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147 results for “chemical diversity”
Inter-Chemical Correlation results for the study: HHEARx2018-2537 (Phthalates and childhood obesity in a racially, ethnically and geographically diverse cohort.)
Title: Phthalates and childhood obesity in a racially, ethnically and geographically diverse cohort. <br>Species: Homo sapiens <br>Number of samples: 630 <br>Number of named analytes: 16 <br>Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=66 <br>
Data and code from: SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration
<h1>TMAP of COCONUT database</h1> <p>The script and data used in SIDERITE paper to generate TMAP picture (Figure S3 in supplementart material).</p> <p>Requirement: tmap</p> <p>You can install tmap by conda.</p> <blockquote> <p>conda create -n tmap python=3.7</p> <p>conda activate tmap</p> <p>conda install -c tmap tmap</p> <p>pip install faerun</p> <p>pip install matplotlib</p> <p>conda install scipy</p> <p>conda install -c rdkit rdkit</p> <p>conda install -c conda-forge mhfp</p> </blockquote> <p> </p> <p>Usage: python plot_COCONUT.py</p> <p>Then it will use COCONUT.csv to generate index.html and index.js. Open index.html to see result.</p> <h1>Other large input files</h1> <p>Tanimoto_COCONUT_SIDERITE.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/predicted_new/Clustering_coconut.m">SIDERITE/predicted_new/Clustering_coconut.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>Sid_structure_output3.xlsx is used in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/statistics/Figure1.m" target="_blank" rel="noopener">SIDERITE/statistics/Figure1.m at main · RuolinHe/SIDERITE</a>, <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a> and <a href="https://github.com/RuolinHe/SIDERITE/blob/main/siderophore_process/Sid_process_code.m" target="_blank" rel="noopener">SIDERITE/siderophore_process/Sid_process_code.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>COCONUT4MetFrag_Canonical.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a>.</p> <p> </p> <p>COCONUT_r.txt is the output file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/tmap_code.m" target="_blank" rel="noopener">SIDERITE/TAMP/tmap_code.m at main · RuolinHe/SIDERITE</a>. and the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/predicted_new/isSiderophore1.py" target="_blank" rel="noopener">SIDERITE/predicted_new/isSiderophore1.py at main · RuolinHe/SIDERITE.</a></p> <p> </p> <p>COCONUT4MetFrag.xlsx is the input file in <a href="https://github.com/RuolinHe/SIDERITE/blob/main/TAMP/CheckSMILES2.py" target="_blank" rel="noopener">SIDERITE/TAMP/CheckSMILES2.py at main · RuolinHe/SIDERITE</a>.</p> <p> </p>
Fig. 3 in Diversity Of Mosquitoes (Diptera, Culicidae) And Physico-Chemical Characterization Of Their Larval Habitats In Tizi-Ouzou Area, Algeria
Fig. 3. Mosquito breeding sites (site 01, a; site 02, b; site 03, c; site 04, d; site 05, e; site 06, f); site 07, g).
A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors
<p>The development of methods to engineer and immobilize amine transaminases (ATAs) to improve their functionality and operational stability is gaining momentum. The quest for robust, fast, and easy-to-use methods to screen the activity of large collections of transaminases, is essential. This work presents a novel and multiplex fluorescence-based kinetic assay to assess ATA activity using 4-dimethylamino-1-naphthaldehyde as an amine acceptor. The developed assay allowed us to screen a battery of amine donors using free and immobilized ATAs from different microbial sources as biocatalysts. As a result, using chromatographic methods, 4-hydroxybenzylamine was identified as the best amine donor for the amination of hydroxy methyl furfural. Finally, we adapted this method to determine the apparent Michaelis-Menten parameters of a model immobilized ATA at the microscopic (single-particle) level. Our studies promote the use of this multiplex, multidimensional assay to screen ATAs for further improvement.</p>
Changes in community-weighted trait mean, functional diversity, soil chemical properties and temperature along an elevational gradient in Tenerife, Canary Islands
<p>This dataset comprises community-weighted trait means and functional diversity of leaf traits, chemical soil properties and temperature recorded in roadside (disturbed) and interior (less disturbed) plots, along an elevational gradient of 2,300 m in Tenerife, Canary Islands. The leaf traits measured were specific leaf area (SLA), nitrogen, nitrogen to phosphorus ratio, leaf dry matter content (LDMC) and carbon to phosphorus ratio. The soil chemical properties measured were pH, nitrogen, nitrogen to phosphorus ratio, carbon to phosphorus ratio, calcium, potassium, magnesium and cation exchange capacity. Also the scores of the three first axes derived from a PCA analysis including the soil chemical properties are included. The temperature variables consist of bioclimatic variables Bio10 (mean temperature of the warmest quarter) and Bio11 (mean temperature of the coldest quarter). This dataset has been used for the analysis presented in Ratier Backes et al. (2021).</p>
Fig. 2 in Diversity Of Mosquitoes (Diptera, Culicidae) And Physico-Chemical Characterization Of Their Larval Habitats In Tizi-Ouzou Area, Algeria
Fig. 2. Study sites location (1— Irdjen; 2 — Ouadhia; 3 — Beni Yenni; 4 — Iboudraren).
