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opencc-by-4.0Sep 2020View details →

Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study

This is the code and associated data that was used to generate conclusions for the following manuscript published in Applied and Environmental Microbiology: DOI: 10.1128/AEM.02278-20 Implementation of ATP and Microbial Indicator Testing for Hygiene Monitoring in a Tofu Production Facility Improves Product Quality and Hygienic Conditions of Food Contact Surfaces: A Case Study Authors: Jonathan H. Sogin(a), Gabriela Lopez Velasco(b), Burcu Yordem(b), Cari K. Lingle(b), John M. David(b), Mario Cobo(a), Randy W. Worobo(a) (a)Department of Food Science, Cornell University, Ithaca, NY, USA (b)3M Company, St. Paul, MN, USA Address correspondence to Jonathan H. Sogin, jhs397@cornell.edu

opencc-by-4.0Nov 2023View details →

ATP Tennis dataset

This dataset contains various information about male tennis players in 2020-2023 and is publicly available.Most of the original data is stored in 3.1_ATP_info.xlsx and can be accessed on the ATP website. On separate sheets, it contains scores like aces, under pressure, breakpoints, etc., for the top players each year. Then, each sheet was preprocessed and converted to csv files.Additionally, heights_weights.csv contains data with heights and weights of tennis players, and final_rankings_{2020-2023}.csv contains rankings at the end of each corresponding year and, additionally, nationalities and ages of tennis players. However, since the year 2023 has not ended yet, we have little data for it.Finally, all the data was merged by year in merged_{2020-2023}.csv.

opencc-by-4.0Feb 2024View details →

All-atom molecular dynamics simulations of incomplete ATP synthase rotor rings with unusually high stoichiometry predicted by the AlphaFold2-based method

The trajectories of all-atom MD simulations of AlphaFold2 4, 11, 16 or 18-mer structures of the subunit c from Candidatus Kryptonium thompsoni (CKt_Nmer_lipid_mix_CHM36m_303K_500ns) and Thalassoglobus polymorphus (Tp_Nmer_lipid_mix_CHM36m_303K_500ns), and AlphaFold2 11-mer structure of the subunit c from Spinacia oleracea (So_11mer-c20_POPC_CHM36m_303K_300ns) in a lipid bilayer. Simulations have been performed using the CHARMM36m force field, running with the GROMACS 2022 package.

opencc-by-4.0Jun 2024View details →

F-Type ATP synthase rotor ring stoichiometry predictions

Stoichiometry prediction data for: 1) rotor rings with experimental structures available 2) representative c subunits 3) c subunits with unexpectedly high predicted stoichiometry 4) all c subunits via matching with corresponding representative sequence

opencc-by-4.0Mar 2023View details →

Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase

We have provided all the necessary files, outputs, as well as the ReadMe file for this work to be redone.

opencc-by-4.0Jul 2023View details →

Effect of burosumab on muscle function and strength, and rates of ATP synthesis in skeletal muscle in adults with X-linked Hypophosphatemia

Abstract Context: Burosumab, a neutralizing antibody to FGF23, is approved for the treatment of X-linked hypophosphatemia. In clinical trials burosumab improves symptoms of pain, fatigue and stiffness and improves performance on certain muscle function studies. Objective: Determine if burosumab would increase ATP synthesis in skeletal muscle of treatment-naïve adults with XLH and if so whether that correlated with improved muscle function. Methods: Ten symptomatic adults, who had not received any treatment for XLH for years, had ATP synthesis rates assessed in the soleus/gastrocnemius muscle complex of the right calf using the 31P magnetic resonance spectroscopy saturation transfer technique. Baseline muscle function tests and symptoms of pain, fatigue, stiffness and lower extremity joint pain were quantified. All participants were treated with burosumab, 1 mg/kg every four weeks for 12 weeks. ATP synthesis rates and muscle function tests were repeated 2-weeks (“peak”) and 4-weeks (“trough”) after the third dose of burosumab. Results: Pain, fatigue, stiffness and lower extremity joint pain all improved with treatment. Performance on the 6-Minute Walk and Sit to Stand tests also improved significantly. Performance on the Timed Up and Go test did not significantly improve (p = 0.057). Muscle strength, measured by dynamometry, did not change significantly in either the upper or lower extremities during the study. ATP synthesis rates did not change over the three months of study in the group as whole. In a sub-analysis comparing individuals whose performances on the 6-Minute Walk Test and Sit to Stand tests were at or better than the mean outcome for those tests, to those whose outcomes were below the mean, no difference was observed in the rate of change in ATP synthesis rates. Despite profound and prolonged hypophosphatemia at baseline, intracellular muscle concentrations of phosphorus were normal. Conclusion: The improvement in the 6-Minute Walk Test and Sit to Stand tests without any observed change in either upper or lower extremity muscle strength or ATP synthesis rates, suggests that improvement in pain, fatigue and stiffness may explain, at least in part, the improved performance on these two tests. The preserved intracellular phosphate levels suggests that adaptive mechanisms are present in skeletal muscle that insulate intracellular phosphorus from life-long FGF23-mediaed hypophosphatemia.

