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Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"

The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making. All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow. The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a> The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a> To obtain maximum compression of the data, the tar command used to generate this tarball was: <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre>

opencc-by-nc-4.0Mar 2023View details →

Image Supplement to Hounshell, "Lines, Points, Waves, Streams. Mapping Ethnographic Types in Swiss Hausforschung, 1880s–1950s"

General description: The images in this repository are provided as a color supplement to the figures printed in black and white or otherwise mentioned in the following article: Eric Hounshell, “Lines, Points, Waves, Streams. Mapping Ethnographic Types in Swiss Hausforschung, 1880s–1950s,” Historische Anthropologie 31:1 (2023), 130-164 [DOI forthcoming]. All images are credited to Jakob Hunziker (1827-1901). Image References: Fig. 1: Die Verbreitung der Hausformen in der Schweiz, in: Jakob Hunziker, Das Schweizerhaus nach seinen landschaftlichen Formen und seiner geschichtlichen Entwicklung, Aarau 1914, volume 8. Fig. 2: Untitled, in: Folder AG54.198, Jakob Hunziker Nachlass, Staatsarchiv Aargau. Appendix 1: Bedachung, in: Folder AG54.198, Jakob Hunziker Nachlass, Staatsarchiv Aargau. Appendix 2: Untitled, in: Folder AG54.198, Jakob Hunziker Nachlass, Staatsarchiv Aargau. Appendix 3: Untitled, in: Folder AG54.198, Jakob Hunziker Nachlass, Staatsarchiv Aargau.

opencc-by-4.0Sep 2022View details →

Data From: B1 Field inhomogeneity correction for qDESS T2 mapping: application to rapid bilateral knee imaging

Purpose: T2 mapping is a powerful tool for studying osteoarthritis (OA) changes and bilateral imaging may be useful in investigating the role of between-knee asymmetry in OA onset and progression. The quantitative double-echo in steady-state (qDESS) can provide fast simultaneous bilateral knee T2 and high-resolution morphometry for cartilage and meniscus. The qDESS uses an analytical signal model to compute T2 relaxometry maps, which require knowledge of the flip angle (FA).  In the presence of B1 inhomogeneities, inconsistencies between the nominal and actual FA can affect the accuracy of T2 measurements. We propose a pixel-wise B1 correction method for qDESS T2 mapping exploiting an auxiliary B1 map to compute the actual FA used in the model.   Methods: The technique was validated in a phantom and in vivo with simultaneous bilateral knee imaging.  T2 measurements of femoral cartilage (FC) of both knees of six healthy participants were repeated longitudinally to investigate the association between T2 variation and B1. Results: The results showed that applying the B1 correction mitigated T2 variations that were driven by B1 inhomogeneities.  Specifically, T2 left-right symmetry increased following the B1 correction (rc = 0.74 > rc = 0.69). Without the B1 correction, T2 values showed a linear dependence with B1. The linear coefficient decreased using the B1 correction (from 24.3 \(\pm\) 1.6 ms to 4.1 \(\pm\) 1.8) and the correlation was not statistically significant after the application of the Bonferroni correction (p-value > 0.01).   Conclusion: the study showed that B1 correction could mitigate variations driven by the sensitivity of the qDESS T2 mapping method to B1, therefore increasing the sensitivity to detect real biological changes. The proposed method may improve the robustness of bilateral qDESS T2 mapping, allowing for an accurate and more efficient evaluation of OA pathways and pathophysiology through longitudinal and cross-sectional studies. This repository contains the raw data for reproducing the results reported in the paper. The data are provided in NIFTI format. The repository also contains the MALTAB scripts used to compute B1 maps from the NIFTI data.

Data set to: Mapping a brain parasite: occurrence and spatial distribution in fish encephalon

Data for the manuscript "Mapping a brain parasite: occurrence and spatial distribution in fish encephalon", doi: 10.1016/j.ijppaw.2023.03.004. Description of the distribution of metacercariae from the trematode species Cardiocephaloides longicollis in the brain of fish.

opencc-zeroMar 2023View details →

dryad36/100

POI-based land use map for Africa

The combination of spatial distribution, semantic characteristics, and sometimes temporal dynamics of POIs inside a geographic region can capture its unique land use characteristics. We developed a scalable POI-based land use modeling framework. By combining POIs with a neural network language model, we developed a spatially explicit approach to learn the embedding representation of POIs and AOIs. We trained supervised classifiers using AOI embeddings as input features to predict AOI land use at different semantic granularities.

openMar 2023View details →

Argument maps as tools to support the development of new media literacies: a systematic review.

