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Supporting files for manuscript: Effect of the coordination environment on the ability of iron to bind/activate N2: relevance to the nitrogenase mechanism

Supporting files for manuscript 'Effect of the coordination environment on the ability of iron to bind/activate N2: relevance to the nitrogenase mechanism':  input files, optimized structures, checkpoint files usable for molecular orbital diagrams.

Data for the manuscript named 'Altitude-dependence response near cusp region after solar wind variations'

Data for the manuscript named 'Altitude-dependence response near cusp region after solar wind variations 1) cluster data, observation from cluster mission 2) MAD6400_2001-10-12_tau1a_59.4@vhfa_041292, EISCAT radar data 3) OMNI: solar wind and IMF data 4) p_shell_5.7Re_011012 is thermal pressure at 5.7 Re-shell, which was carried out in real-time solar wind conditions during 08:30-10:00UT (real-time-density run) 5) p_shell_5.7Re_011012cd is thermal pressure at 5.7 Re-shell, which was carried out in real-time solar wind conditions except for solar wind density  during 08:30-10:00UT (no-density-increasing run)  “1_5.7Rshell_out.txt”time_latitude_out “1P_shell_5.7Re.csv”time_shell_5.7Re data range: MLT 08:00~16:00, latitude -90°~ -30°

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>

Appendix Data for Manuscript : Application of OSL surface exposure dating with the use of two-dimensional OSL laser scanning instruments and energy-dispersive x-ray spectroscopy

Appendix Data for Manuscript 'Application of OSL surface exposure dating with the use of two-dimensional OSL laser scanning instruments and energy-dispersive x-ray spectroscopy'.

R scripts for manuscript "The circulating phageome reflects bacterial infections"

These are documents and an R script associated with the manuscript "The circulating phageome reflects bacterial infections". These include: 1. allphagedf_seqids.csv which is a table including number of BLAST hits to unique phage Genbank IDs by sample. The samples used in this table are the 71 (61 septic, 10 asymptomatic controls) sequenced in this study. The rows of this table correspond to samples (rownames are library IDs) and columns correspond to all identified phage Genbank IDs from the blast output. 2. Phageome Summaries.RMD which is an R markdown document which demonstrates i) processing of blast output into a new allphagedf_seqids document, ii) use of the phage dictionary to summarize representation of phage taxonomic families as well as host genuses, and iii) use of the coliphage dictionary to assess how E. coli phages represent known host bacterial characteristics across samples. 3. Readme.txt which summarizes the above as well as provides links to other relevant data.

AMPSphere pre-computed resources and auxiliary files for the manuscript codes

AMPSphere is a comprehensive catalog of antimicrobial peptides predicted using Macrel (DOI: 10.7717/peerj.10555) from 63,410 public metagenomes, ProGenomes v2.2 database (82,400 high-quality microbial genomes), and c.a. 4k non-whitelisted microbial genomes from NCBI. Currently, AMPSphere is available as a web resource at https://ampsphere.big-data-biology.org/. AMPSphere v.2022-03 contains 863,498 sequences (avg length: 36 amino acids, range 8-98). DRAMP database was used to find confirmed sequences with strict homology to reference. This approach showed that 2,488 peptides were previously confirmed in our dataset. The present repository is a data dump for the precomputed resources and files needed for its generation and analysis as a complement to the GitHub repository. The complementary documentation is also available for each one of the files. To use the files just download them and apply the command `untar` to decompress the folders.

Data used to create figures and tables in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China"

This dataset contains all simulation output and observational data of ground-based/satellite-retrieved meteorological and air quality for computing statistical metrics in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China", as follows: 1. Simulation and observational results of meteorological and air quality including four folders:      Day_PBLH: Daily PBLH data      Hour_air: Hourly air quality data regarding PM2.5, O3, SO2, NO2 and CO      Hour_met: Hourly meteorological data regarding T2, Q2, RH2, WS10 and precipitation      Hour_radiation: Hourly surface radiation data 2. Simulation and satellite-retrieved results of meteorological and air quality including nine folders:     AOD: Yearly and seasonal AOD data     CF: Yearly and seasonal CF data     CO: Yearly and seasonal CO data     LWP: Yearly and seasonal LWP data     NO2: Yearly and seasonal NO2 data     O3: Yearly and seasonal O3 data     Precipitation: Yearly and seasonal precipitation data     Radiation: Yearly and seasonal radiation data     SO2: Yearly and seasonal SO2 data

Dataset for manuscript "Host-related and environmental factors influence long-term ectoparasite infestation dynamics of mouse lemurs in northwestern Madagascar" to be published in the American Journal of Primatology

This Excel-file contains three datasets, corresponding to the initial raw dataset resulting from all ectoparasite inspections (n = 2,241), the merged dataset used for host-related and temporal modeling (n = 1940), and the even more condensed dataset with one datapoint per individual used for climatic modeling (n = 583), respectively.

