "Identifying Mediterranean Hotspots: The MED-HOT Index".</p>
"Power system investment optimization to identify carbon neutrality scenarios for Italy", scripts and data
<p>Script and data to reproduce the main results of "Power system investment optimization to identify carbon neutrality scenarios for Italy"</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Pieter Huybrechts, <a href="https://orcid.org/0000-0002-6658-6062">https://orcid.org/0000-0002-6658-6062</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Single cell multiomic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
<p>Innate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. To gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omic approach consisting of Abseq and targeted mRNA sequencing to respectively probe the surface marker expression, transcriptional profile and heterogeneity of ILCs in peripheral blood of patients with COVID-19 compared with healthy controls. We found that the frequency of ILC1 and ILC2 cells was significantly increased in COVID-19 patients. Moreover, all ILC subsets displayed a significantly higher frequency of CD69-expressing cells, indicating a heightened state of activation. ILC2s from COVID-19 patients had the highest number of significantly differentially expressed (DE) genes. The most notable genes DE in COVID-19 vs healthy participants included a) genes associated with responses to virus infections and b) genes that support ILC self-proliferation, activation and homeostasis. In addition, differential gene regulatory network analysis revealed ILC-specific regulons and their interactions driving the differential gene expression in each ILC. Overall, this study provides mechanistic insights into the characteristics of ILC subsets activated during COVID-19 infection.</p>
Identifying one-to-one communication themes on HPV and HPV vaccination
<p>The aim of this study is to examine the factors that impact communication between doctors, young adolescents, parents, and caregivers when discussing HPV vaccination recommendations. We are interested in understanding how different topics are discussed based on patient characteristics. Specifically, we would like to explore the influence of factors such as religion, country of origin, educational level, and gender.</p> <p>Survey was carried out in the framework of the European project PROTECT-EUROPE (EU4H-1, Project ID 101080046). PROTECT-EUROPE is an EU4Health Project that champions gender-neutral vaccination programme in EU Member States to provide protection for everyone against cancers caused by HPV e.g. cervical, anal, penile, vaginal, vulval and oropharyngeal.</p>
Archival mitogenomes identify invasion by the Batrachochytrium dendrobatidis CAPE lineage caused an African amphibian extinction in the wild
<p>Outbreaks of emerging infectious diseases are influenced by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Deterioration in the population of the microendemic Tanzanian Kihansi spray toad (<em>Nectophrynoides asperginis</em>) occurred after the construction of a hydropower dam, implicating habitat modification in this species decline. Population recovery followed habitat augmentation, however a subsequent outbreak of chytridiomycosis caused by <em>Batrachochytrium dendrobatidis </em>(<em>Bd</em>) led to the spray toads extinction in the wild. We show using spatiotemporal surveillance and mitogenome assembly of <em>Bd </em>from archived toad mortalities that the outbreak was caused by invasion of the <em>Bd</em>CAPE lineage and not the panzootic lineage <em>Bd</em>GPL. Molecular dating reveals an emergence of <em>Bd</em>CAPE across Southern Africa overlapping with the timing of the spray toads extinction. That our post-outbreak surveillance of co-occurring amphibian species in the Udzungwa Mountains shows widespread infection by <em>Bd</em>CAPE yet no signs of ill-health or decline suggests these other species can tolerate <em>Bd</em> when environments are stable. We conclude that, despite transient success in mitigating the impact caused by dams' construction, invasion by <em>Bd</em>CAPE caused the ultimate die-off that led to the extinction of the Kihansi spray toad.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Adam Cohen, <a href="https://orcid.org/0000-0003-4881-3636">https://orcid.org/0000-0003-4881-3636</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Supplemental Data for "Identifying novel variants of small molecules through database search of mass spectra"
<p>Supplemental Dataset 1 contains GNPS dataset information for the large scale search of GNPS vs Pubchem.</p> <p>Supplemental Dataset 2a contains the top scoring exact mode hit for each spectrum against PubChem and COCONUT. Files are split into "*chunk*" files of up to 10 million records each.</p> <p>Supplemental Dataset 2b contains the top scoring variable mode hit for each spectrum against COCONUT.</p> <p>Supplemental Dataset 3 contains mass spectra provided by Waters Corporation to analyze impurities of Imatinib.</p>
Results outputs for "Beyond the Hype: Identifying and Analyzing Math Word Problem-Solving Challenges for Large Language Models"
<p>The provided files contain outputs generated by various Large Language Models (LLMs) for solving problems in the SVAMP dataset. Additionally, they include tagged statements of problems that LLMs incorrectly resolved.</p> <p>This repository includes the following two files:</p> <ul> <li>all_data.json --> Contains the generated samples for the SVAMP dataset.</li> <li>df_combined.pkl --> Contains the tagged SVAMP statements of problems that CodeLlama failed to resolve.</li> </ul>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Quentin J. Groom, <a href="https://orcid.org/0000-0002-0596-5376">https://orcid.org/0000-0002-0596-5376</a>. Claims or attributions were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Identifying genetic variants associated with chromatin looping and genome function
<p><span>Here<span> we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of HiChIP contacts defining loops between active regulatory regions (iQTLs). We observe a substantial overlap between iQTLs and previously defined eQTLs and histone QTLs, and an enrichment for fine-mapped QTLs and GWAS variants. Furthermore, we describe a distinct subset of nCD4 iQTLs, for which the significant variation of chromatin contacts in nCD4 are translated into significant eQTL trends in CD4 T cell memory subsets. Finally, we define connectivity-QTLs as iQTLs that are significantly associated with concordant genotype-dependent changes in chromatin contacts over a broad genomic region (e.g., GWAS SNP in the <em>RNASET2</em> locus). Our results demonstrate the importance of chromatin contacts as a complementary modality for QTL mapping and their power in identifying novel classes of QTLs linked to cell-specific gene expression and connectivity.</span></span></p> <p> </p> <p><span><span>This repository contains the source code, supplementary datasets for the manuscript (Nature Communications 2024).</span></span></p>
ScienceDex guides
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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.