opencc-by-4.0Sep 2023View details →

MM and QMMM trayectories from "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations"

Here are provided two trayectories from the results of "Conformational Changes and ATP Hydrolysis in Zika Helicase. The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations". ZikaNS3h-MMtrajectory.nc contains a Molecular Mechanics MD simulation of the system with ATP bound to the active site. TS1-mech1-QMMMtrajectory.nc contains a QMMM MD simulation of the system with TS1 of the base-assisted mechanism bound to the active site. ZikaNS3h.prmtop is the parameter file.

opencc-by-4.0Apr 2023View details →

ATP synthase evolution on a cross-braced dated tree of life

AbstractThe timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19Ga) and bacterial (2.58-2.12Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.Repository Contents1_100Eukaryote_genomes.tar.gz: includes all protein sequence files for the 100 Eukaryotes sampled in this study. 2_Phylogenies.tar.gz: includes all files used for phylogenetic analyses. Folders are organized as follows: <ul><li>1_ATPsynthase_gene_trees: this folder contains all sequence, alignment, and tree files for the ATP synthase gene trees. Files are organized as follows and are associated with the corresponding parts of the manuscript: Figure 3, Figure 5B, Supplementary Figures 5-10, Supplementary Figures 18-19<ul><li>Folder '1_sequences' includes all unaligned fasta sequence files for each ATP synthase gene tree (see Methods)</li><li>Folder '2_alignments' includes all alignments generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with BMGE (subdirectory: 2_trimmed)</li><li>Folder '3_treefiles' includes all IQ-TREE2 output files for all ATP synthase gene phylogenies. Any files with suffix *taxa.treefile contain the full taxonomic string for each accession. </li><li>Folder '4_pdfs' includes PDF files for each ATP synthase gene tree</li></ul></li><li>2_Eukaryotic_subsets: this folder contains all sequence, alignment, and tree files for ATP synthase Eukaryotic subset gene trees. Files are organized as follows and are associated with the corresponding parts of the manuscript: Supplementary Figure 11 <ul><li>Folder '1_sequences' includes all unaligned fasta sequence files for the eukaryotic subsets.</li><li>Folder '2_alignments' includes all alignments generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with BMGE (subdirectory: 2_trimmed).</li><li>Folder '3_treefiles' includes all Bayesian trees inferred for eukaryotic subsets.</li><li>Folder '4_pdfs' includes PDF files for each eukaryotic subset tree </li></ul></li><li>3_21eLife_concatenated_species_tree: this folder contains all sequence, alignment, and tree files for the single gene tree and concatenated phylogeny analyses (inferred using 21 single-copy marker genes, see Methods). Files are organized as follows and are associated with the following parts of the manuscript: Figure 1, Supplementary Figure 20 <ul><li>Folder '1_inspection_start' corresponds to the initial manual inspection of the single gene trees and includes the following subdirectories:<ul><li>Folder '1_sequences' includes all protein sequence fasta files corresponding to the 27 original single-copy marker genes</li><li>Folder '2_alignments' includes all alignment files generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with BMGE (subdirectory: 2_untrimmed)</li><li>Folder '3_treefiles' includes all IQ-TREE2 output files for all phylogenies (27 single-copy marker genes)</li><li>Folder '4_pdfs' includes PDF files for each single gene tree</li></ul></li><li>Folder '2_inspection_final' corresponds to the final manual inspection of the single gene trees and includes the following subdirectories:<ul><li>Folder '1_sequences' includes all protein sequence fasta files corresponding to the final 21 single-copy marker genes</li><li>Folder '2_alignments' includes all alignment files generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with BMGE (subdirectory: 2_untrimmed)</li><li>Folder '3_treefiles' includes all IQ-TREE2 output files for all phylogenies (21 single-copy marker genes)</li><li>Folder '4_pdfs' includes PDF files for each single gene tree</li></ul></li><li>Folder '3_concatenated_phylogeny' contains concatenated alignment generated from the final 21 single-copy marker gene alignments<ul><li>Folder '1_alignment' includes the concatenated alignment generated from the 21 trimmed alignments from the final inspection</li><li>Folder '2_treefiles' includes all IQ-TREE2 output files for trees inferred using the two different models (subdirectories: LG+C20+R+F and LG+C60+R+F)</li></ul></li><li>Folder '4_Eukaryote_only_phylogeny' contains sequence, alignment, and tree files for 21 single-copy marker genes used to infer a Eukaryote-only phylogeny. Folder is organized as follows and files correspond to Supplementary Figure 3: <ul><li>Folder '1_sequences' includes all protein sequence fasta files corresponding to the 21 single-copy marker genes with only Eukaryotes</li><li>Folder '2_alignments' includes all alignment files generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with BMGE (subdirectory: 2_untrimmed)</li><li>Folder '3_concatenated_phylogeny' includes concatenated alignment generated from 21 single-copy markers with only Eukaryotes (subdirectory: 1_alignment) and all IQ-TREE2 output files for the concatenated phylogeny (subdirectory: 2_treefiles)</li><li>Folder '4_pdfs' includes PDF files for the concatenated Eukaryote tree</li></ul></li></ul></li><li>4_Ribosomal_species_tree: this folder contains all sequence, alignment, and tree files for the single gene tree and concatenated phylogeny analyses (inferred using 12 ribosomal marker genes, see Methods). Files are organized as follows and are associated with the corresponding parts of the manuscript: Figure 5A, Figure 5C, Supplementary Figures 12-16, Supplementary Figure 21<ul><li>Folder '1_sequences' includes all protein sequence fasta files for the original 15 ribosomal proteins. Sequence sets include the best-hit Archaea and Bacteria, and nuclear, mitochondrial, and plastid eukaryotic homologs</li><li>Folder '2_alignments' includes all alignment files generated using MAFFT L-INS-i (subdirectory: 1_untrimmed) and trimmed with TRIMAL (gappy-out) (subdirectory: 2_trimmed)</li><li>Folder '3_treefiles' includes all original FastTree tree files, tree files with highlighted sequences to remove (*blue-to-rem = eukaryotic nuclear homolog only; *colored-to-rem = eukaryotic nuclear, mitochondrial, and plastid homologs). PDFs of each marker gene tree are also included that depict highlighting of sequences to keep and/or remove. </li><li>Folder '4_concatenated_phylogeny' contains concatenated alignment generated from the final 12 ribosomal marker genes<ul><li>Folder '1_alignment' includes the concatenated alignment generated with 12 ribosomal marker proteins in MAFFT L-INS-i and trimmed with TRIMAL (gappy-out)</li><li>Folder '2_phylogeny' includes all IQ-TREE2 output files for the species tree inferred using the LG+C60+R+F model</li></ul></li></ul></li><li>5_Dating_analysis: includes all Mcmcdate output files for the dating analyses (species tree and ATP synthase gene tree, see Methods). <ul><li>Folder '0_Starting_species_phylogenies' includes the treefiles (with and without taxonomic string) for the Edited1 and Edited2 topologies that were used in the dating analyses (see Methods). </li><li>Folder '1_Edited1_dating' includes all dated tree files and monitor files for braced and unbraced analyses of the Edited1 species tree topology. Data corresponds to Supplementary Figure 12, Supplementary Figure 14-15 </li><li>Folder '2_Edited2_dating' includes all dated tree files and monitor files for braced and unbraced analyses of the Edited2 (focal) species tree topology. Data corresponds to Figure 5A, Figure 5C, Supplementary Figure 13, Supplementary Figure 16.</li><li>Folder '3_ATP_synthase_dating' includes all dated tree files and monitor files for braced and unbraced analyses of the ATP synthase gene tree. Data corresponds to Figure 5B, Supplementary Figures 18-19.</li></ul></li></ul>3_Scripts.tar.gz: includes all workflows and scripts used for phylogenetic analyses. <ul><li>1_workflows: includes bash workflows for phylogenetic analyses (details on software versions are included in each workflow summary): <ul><li>Workflow_ATPsynthase_gene_trees.sh: generation of the ATP synthase phylogenies</li><li>Workflow_21eLife_marker_phylogeny.sh: inferring the 21 marker-gene species tree </li><li>Workflow_Ribosomal_species_tree.sh: inferring the 12 ribosomal marker-gene species tree </li><li>Workflow_Database_annotations.sh: workflow for gene annotation for 800 sampled Archaea, Bacteria, and Eukaryota</li></ul></li><li>2_R_scripts: includes R scripts used for the Eukaryote sequence contamination screening (Figure 1, Figure 2, Supplementary Figure 2, Supplementary Figures 4, 5, 8-10), presence-absence analyses (Figure 1, Figure 2, Supplementary Figure 2), and plotting tree figures (Supplementary Figures 4-10). Input mapping files and R output files are included.<ul><li>Folder '1_Euk_contamination_screen' contains workflow 'Eukaryote_contamination_screen.Rmd' used to inspect Eukaryotic ATP synthase sequences for bacterial contamination</li><li>Folder '2_Presence_absence' includes sub-directories:<ul><li>Folder '1_Species_tree' includes the treefile(s) used for ordering the plots in Figure 1 and Supplementary Figure 2 ('1_tree'), the taxonomic and COG mapping files and the list of putative contamination to remove ('2_input_files'), the raw count table for all 800 taxa ('3_Output_files'), R output plot(s) ('4_Plotting'), and the script to generate presence-absence plots 'Presence-absence.R'. </li><li>Folder '2_Eukaryotes_only'  includes organelle information, protein mapping files, taxonomic mapping files, and list of putative contamination to remove ('1_Input_files'); raw count table of ATP synthase subunits ('2_Output_files'); and R output plots ('3_Output_files'). Please see 'Eukaryote_contamination_screen.Rmd' in parent directory '2_R_scripts' for more information on how Eukaryotic sequences were screened, how the list of contaminating sequences was curated, and how the plot for Figure 2 was generated. </li></ul></li><li>Folder '3_Plotting_trees' includes the rectangular and radial trees generated for each ATP synthase trees (see Supplementary Figures 5-10). Trees were generated from the treefiles for the ATP synthase gene trees (see above), and script 'Plotting_trees.Rmd'</li><li>'Marker_gene_counts.R' script used to count marker genes per genome (see Methods)</li></ul></li><li>3_TimeTree: includes python scripts used to generate the time-trees (Figure 5C, Supplementary Figures 15 and 19)</li><li>4_ALE_workflow: example bash workflow used to run ALE. For details see Methods. </li></ul>