The post-digital era is characterized by the vast presence of platforms imposing their digital affordances and algorithmic control on our behavior. This environment is challenging education and training, with implications for digital and transmedial literacy. Investigating instructional methodologies is crucial to foster critical comprehension of such novel informational environments. The argument maps (AM), which were first created and evaluated in static information contexts (analogical/old web), could be useful in the emergence of dynamic (post-digital) textual forms. The current paper describes a comprehensive literature review based on the assumptions above. We looked into state of the art in research on using AM to handle dynamic information. We found 150 papers using a PRISMA procedure and then examined 25 of them. Our review produced pertinent data about the current state of AM, including the sorts of texts on which they are used and the tools (especially digital and AI-based) that have been employed. Our research lays the groundwork for teaching the literacies needed in new informational settings, such as multimodal, dynamic, algorithmic, and data-driven contexts, with a specific focus on AM as an effective mediational tool. This Zenodo record presents the full dataset composed of the following sheets: <ol> <li>Codebook</li> <li>Italian Journals</li> <li>List of articles extracted from SCOPUS</li> <li>List of articles extracted from ERIC</li> <li>List of articles extracted from WOS</li> <li>List of articles extracted from DOAJ</li> <li>PRISMA workflow</li> <li>Analysis - First Level (classification of 25 articles selected)</li> <li>Analysis - Second Level (List of 19 articles selected)</li> <li>Final Dataset</li> <li>Interrater Agreement.</li> </ol> As for the Keywords' Map, a primo file .txt displays the text over which basis was performed the keyword maps analysis. The second .txt file shows notes relating to the analysis procedures using the software VOS-Viewer <a href="http://www.vosviewer.com/">http://www.vosviewer.com/</a>  Any comments or improvements are welcome!

openDec 2022View details →

Sentinel-2 based maps of irrigated fields in Vojvodina, Serbia

This dataset consists of classified irrigated fields of the three most irrigated crops in Vojvodina (Serbia): maize, soybean, and sugar beet. Maps were generated for three years (2020, 2021, 2022), characterized by different climate conditions using Sentinel-2 satellite data and machine learning algorithms. All maps are in GIS format (.tiff) where label 0 corresponds to non-irrigated fields while label 1 corresponds to irrigated fields in Vojvodina and as if could be used for further research.

Shifting cultivation and other forest disturbance drivers maps in Laos

This dataset includes maps of shifting cultivation and other forest disturbance drivers in Laos. Annual map classes (numbers are class values): 1. Forest,   2. Plantation,   3. Non-forest,    4. Subtle disturbances  5. Severe drought,   6. New Plantation,   7. Deforestation,  8. Shifting cultivation The aggregate map classes (numbers are class values): 1.Stable forest, 2,Non-forest, 3.Shifting cultivation, 4.Deforestation, 5.New plantation Please cite the two references if you use the datasets: Chen, S., Woodcock, C. E., Saphangthong, T., & Olofsson, P. (2023). Satellite data reveals a recent increase in shifting cultivation and associated carbon emissions in Laos. Environmental Research Letters, 18(11), 114012. Chen, S., Olofsson, P., Saphangthong, T., & Woodcock, C. E. (2023). Monitoring shifting cultivation in Laos with Landsat time series. Remote Sensing of Environment, 288, 113507. Please visit https://github.com/shijuanchen/shift_cult and https://sites.google.com/view/shijuanchen/research/shift_cult for Google Earth Engine applications, visualization and more datasets.

opencc-by-4.0Nov 2022View details →

Analysis results reported in "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps"