Invasive plant species that experience lower herbivory pressure may evolve lower diversities of chemical defence compounds in the exotic range
<p><strong>ABSTRACT</strong></p> <p><strong>PREMISE</strong></p> <p>Invasive plant species often escape from specialist herbivore species and are likely to experience herbivory mostly from generalist herbivore species in the exotic range. Consequently, the Shifting Defence Hypothesis (SDH) predicts that invasive plants will express higher concentrations of qualitative defence compounds to deter dominant generalist herbivores in the exotic range. Here, I additionally propose a Reduced Chemical Diversity Hypothesis (RCDH), which predicts that reduced herbivory pressure will select for invasive plant genotypes that produce lower diversities of defence compounds in the exotic range.</p> <p><strong><span>METHODS</span></strong></p> <p>I tested whether: (1) Invasive <em>Brassica nigra</em> populations express a lower diversity and an overall higher concentration of glucosinolate compounds than native-range <em>B. nigra</em>; (2) <em>Brassica nigra</em> individuals that express high diversities and concentrations of glucosinolates are more attractive to specialist and deterrent to generalist herbivores; (3) Tissues of invasive <em>B. nigra </em>are less palatable to two generalist herbivores <em>Theba pisana</em> and <em>Helix aspersa</em> than tissues of native-range<em> B. nigra</em>.</p> <p><strong><span>RESULTS</span></strong></p> <p>Invasive <em>B. nigra </em>populations expressed a significantly lower diversity of glucosinolate compounds and a marginally higher concentration of total glucosinolate compounds. Leaf tissues of the invasive <em>B. nigra</em> were significantly less palatable to <em>T. pisana</em> and marginally less so to <em>H. aspersa</em>. <em>Brassica nigra</em> individuals that expressed high concentrations of total glucosinolate compounds were visited by a low diversity of generalist herbivore species in the field.</p> <p><strong><span>CONCLUSIONS</span></strong></p> <p>The biogeographical differences in glucosinolate profiles of invasive and native-range populations of <em>B. nigra</em> may be the result of differential herbivore selection pressures in the respective ranges.</p>
The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity - dataset
<p>Dataset to paper: Błońska E., Jankowiak R., Lasota J., Krzemińska N., Zbyryt A., Ciach M. 2024. The role of chemical properties of the material deposited in nests of white stork in shaping enzymatic activity and fungal diversity. Environmental Science and Pollution Research 31, 2: 2583-2594. https://doi.org/10.1007/s11356-023-31383-x</p> <p>This study was financially supported by the National Science Centre, Poland (grant no. 2021/41/B/NZ8/03456).</p>
Accompanying dataset for: "IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues"
<p>These datasets were acquired using either the manual or automated IBEX multiplex imaging protocols and accompany the manuscript “IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, A. Radtke <em>et al.</em>, 2021, Nature Protocols.</p> <p>All image data are stored using the <a href="https://imaris.oxinst.com/support/imaris-file-format">Imaris file format</a>. To view these multi-channel images, you can either use one of these <strong>free</strong> viewers, <a href="https://imaris.oxinst.com/imaris-viewer">Imaris viewer</a>, <a href="https://imagej.net/Fiji">Fiji</a>.</p> <p>Each experiment has an associated imaging meta-data file in xlsx format and the resulting image in Imaris format.</p> <p><strong>Human Jejunum (Automated)</strong></p> <p>Dataset is a 24 parameter IBEX experiment performed on a human jejunum section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Kidney (Automated)</strong></p> <p>Dataset is a 16 parameter IBEX experiment performed on a human kidney Formalin-Fixed Paraffin-Embedded (FFPE) section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Lymph Node (Automated)</strong></p> <p>Dataset is a 25 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Skin (Automated)</strong></p> <p>Dataset is an 18 parameter IBEX experiment performed on a human skin section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Thunder 3D Cell Culture microscope with a high precision (Quantum) stage, a high quantum efficiency sCMOS camera (DFC9000 GTC), and a 40x (1.3) NA oil objective. The light source was an LED8 with 8 individual LED lines for excitation with millisecond triggering. All images were captured at a 16-bit depth with the following pixel dimensions: x (0.160 μm), y (0.160 μm), and z (1 μm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.7.1.21655).