Dataset and R code for the manuscript: Interspecific facilitation favors rare species establishment and reduces performance disparities among adults

The following directory contains the data necessary to replicate the results obtained in the manuscript entitled: Interspecific facilitation favors rare species establishment and reduces performance disparities among adults. We provided an R workspace containing the data "Dataset1.RData", a "ReadMe.txt" archive with detailed information on the variables included in "Dataset1.RData", and the R code necessary to replicate the results ("Rcode1.txt")

Supplementary data for the manuscript titled 'Energy metabolism and aerobic respiratory chain of Vitreoscilla sp. C1: Comparison with beta-proteobacteria'

This dataset contains the supplementary data files for the manuscript titled, 'Energy metabolism and aerobic respiratory chain of Vitreoscilla sp. C1: Comparison with beta-proteobacteria.'

Dataset for Manuscript: Comparing Urban Anthropogenic NMVOC Measurements with Representation in Emission Inventories - A Global Perspective

Urban observations of individual NMVOCs and the calculated or reported emission ratios used for comparison to emission inventories.

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor" by Jie Heng, Yunfei Hu, Guillermo Pérez-Hernández, Asuka Inoue, Jiawei Zhao, Xiuyan Ma, Xiaoou Sun, Kouki Kawakami, Tatsuya Ikuta, Jienv Ding, Yujie Yang, Lujia Zhang, Sijia Peng, Xiaogang Niu, Hongwei Li, Ramon Guixà-González, Changwen Jin, Peter W. Hildebrand, Chunlai Chen & Brian K. Kobilka Nature Communications 2023, <a href="https://doi.org/10.1038/s41467-023-37233-1">https://doi.org/10.1038/s41467-023-37233-1</a> The representative molecular dynamics (MD) trajectories shown in the Supplementary Fig. 8, Variable contacts of the β2AR CT can be 3D visualized in the browser in the following link: <ul> <li><a href="https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl"> https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl</a></li> </ul>

opencc-by-4.0Apr 2024View details →

Datasets for the manuscript "Metabolomic and Sphingolipidomic Profiling of Human Hepatoma Cells Exposed to Widely Used Pharmaceuticals"

See experimental details on the main text of the manuscript "Metabolomic and Sphingolipidomic Profiling of Human Hepatoma Cells Exposed to Widely Used Pharmaceuticals" <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jpba.2024.116378" target="_blank" rel="noreferrer noopener">https://doi.org/10.1016/j.jpba.2024.116378</a> <h2>Data description</h2> This study investigates the impact of three commonly used pharmaceuticals (amoxicillin, carbamazepine, and trazodone) on human liver cells. To mimic real-world conditions, liver cells were encapsulated in spheroids and exposed to various concentrations of these drugs for 24 hours. The study employs metabolomic and sphingolipid analyses to identify metabolic changes induced by drug exposure. <div></div> <div> <div> <div> <h3>LC-MS/MS Method for Sphingolipid Analysis</h3> Targeted sphingolipid analysis was conducted using a Waters ACQUITY UPLC System coupled to a Waters Xevo TQ-S system equipped with an Electrospray Ion Source (ESI) and ScanWave™ collision cell technology, operating in positive mode [16]. Sphingolipids were quantified using a Zorbax Rapid Resolution RRHD C18 Column (80 Å, 1.8 µm, 2.1 mm × 100 mm). <h3>LC-HRMS Method for Semi-Targeted Metabolomic Analysis</h3> LC-HRMS analysis was performed on an Agilent 1290 Affinity II HPLC system coupled to an Agilent 6550 iFunnel QTOF mass spectrometer equipped with a dual AJS electrospray ionization source operating in both positive and negative modes. Polar metabolite screening was conducted using a SeQuant® ZIC®-pHILIC 5 µm polymer 100 × 2.1 mm column. </div> </div> </div>   <h2>Funding</h2> The research leading to these results has received funding from the Spanish Ministry of Science and Innovation MCIN/AEI/ 10.13039/501100011033, Grants CTQ2017-82598-P and CEX2018-000794-S. The authors also want to grant support from the Catalan Agency for Management of University and Research Grants (AGAUR, Grant 2017SGR753). Miriam Pérez-Cova acknowledges a predoctoral FPU 16/02640 scholarship from the Spanish Ministry of Education and Vocational Training (MEFP), and Post-graduate department from CSIC for the funding of the research stay in Karolinska Institute, via the award to best outreach video in the YoInvestigoYosoyCsic contest, 2019 edition.