Analysis results reported in "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps" (<a href="https://www.biorxiv.org/content/10.1101/2022.05.07.490900v1">biorxiv</a>) of <a href="https://doi.org/10.5281/zenodo.7299516">4i data</a>. Analysis of this dataset was done with <a href="https://pypi.org/project/campa/">CAMPA</a>, and all scripts to reproduce these results are available in the<a href="https://github.com/theislab/campa_ana"> CAMPA reproducibility repository</a>.

opencc-by-4.0Nov 2022View details →

4i dataset for "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps"

4i dataset described and analysed in "Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps" (<a href="https://www.biorxiv.org/content/10.1101/2022.05.07.490900v1">biorxiv</a>). Analysis of this dataset was done with <a href="https://pypi.org/project/campa/">CAMPA</a>. The data is in CAMPA-readable format; for more information on the data format, see the <a href="https://campa.readthedocs.io/en/develop/overview.html#data-format">CAMPA documentation</a> . The data contains preprocessed wells of 184A1 and HeLa cells with different chemical treatments and 43 channels. For more information on the data, see the <a href="https://github.com/theislab/campa_ana/blob/develop/workflow/00_setup_and_download_data.ipynb">CAMPA reproducibility repository</a>.

Gene/Protein BridgeDb ID Mapping Database (Ensembl Fungi 52)

Mapping databases derived from Ensembl Fungi 52. These files can be used with BridgeDb. This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

opencc-zeroMar 2021View details →

Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event TEST_EVENT Preliminary

Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event TEST_EVENT Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2020arXivNicePaper

opencc-zeroMar 2021View details →

Submitted Completed pointings to the Gravitational Wave Treasure Map for event TEST_EVENT

Attached in a .json file is the completed pointing information for 1 observation(s) for the EM counterpart search associated with the gravitational wave event TEST_EVENT. These observations were taken on the DLT40 instrument.

Gene/Protein BridgeDb ID Mapping Database (Ensembl 106)

Ensembl 106 derived ID mapping databases for use with BridgeDb. This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 52)

Mapping databases derived from Ensembl Plants 52. These files can be used with BridgeDb. This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts which were used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

Gene/Protein BridgeDb ID Mapping Database (Ensembl 107)

Ensembl 107 derived ID mapping databases for use with BridgeDb. This version doesn't have the issue of not could be searched using gene names (e.g. in PathVisio). The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

openother-openMar 2023View details →

Gene/Protein BridgeDb ID Mapping Database (Ensembl 108)

Ensembl 108 derived ID mapping databases for use with BridgeDb. The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>.

Marmoset Functional Maps, "A Vocalization-Processing Network in Marmosets"

Marmoset data and functional maps used in the article "A vocalization-processing network in marmosets". (Jafari et al., 2023)

opencc-zeroDec 2022View details →

dryad36/100

Data from: Genome-wide epitope mapping reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection

Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of infection. Vaccination is a key control measure and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin preparations. Subunit vaccines based on recombinant proteins offer significant advantages, as they can be designed to reduce reactogenicity and can be co-designed with defined antigen serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 ORFs in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different C. burnetii exposure statuses. However, C. burnetii exposure did result in more uniform seroreactivity across species. Through the implementation of three different vaccine candidate methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic, out of which 65 have been previously described. This is the first study to investigate seroreactivity against the entire C. burnetii genome presented as overlapping linear peptides and provides the basis for selection of antigen targets for next generation Q fever vaccines and diagnostic tests.

CRLC: Cross-resolution national-scale land-cover mapping based on noisy label learning: a case study of China

CRLC are the 10-meter resolution land cover maps for China in 2020 achieved by a deep classification network. The maps include eight land cover classes: 1: Cropland 2: Forest 3: Grass/shrubland 5: Wetland 6: Water bodies 8: Impervious 9: Bareland 10: Snow/ice   Reference: <pre>@article{liu2023cross, title={Cross-resolution national-scale land-cover mapping based on noisy label learning: A case study of China}, author={Liu, Yinhe and Zhong, Yanfei and Ma, Ailong and Zhao, Ji and Zhang, Liangpei}, journal={International Journal of Applied Earth Observation and Geoinformation}, volume={118}, pages={103265}, year={2023}, publisher={Elsevier} }</pre>