closedIPD-NOFeb 2026View details →

Assessment of Primary Prevention Patients Receiving An ICD - Systematic Evaluation of ATP

ClinicalTrials.gov study NCT02923726. IPD Sharing: NO. Countries: 8. Publications: 1.

restrictedIPD-UNDECIDEDFeb 2026View details →

ADVANCE CRT - D: Antitachycardia Pacing (ATP) Delivery for Painless Implantable Cardioverter Defibrillator (ICD) Therapy

ClinicalTrials.gov study NCT00147290. IPD Sharing: Not stated. Countries: 1. Publications: 4.

closedIPD-NOFeb 2026View details →

Functional Magnetic Resonance Imaging of ATP Cough in Chronic Cough Patients

ClinicalTrials.gov study NCT03722849. IPD Sharing: NO. Countries: 1. Publications: 6.

restrictedIPD-UNDECIDEDFeb 2026View details →

ADVANCE-D: Antitachycardia Pacing (ATP) Delivery for Painless Implantable Cardioverter Defibrillator (ICD) Therapy

ClinicalTrials.gov study NCT00147277. IPD Sharing: Not stated. Countries: 1. Publications: 1.

publicAug 2025View details →

Data from: Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein C termini

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publicSep 2025View details →

Supplemental information and raw data: Developmental and caste-specific expression patterns of ATP-Binding Cassette (ABC) transporters in honey bees (Apis mellifera)

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publicMar 2025View details →

Loss of intracellular ATP affects axoplasmic viscosity and pathological protein aggregation in mammalian neurons

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