</p> <p><strong>Human Liver (Manual)</strong></p> <p>Dataset is a 22 parameter IBEX experiment performed on a human liver section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Human Lymph Node (Manual)</strong></p> <p>Dataset is a 38 parameter IBEX experiment performed on a human lymph node section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p> <p><strong>Human Spleen (Manual)</strong></p> <p>Dataset is a 25 parameter IBEX experiment performed on a human spleen section labeled with the nuclear marker Hoechst and antibodies directed against the indicated markers. Images were acquired using an inverted Leica TCS SP8 X confocal microscope equipped with a 40X objective (NA 1.3), 4 HyD and 1 PMT detectors, a white light laser that produces a continuous spectral output between 470 and 670 nm as well as 405, 685, and 730 nm lasers. All images were captured at an 8-bit depth, with a line average of 3, and 1024x1024 format with the following pixel dimensions: x (0.284 µm), y (0.284 µm), and z (1 µm). Images were tiled and merged using the LAS X Navigator software (LAS X 3.5.5.19976).</p>
Rapid and chemically diverse C transfer from trees to mycorrhizal fruit bodies in the forest
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Changes in community-weighted trait mean, functional diversity, soil chemical properties and temperature along an elevational gradient in Tenerife, Canary Islands
Open the record for dataset details and reuse information.
Invasive plant species that experience lower herbivory pressure may evolve lower diversities of chemical defence compounds in the exotic range
Open the record for dataset details and reuse information.
ToPoRg-18k: dataset of single-chain radii of gyration distribution for 18,450 architecturally diverse and chemically patterned coarse-grained polymers
<blockquote> <p>Revision: This revision includes four independent trajectory values of the ensemble averages of the mean squared radii of gyration and their standard deviations, which can be used to compute statistical measures such as the standard error.</p> </blockquote> <p>This distribution provides access to 18,450 configurations of coarse-grained polymers. The data is provided as a serialized object using the `pickle' Python module and in csv format. The data was compiled using Python version 3.8. </p> <p><strong>References<br></strong>The specific applications and analyses of the data are described in <br>1. Jiang, S.; Webb, M.A. "Physics-Guided Neural Networks for Transferable Prediction of Polymer Properties"</p> <p><strong>Data<br></strong>There are seven .pickle files that contain serialized Python objects.</p> <ul> <li><strong>pattern_graph_data_*_*_rg_new.pickle</strong>: squared radii of gyration distribution from MD simulation. The number indicates the molecular weight range.</li> <li><strong>rg2_baseline_*_new.pickle</strong>: squared radii of gyration distribution from Gaussian chain theoretical prediction.</li> <li><strong>delta_data_v0314.pickle</strong>: torch_geometric training data.</li> </ul> <p><strong>Usage</strong><br>To access the data in the .pickle file, users can execute the following:</p> <blockquote> <p># LOAD SIMULATION DATA<br>DATA_DIR = "your/custom/dir/"<br>mw = 40 # or 90, 190 MWs</p> <p>filename = os.path.join(DATA_DIR, f"pattern_graph_data_{mw}_{mw+20}_rg_new.pickle")<br>with open(filename, "rb") as handle:<br> graph = pickle.load(handle)<br> label = pickle.load(handle)<br> desc = pickle.load(handle)<br> meta = pickle.load(handle)<br> mode = pickle.load(handle)<br> rg2_mean = pickle.load(handle)<br> rg2_std = pickle.load(handle) ** 0.5 # var</p> <p># combine asymmetric and symmetric star polymers<br>label[label == 'stara'] = 'star'<br># combine bottlebrush and other comb polymers<br>label[label == 'bottlebrush'] = 'comb' </p> <p># LOAD GAUSSIAN CHAIN THEORETICAL DATA<br>with open(os.path.join(DATA_DIR, f"rg2_baseline_{mw}_new.pickle"), "rb") as handle:<br> rg2_mean_theo = pickle.load(handle)[:, 0]<br> rg2_std_theo = pickle.load(handle)[:, 0]</p> </blockquote> <ul> <li><strong>graph</strong>: NetworkX graph representations of polymers.</li> <li><strong>label</strong>: Architectural classes of polymers (e.g., linear, cyclic, star, branch, comb, dendrimer).</li> <li><strong>desc</strong>: Topological descriptors (optional).