Dataset for "The VLF Transmitter, Narrowband Receiver, and Tuner Investigation on the DSX Spacecraft" manuscript

Dataset for "The VLF Transmitter, Narrowband Receiver, and Tuner Investigation on the DSX Spacecraft" publication submitted to JGR Space Physics

Data for the manuscript "Ion-mediated condensation controls the mechanics of mitotic chromosomes"

Data accompanying the manuscript "Ion-mediated condensation controls the mechanics of mitotic chromosomes". Each folder contians data to one set of experiments together with scripts to analyse the data and produce plots.

Data set related to the manuscript "Investigating particle size effects on NMR spectra of ions diffusing in porous carbons through a mesoscopic model"

Graphical files in the agr format for all the figures in the manuscript entitled "Investigating particle size effects on NMR spectra of ions diffusing in porous carbons through a mesoscopic model". Examples of input files for the lattice simulations are also provided.

Data used to simulations in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China"

This dataset contains input data of simulations by WRF-CMAQ, WRF-Chem and WRF-CHIMERE in the GMD manuscript "Inter-comparison of multiple two-way coupled meteorology and air quality models (WRF v4.1.1-CMAQ v5.3.1, WRF-Chem v4.1.1 and WRF v3.7.1-CHIMERE v2020r1) in eastern China", as follows: 1. WRF-CMAQ input data including emission, ICs and lateral BCs of meteorology and air quality: YYYYMM.zip represents the input data for each month for simulations. Due to the large size of the compressed file containing input data each month, there may be interruptions when uploading it to Zenodo. Therefore, we will split each compressed file into 50MB. If users want to browse the file, they can download the segmented files, and then merge them into the YYYYMM.zip file using the Linux command line "unzip 'YYYYMM.zip.*' -d combined"

Online supplement to manuscript: "Ability of ChatGPT to generate competent radiology reports for distal radius fracture by use of RSNA template items and integrated AO classifier." Current problems in diagnostic radiology (2023).

Online supplement to manuscript:  Bosbach, Wolfram A., Jan F. Senge, Bence Nemeth, Siti H. Omar, Milena Mitrakovic, Claus Beisbart, András Horváth, Johannes Heverhagen, and Keivan Daneshvar. "Ability of ChatGPT to generate competent radiology reports for distal radius fracture by use of RSNA template items and integrated AO classifier." Current problems in diagnostic radiology (2023). <a href="https://doi.org/10.1067/j.cpradiol.2023.04.001">doi.org/10.1067/j.cpradiol.2023.04.001</a>

MMCFSv2 and MMCFSv1 Processed data for GMD Manuscript

This dataset was used to make all the plots in the manuscript titled "Monsoon Mission Coupled Forecast System Version 2.0: Model Description and Indian Monsoon Simulations" submitted to GMD

Simulations for manuscript Unravelling the forcing and feedbacks contributing to Pliocene Arctic warming in EC-Earth simulations

Nine PlioMIP2 experiments were conducted to investigate the mid-Pliocene Arctic climate. These experiments considered three CO2 levels (280, 400 and 560 ppm), modern or Pliocene ice sheet conditions in Greenland and Antarctica and either prescribed or dynamic vegetation. Simulations were performed by the EC-Earth3-LR Veg climate model with a horizontal resolution of ~1.125°. The dataset contains selected output data from the simulations. Simulations were run for 1000 years. The last 200 years were used for analysis after the model reached an equilibrium as measured by global surface air temperature trend less than 0.05 K per century.  The dataset contains Earth system model results from EC-Earth3 presented in the study by Power et al. (2023).