</li> <li><strong>meta</strong>: Identifiers for unique architectures (optional).</li> <li><strong>mode</strong>: Identifiers for unique chemical patterns (optional).</li> <li><strong>rg2_mean</strong>: Mean squared radii of gyration from simulations.</li> <li><strong>rg2_std</strong>: Corresponding standard deviation from simulations.</li> <li><strong>rg2_mean_theo</strong>: Mean squared radii of gyration from theoretical models.</li> <li><strong>rg2_std_theo</strong>: Corresponding standard deviation from theoretical models.</li> </ul> <p><strong>Help, Suggestions, Corrections?</strong><br>If you need help, have suggestions, identify issues, or have corrections, please send your comments to Shengli Jiang at sj0161@princeton.edu</p> <p><strong>GitHub</strong><br>Additional data and code relevant for this study is additionally accessible at <a href="https://github.com/webbtheosim/gcgnn">https://github.com/webbtheosim/gcgnn</a> </p>
Chemical Diversity of Filamentous Benthic Cyanobacteria
<p><span>Genomic and chemical analysis has revealed that numerous species of filamentous cyanobacteria harbor complex secondary metabolisms tailored to their particular ecological niche. The metabolomic analysis of strains isolated and cultivated from cyanobacterial benthic mats has the potential to expand the library of marine algal-derived natural products. Strains were isolated from phytobenthos collected from coral reefs in Abrolhos, Brazil and Ishigaki, Japan. Phylogenetic analysis of isolates shows high similarity to previously-described members of benthic mats and also suggests the geographic expansion of the </span><span>Adonisia</span><span> lineage. Chemical analysis by LC-HRMS and data processing via MZmine and FBMN-GNPS of environmental samples and isolated cyanobacterial strains confirmed the presence of a wide chemical diversity. In addition, similarity analysis applying DBsimilarity indicated the broad coverage of various biosynthetic and chemical classes of compounds previously reported for cyanobacteria. </span></p>
Evolution of binary gender and geographic diversity in the editorial boards of Geochimica et Cosmochimica Acta and Chemical Geology
<p>Dataset from article</p> <p><strong>Evolution of diversity in the editorial boards of <em>Geochimica et Cosmochimica Acta </em>and <em>Chemical Geology</em> </strong></p> <p>by Pourret et al. published in European Science Editing</p>
Chemical Diversity of Cyanobacterial Natural Products (2010-2023)
<p>Cyanobacterial natural products reported from 2010 to 2023.</p> <p> </p>
Screening of 165,988 compounds reflecting biological and chemical diversity in the Janssen Library for anti-SARS-CoV-2 activity
<p>This report describes the most relevant results of screening a diversity set of the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 in a stable eGFP-expressing VeroE6 cell line infected with SARS-CoV-2.</p>
Figure 16 in Fossil diversity in 'dawn' hexapods (Diplura: Projapygoidea), with direct evidence for being chemically predaceous in the Cretaceous
Figure 16. Scanning electron micrographs of the secretion. A, distal end of the infudibuliform complex with the extruded filaments. B, C, detail of filaments showing the granular surface.
Figure 15 in Fossil diversity in 'dawn' hexapods (Diplura: Projapygoidea), with direct evidence for being chemically predaceous in the Cretaceous
Figure 15. Scanning electron micrographs of the cerci of Recent projapygids (genera indet.) expelling the glandular substance. A–C, different magnifications of cerci of a specimen from Brazil showing the solidified secretion forming filamentous masses. D, distal part of cerci of a Costa Rican specimen showing an incipient secretion. Arrows indicate the glandular substance in C and D. In A, the box labelled B corresponds to panel B; In B, the box labelled C corresponds to panel C. Abbreviations: ids, infundibuliform distal segment; ipds, infundibuliform predistal segment; ss, simple setae; tp, longitudinal tegumentary pleats. Scale bars: 1 mm in A; 0.2 mm in B; 0.05 mm in C, D.
Figure 14 in Fossil diversity in 'dawn' hexapods (Diplura: Projapygoidea), with direct evidence for being chemically predaceous in the Cretaceous
Figure 14. Palaeoecological reconstruction of Electroprojapyx alchemicus gen. et sp. nov, using their cerci as chemical weapons for hunting a springtail in the Cretaceous amber forest. Illustration by O. Sanisidro, with scientific supervision.
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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.